Chem Office Enterprise 2006

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Users Guide
Chem & Bio Office Enterprise 2006

for Windows
Chem & Bio Office Enterprise is an Enterprise and Workgroup solution including: Knowledge Management: E-Notebook, CombiChem and Reaction Planner Biological Informatics: BioAssay Enterprise, BioSAR and BioViz Chemical Informatics: Inventory Enterprise and Registration Enterprise Scientific Databases: The Merck Index and ChemACX Database
Chem & Bio Office
Enterprise, Workgroup and Databases
: IS IT OK TO COPY MY COLLEAGUES SOFTWARE? NO, its not okay to copy your colleagues software. Software is protected by federal copyright law, which says that you can't make such additional copies without the permission of the copyright holder. By protecting the investment of computer software companies in software development, the copyright law serves the cause of promoting broad public availability of new, creative, and innovative products. These companies devote large portions of their earnings to the creation of new software products and they deserve a fair return on their investment. The creative teams who develop the softwareprogrammers, writers, graphic artists and othersalso deserve fair compensation for their efforts. Without the protection given by our copyright laws, they would be unable to produce the valuable programs that have become so important to our daily lives: educational software that teaches us much needed skills; business software that allows us to save time, effort and money; and entertainment and personal productivity software that enhances leisure time. Q: That makes sense, but what do I get out of purchasing my own software? A: When you purchase authorized copies of software programs, you receive user guides and tutorials, quick reference cards, the opportunity to purchase upgrades, and technical support from the software publishers. For most software programs, you can read about user benefits in the registration brochure or upgrade flyer in the product box. Q: What exactly does the law say about copying software? A: The law says that anyone who purchases a copy of software has the right to load that copy onto a single computer and to make another copy for archival purposes only or, in limited circumstances, for purposes only of maintenance or repair. It is illegal to use that software on more than one computer or to make or distribute copies of that software for any other purpose unless specific permission has been obtained from the copyright owner. If you pirate software, you may face not only a civil suit for damages and other relief, but criminal liability as well, including fines and jail terms of up to one year
Q: So I'm never allowed to copy software for any other reason? A: Thats correct. Other than copying the software you purchase onto a single computer and making another copy for archival purposes only or purposes only of maintenance or repair, the copyright law prohibits you from making additional copies of the software for any other reason unless you obtain the permission of the software company. Q: At my company, we pass disks around all the time. We all assume that this must be okay since it was the company that purchased the software in the first place. A: Many employees dont realize that corporations are bound by the copyright laws, just like everyone else. Such conduct exposes the company (and possibly the persons involved) to liability for copyright infringement. Consequently, more and more corporations concerned about their liability have written policies against such softlifting. Employees may face disciplinary action if they make extra copies of the companys software for use at home or on additional computers within the office. A good rule to remember is that there must be one authorized copy of a software product for every computer upon which it is run Q: Can I take a piece of software owned by my company and install it on my personal computer at home if instructed by my supervisor? A: A good rule of thumb to follow is one software package per computer, unless the terms of the license agreement allow for multiple use of the program. But some software publishers licenses allow for remote or home use of their software. If you travel or telecommute, you may be permitted to copy your software onto a second machine for use when you are not at your office computer. Check the license carefully to see if you are allowed to do this. Q: What should I do if become aware of a company that is not compliant with the copyright law or its software licenses? A: Cases of retail, corporate and Internet piracy or noncompliance with software licenses can be reported on the Internet at http://www.siia.net/piracy/report.asp or by calling the Anti-Piracy Hotline: (800) 388-7478.
Q: Do the same rules apply to bulletin boards and user groups? I always thought that the reason they got together was to share software. A: Yes. Bulletin boards and user groups are bound by the copyright law just as individuals and corporations. However, to the extent they offer shareware or public domain software, this is a perfectly acceptable practice. Similarly, some software companies offer bulletin boards and user groups special demonstration versions of their products, which in some instances may be copied. In any event, it is the responsibility of the bulletin board operator or user group to respect copyright law and to ensure that it is not used as a vehicle for unauthorized copying or distribution. Q: I'll bet most of the people who copy software don't even know that they're breaking the law. A: Because the software industry is relatively new, and because copying software is so easy, many people are either unaware of the laws governing software use or choose to ignore them. It is the responsibility of each and every software user to understand and adhere to copyright law. Ignorance of the law is no excuse. If you are part of an organization, see what you an do to initiate a policy statement that everyone respects. Also, suggest that your management consider conducting a software audit. Finally, as an individual, help spread the word that users should be software legal. Q: What are the penalties for copyright infringement? A: The Copyright Act allows a copyright owner to recover monetary damages measured either by: (1) its actual damages plus any additional profits of the infringer attributable to the infringement, or (2) statutory damages, of up to $150,000 for each copyrighted work infringed. The copyright owner also has the right to permanently enjoin an infringer from engaging in further infringing activities and may be awarded costs and attorneys fees. The law also permits destruction or other reasonable disposition of all infringing copies and devices by which infringing copies have been made or used in violation of the copyright owners exclusive rights. In cases of willful infringement, criminal penalties may also be assessed against the infringer.
SIIA also offers a number of other materials designed to help you comply with the Federal Copyright Law. These materials include: "It's Just Not Worth the Risk" video. This 12minute video, available $10, has helped over 20,000 organizations dramatize to their employees the implications and consequences of software piracy. Dont Copy that Floppy video This 9 minute rap video, available for $10, is designed to educate students on the ethical use of software.
Other education materials including, Software Use and the Law, a brochure detailing the copyright law and how software should be used by educational institutions, corporations and individuals; and several posters to help emphasize the message that unauthorized copying of software is illegal. To order any of these materials, please send your request to: SIIA Anti-Piracy Materials Software & Information Industry Association 1090 Vermont Ave, Sixth Floor, Washington, D.C. 20005 (202) 289-7442 We urge you to make as many copies as you would like in order to help us spread the word that unauthorized copying of software is illegal.
A Guide to CambridgeSoft Manuals

Includes Chem & Bio Draw Chem & Bio 3D Software Chem & Bio Finder BioAssay Desktop BioViz Desktop Inventory Desktop E-Notebook Desktop ChemDraw/Excel Desktop Applications Struct <=> Name CombiChem/Excel ChemNMR ChemFinder/Office MOPAC, GAMESS, MM2 CS Gaussian, Jaguar Interface Chem & Bio Office Enterprise E-Notebook Enterprise, Workgroup Enterprise Solutions Document Enterprise BioAssay Enterprise, Workgroup BioSAR Enterprise Inventory Enterprise, Workgroup Registration Enterprise Formulations & Mixtures Oracle Cartridge The Merck Index ChemACX, ChemMSDX Databases Sigma Aldrich MSDS ChemINDEX, NCI & AIDS, ChemRXN Ashgate Drugs, Traditional Chinese Medicines ChemSynth, ChemReact68 Medicinal Chemistry Structure Drawing Tips Tips Searching Tips Importing SD Files
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Contents
About the Manual . . . . . . . . . . . . . . . . . . . . 1
Manual Organization . . . . . . . . . . . . . . . . . . . . . . . 1 Helpful CambridgeSoft Links . . . . . . . . . . . . . . . . 1 Moving a Protocol or Project . . . . . . . . . . . . . .20 Duplicating a Protocol . . . . . . . . . . . . . . . . . . . .20 Viewing a Protocols Properties (Renaming) . . .20 Protocol Data and Definitions . . . . . . . . . . . . . .21 Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21 Protocol Data . . . . . . . . . . . . . . . . . . . . . . . . . .23 Protocol Definitions . . . . . . . . . . . . . . . . . . . . .26 Designing a New Protocol . . . . . . . . . . . . . . . . . .29 Defining Tables and Fields . . . . . . . . . . . . . . . .30 Expose Table in BioSAR Browser . . . . . . . . . . .34 Assigning a Calculation to a Field . . . . . . . . . . .34 Summary Tables . . . . . . . . . . . . . . . . . . . . . . . .42 Defining Security . . . . . . . . . . . . . . . . . . . . . . . .43 Importing and Viewing Data . . . . . . . . . . . . . . . .43 File Import Templates . . . . . . . . . . . . . . . . . . . .43 Importing Data . . . . . . . . . . . . . . . . . . . . . . . . .47 Searching for and Viewing Data in Tables . . . . .48 Validating Protocol Data . . . . . . . . . . . . . . . . . .48 Data Manipulation and Curve Fitting . . . . . . . . .49 Plotting Data using a Graph Template . . . . . . . .50 Fitting Data to a Curve . . . . . . . . . . . . . . . . . . .51 Viewing the Plotted Data . . . . . . . . . . . . . . . . . .52 Invalidating Data Points . . . . . . . . . . . . . . . . . .52 Graphing Options . . . . . . . . . . . . . . . . . . . . . . .53 Compound Lists . . . . . . . . . . . . . . . . . . . . . . . . . . .54 Manipulating Compound Lists . . . . . . . . . . . . . .55 Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55 Editing the settings tables . . . . . . . . . . . . . . . . . .55 Adding an entry . . . . . . . . . . . . . . . . . . . . . . . . .55 Deleting an entry . . . . . . . . . . . . . . . . . . . . . . . .55 Canceling/Discarding Changes . . . . . . . . . . . . .56 Plate Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . .56 Defining a Plate Format . . . . . . . . . . . . . . . . . .56 Well Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . .56 Protocol Picklist . . . . . . . . . . . . . . . . . . . . . . . . . .57 Adding a Picklist to the Picklist Table . . . . . . . .57 Adding Picklist Options . . . . . . . . . . . . . . . . . . .57 Using a Picklist . . . . . . . . . . . . . . . . . . . . . . . . .57 Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58 Managing Users . . . . . . . . . . . . . . . . . . . . . . . . . .58 Managing Groups . . . . . . . . . . . . . . . . . . . . . . . . .59 Creating New Groups . . . . . . . . . . . . . . . . . . . .59 Adding a User to a Group . . . . . . . . . . . . . . . . .59
ChemOffice Enterprise and Workgroup Solutions . . . . . . . . . . . . . . . . . . . . . . . . 3

Enterprise and Workgroup Solutions. . . . . . . . . . . 3 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Section I: Knowledge Management . . . 5

Chapter 1: E-Notebook Enterprise . . . . . . .7 Chapter 2: DocManager Enterprise . . . . . .9
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Logging In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Submitting Documents . . . . . . . . . . . . . . . . . . . . . 10 Add Document Details . . . . . . . . . . . . . . . . . . . . 10 Batch Submission . . . . . . . . . . . . . . . . . . . . . . . . . Recent Activities . . . . . . . . . . . . . . . . . . . . . . . . . . Searching for Documents . . . . . . . . . . . . . . . . . . . Performing a Search . . . . . . . . . . . . . . . . . . . . . . 10 11 11 12
Manage Users and Roles . . . . . . . . . . . . . . . . . . . 12
Section II: Biological Informatics . . . 13

Chapter 3: BioAssay . . . . . . . . . . . . . . . . . . 15
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Logging in to BioAssay . . . . . . . . . . . . . . . . . . . . . Terminology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Navigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Resizing and Moving Columns . . . . . . . . . . . . . . Sorting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . Filtering Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Refreshing the Data View . . . . . . . . . . . . . . . . . . Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Exporting Data to Excel . . . . . . . . . . . . . . . . . . . Table and Form View . . . . . . . . . . . . . . . . . . . . . Getting Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 15 16 17 17 18 18 18 19 19 19 19 19
Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Viewing Protocols in the Navigator . . . . . . . . . . 19
Chem & Bio Office Enterprise, Workgroup & Databases 2006
Contents
Chapter 4: BioSAR Enterprise . . . . . . . . . 61

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61 Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61 Schema . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61 Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61 View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61 Formgroup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61 Login to BioSAR Enterprise . . . . . . . . . . . . . . . . .62 Schema Management . . . . . . . . . . . . . . . . . . . . . . .62 Refreshing Tables . . . . . . . . . . . . . . . . . . . . . . . . .62 Add/Remove Schemas. . . . . . . . . . . . . . . . . . . . .63 Add a Schema . . . . . . . . . . . . . . . . . . . . . . . . . .63 Remove a Schema . . . . . . . . . . . . . . . . . . . . . . .63 Edit Schema Description/Password . . . . . . . . . .64 Schema Display Name . . . . . . . . . . . . . . . . . . . .64 Schema Password . . . . . . . . . . . . . . . . . . . . . . .64 Edit Exposed Tables . . . . . . . . . . . . . . . . . . . . . .64 Edit Table Details . . . . . . . . . . . . . . . . . . . . . . . . .65 Edit a Table's Primary Key . . . . . . . . . . . . . . . .65 Edit a Table's Default Column Order . . . . . . . .66 Edit Table Display Name . . . . . . . . . . . . . . . . .66 Table Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . .66 Manage Your Forms . . . . . . . . . . . . . . . . . . . . . . . .68 Create a New Form . . . . . . . . . . . . . . . . . . . . . . .69 Selecting a Base Table . . . . . . . . . . . . . . . . . . . .69 Selecting Child Tables . . . . . . . . . . . . . . . . . . . .72 Edit Integration Options . . . . . . . . . . . . . . . . . .72 Form Roles and Users . . . . . . . . . . . . . . . . . . . .72 Assign the Form to Project(s) . . . . . . . . . . . . . .73 Editing a Form . . . . . . . . . . . . . . . . . . . . . . . . . . .73 Renaming a Form . . . . . . . . . . . . . . . . . . . . . . . . .74 Duplicating a Form . . . . . . . . . . . . . . . . . . . . . . .74 Delete an Existing Form . . . . . . . . . . . . . . . . . . .74 Opening a Form/Searching Using a Form . . . . .74 Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75 Search Using a Saved Query . . . . . . . . . . . . . . . .75 Searching Using the History . . . . . . . . . . . . . . . .76 Viewing Search Results . . . . . . . . . . . . . . . . . . . .76 Sorting Results . . . . . . . . . . . . . . . . . . . . . . . . . .77 Dynamically Editing a Form . . . . . . . . . . . . . . .77 Displaying Search Results in MS Excel . . . . . . .77 List View Options . . . . . . . . . . . . . . . . . . . . . . .77 Details View Options . . . . . . . . . . . . . . . . . . . .78 Generating Reports . . . . . . . . . . . . . . . . . . . . . . .78 Create a New Profile . . . . . . . . . . . . . . . . . . . . .80 Edit a Profile . . . . . . . . . . . . . . . . . . . . . . . . . . .82 View a Profile . . . . . . . . . . . . . . . . . . . . . . . . . .83 Duplicate a Profile . . . . . . . . . . . . . . . . . . . . . . .83
Delete a Profile . . . . . . . . . . . . . . . . . . . . . . . . . 84 Ordering Fields and Changing Label Sizes in Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Manage Users and Roles. . . . . . . . . . . . . . . . . . . . 85
Administrator
Section III: Chemical Informatics . . .87

Chapter 5: Inventory . . . . . . . . . . . . . . . . . 89
Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Substance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Inventory Desktop/Workgroup . . . . . . . . . 91
Whats New in CS Inventory 10? . . . . . . . . . . . . 91 Login and Logout . . . . . . . . . . . . . . . . . . . . . . . . 91
The User Interface. . . . . . . . . . . . . . . . . . . . . . . . . 91 Forms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 Managing Locations . . . . . . . . . . . . . . . . . . . . . . 93 Creating a New Location . . . . . . . . . . . . . . . . . 93 Editing a Location . . . . . . . . . . . . . . . . . . . . . . 94 Moving a Location . . . . . . . . . . . . . . . . . . . . . . 94 Deleting a Location . . . . . . . . . . . . . . . . . . . . . 94 Refreshing the Location Tree . . . . . . . . . . . . . . 94 Managing Substances . . . . . . . . . . . . . . . . . . . . . 95 Creating a New Substance . . . . . . . . . . . . . . . . 95 Material Safety Data Sheets . . . . . . . . . . . . . . . . 96 Using ACX . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Mixtures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Conflict Resolution . . . . . . . . . . . . . . . . . . . . . . 97 Editing a Substance . . . . . . . . . . . . . . . . . . . . . 98 Managing Containers. . . . . . . . . . . . . . . . . . . . . . 98 Editing a Container . . . . . . . . . . . . . . . . . . . . . . 99 Moving a Container . . . . . . . . . . . . . . . . . . . . . 99 Check-in/out, Changing Quantities, and Other Shortcuts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 Multi Select . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 Managing EHS Data . . . . . . . . . . . . . . . . . . . . . 100 Searching Inventory. . . . . . . . . . . . . . . . . . . . . . . 101 Searching for Containers . . . . . . . . . . . . . . . . . . 101 Advanced Search . . . . . . . . . . . . . . . . . . . . . . 102 Substructure Search . . . . . . . . . . . . . . . . . . . . 102 Searching for Substances. . . . . . . . . . . . . . . . . . 103 Printing Labels and Reports . . . . . . . . . . . . . . . . 104 Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 Inventory Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Managing Users and Roles . . . . . . . . . . . . . . . . 108 Managing Roles . . . . . . . . . . . . . . . . . . . . . . . 108 Managing Users . . . . . . . . . . . . . . . . . . . . . . . 109
Contents
CambridgeSoft
Managing Tables . . . . . . . . . . . . . . . . . . . . . . . . 110 Custom Fields . . . . . . . . . . . . . . . . . . . . . . . . . . 110

Record Locking . . . . . . . . . . . . . . . . . . . . . . . 111
Managing the Container list display . . . . . . . . . 111 Backup/Restore Database . . . . . . . . . . . . . . . . 111 Audit Trail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Printing an Audit Report . . . . . . . . . . . . . . . . 113
Inventory Enterprise . . . . . . . . . . . . . . . . 115

Logging in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 Searching Inventory Enterprise . . . . . . . . . . . . 115
Simple Search . . . . . . . . . . . . . . . . . . . . . . . . . 115 Advanced Search . . . . . . . . . . . . . . . . . . . . . . 116 Substructure Search . . . . . . . . . . . . . . . . . . . . 116 Global Search . . . . . . . . . . . . . . . . . . . . . . . . . 117 Plate Search . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Substance Management. . . . . . . . . . . . . . . . . . . 118 Creating a New Substance . . . . . . . . . . . . . . . 118 Searching for a Substance . . . . . . . . . . . . . . . . . 120 Editing a Substance's Details . . . . . . . . . . . . . 120 Delete a Substance . . . . . . . . . . . . . . . . . . . . . 121 View History . . . . . . . . . . . . . . . . . . . . . . . . . 121 Synonym Management . . . . . . . . . . . . . . . . . . 122 Link Management . . . . . . . . . . . . . . . . . . . . . . 122 Container Management . . . . . . . . . . . . . . . . . . . 123 Location Management . . . . . . . . . . . . . . . . . . . 123 Current Location Frame . . . . . . . . . . . . . . . . . 123 Location Tree Frame . . . . . . . . . . . . . . . . . . . 124 Creating a New Container . . . . . . . . . . . . . . . 128 Searching for a Container . . . . . . . . . . . . . . . . 130 Viewing the Contents of a Container . . . . . . . 130 Viewing the Contents of a Container . . . . . . . 131 Plate Inventory. . . . . . . . . . . . . . . . . . . . . . . . . . . 141 Creating New Plates . . . . . . . . . . . . . . . . . . . . . 142 Searching for a Plate . . . . . . . . . . . . . . . . . . . . 142 Viewing the Contents of a Plate . . . . . . . . . . . 142 Available Functions from Plate Details Frame 142 Plate Viewing Form Tabs . . . . . . . . . . . . . . . . 146 Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 Managing Users and Roles . . . . . . . . . . . . . . . . 147 Inventory Loader. . . . . . . . . . . . . . . . . . . . . . . . 147 Loading Compounds into Plates . . . . . . . . . . . 147 Import Compounds Only . . . . . . . . . . . . . . . . 150 Inventory Tasks . . . . . . . . . . . . . . . . . . . . . . . . . 150 Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 New Location . . . . . . . . . . . . . . . . . . . . . . . . . 150 Edit Location . . . . . . . . . . . . . . . . . . . . . . . . . 150 Move Location . . . . . . . . . . . . . . . . . . . . . . . . 150 Delete Location . . . . . . . . . . . . . . . . . . . . . . . 150 Plate Settings . . . . . . . . . . . . . . . . . . . . . . . . . 150
Change Password . . . . . . . . . . . . . . . . . . . . . .153 Manage Users . . . . . . . . . . . . . . . . . . . . . . . . .153 Manager Roles . . . . . . . . . . . . . . . . . . . . . . . . .153 Manage Container Requests . . . . . . . . . . . . . . .153 Manage Sample Requests . . . . . . . . . . . . . . . . .154 Manage Orders . . . . . . . . . . . . . . . . . . . . . . . .157 Receive an Order . . . . . . . . . . . . . . . . . . . . . . .158 Manage Approvals . . . . . . . . . . . . . . . . . . . . . .158 Manage Tables . . . . . . . . . . . . . . . . . . . . . . . . .159 Analyze Audit Trail . . . . . . . . . . . . . . . . . . . . .159 Create Plates from Excel . . . . . . . . . . . . . . . . .161 Create Plates from Text File . . . . . . . . . . . . . .161 Custom Reports . . . . . . . . . . . . . . . . . . . . . . .161
Chapter 6: Registration Enterprise . . . . . 163

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .163 Registration Enterprise Workflow . . . . . . . . . . .163 Chemical Registry Number Assignment . . . . . .163 Starting Registration Enterprise . . . . . . . . . . . . .163 Add to Temporary. . . . . . . . . . . . . . . . . . . . . . . . .164 Adding a Compound . . . . . . . . . . . . . . . . . . . . .164 Adding a Batch/Lot . . . . . . . . . . . . . . . . . . . . . .165 Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .167
Searching and Viewing Records in the Temporary Table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .167 Registering Records in the Temporary Table . .168
Editing Records in the Temporary Table . . . . .168 Deleting Records in the Temporary Table . . . .168 Registering a Record. . . . . . . . . . . . . . . . . . . . . .169 Adding Identifier Information to Records . . . .170 Adding Analytics Data to a Record . . . . . . . . . .171 Query and Reporting . . . . . . . . . . . . . . . . . . . . . .171 Searching for Registered Compounds . . . . . . . .171 Analytics Spreadsheets . . . . . . . . . . . . . . . . . . . .172 Administration . . . . . . . . . . . . . . . . . . . . . . . . . . .173 Managing Tables . . . . . . . . . . . . . . . . . . . . . . . . .173 Defining Projects . . . . . . . . . . . . . . . . . . . . . . .173 Defining Sequences . . . . . . . . . . . . . . . . . . . . .174 Defining Structure Comments . . . . . . . . . . . . .175 Defining Registration Enterprise People . . . . .176 Defining Salts . . . . . . . . . . . . . . . . . . . . . . . . .177 Defining Solvates . . . . . . . . . . . . . . . . . . . . . . .178 Managing Users and Roles . . . . . . . . . . . . . . . . .179 Defining New Experiments . . . . . . . . . . . . . . . .179 Managing Analytics Data . . . . . . . . . . . . . . . . . .179 Defining Result Type . . . . . . . . . . . . . . . . . . . .180 Defining Experiment Type . . . . . . . . . . . . . . .180 Defining Parameter Type . . . . . . . . . . . . . . . . .181 Managing Workgroups . . . . . . . . . . . . . . . . . . . .182
Contents
Importing SDFiles . . . . . . . . . . . . . . . . . . . . . . . .182 Steps to Import a SDFile . . . . . . . . . . . . . . . . . .182 Choosing Input and Output Databases. . . . . . .182
Matching Fields in the Input and Output Databases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .183 View Matches and Import . . . . . . . . . . . . . . . . .184
Optional Features . . . . . . . . . . . . . . . . . . . . . . . . .185 Row Level Security (RLS) . . . . . . . . . . . . . . . . .185 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . .185 The User Interface . . . . . . . . . . . . . . . . . . . . . .185 How are Projects linked to People . . . . . . . . . .185 The Unspecified Project . . . . . . . . . . . . . . . . .185 Duplicate Checking . . . . . . . . . . . . . . . . . . . . .186 Activating RLS . . . . . . . . . . . . . . . . . . . . . . . .186 Salt and Solvate Recognition . . . . . . . . . . . . . . .186 Customizable Fields . . . . . . . . . . . . . . . . . . . . . .186 Choosing Preferences. . . . . . . . . . . . . . . . . . . . . .187 Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .187 Logging Off. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .187
Viewing Results in Form View . . . . . . . . . . . . 203 Browsing Other Records . . . . . . . . . . . . . . . . 204 Viewing All Records . . . . . . . . . . . . . . . . . . . . 204 Marking and Unmarking Records . . . . . . . . . . 205 Manipulating Queries . . . . . . . . . . . . . . . . . . . . 205 Restoring Queries . . . . . . . . . . . . . . . . . . . . . . 205 Saving Queries . . . . . . . . . . . . . . . . . . . . . . . . 206 Managing Queries . . . . . . . . . . . . . . . . . . . . . . 207 Manipulating Hit Lists. . . . . . . . . . . . . . . . . . . . 208 Restoring Hit Lists . . . . . . . . . . . . . . . . . . . . . 208 Saving Hit Lists . . . . . . . . . . . . . . . . . . . . . . . 208 Managing Hit Lists . . . . . . . . . . . . . . . . . . . . . 209 Refining Search Results . . . . . . . . . . . . . . . . . . . 210 Refining Over Current Records Found . . . . . . 210 Undoing a Refined Search . . . . . . . . . . . . . . . 210 Exporting Search Results . . . . . . . . . . . . . . . . . 210 Histories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211 Setting Your Display and Search Preferences . . 211 Server Information. . . . . . . . . . . . . . . . . . . . . . . . 213 Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Administrator
Section IV: ChemOffice Enterprise . 189

ChemOffice Enterprise . . . . . . . . . . . . . . . . . . . .189 CS Oracle Cartridge . . . . . . . . . . . . . . . . . . . . . . .189
Chapter 8: CS Oracle Cartridge . . . . . . . 215

Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 Minimum Requirements . . . . . . . . . . . . . . . . . . 215 Before Installation . . . . . . . . . . . . . . . . . . . . . . . 215 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 Un-installation . . . . . . . . . . . . . . . . . . . . . . . . . . 216 Re-installation . . . . . . . . . . . . . . . . . . . . . . . . . . 216 Multiple Installations . . . . . . . . . . . . . . . . . . . . . 217 Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217 DDL Considerations . . . . . . . . . . . . . . . . . . . . . . 217 Creating The Index . . . . . . . . . . . . . . . . . . . . . . 218 Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220 Maintenance of the Index . . . . . . . . . . . . . . . . . 220 Unique index . . . . . . . . . . . . . . . . . . . . . . . . . 221 DML Considerations . . . . . . . . . . . . . . . . . . . . . . 222 Fast Substructure Search . . . . . . . . . . . . . . . . . . 222 Simple Example . . . . . . . . . . . . . . . . . . . . . . . 224 Querying Large Structures . . . . . . . . . . . . . . . 224 Using Optimizer Hints . . . . . . . . . . . . . . . . . . 225 Query Optimization . . . . . . . . . . . . . . . . . . . . 225 Formula Query . . . . . . . . . . . . . . . . . . . . . . . . 226 MolWeight Query . . . . . . . . . . . . . . . . . . . . . . 226 Support Functions . . . . . . . . . . . . . . . . . . . . . . . . 226 Distributing databases . . . . . . . . . . . . . . . . . . . . 229 Using data maintained by the cartridge . . . . . . 229 Error Handling . . . . . . . . . . . . . . . . . . . . . . . . . 231
Chapter 7: ChemOffice Enterprise . . . . . 191

About ChemOffice Enterprise. . . . . . . . . . . . . . .191 Installation and Administration . . . . . . . . . . . . .191 Global Login and Security . . . . . . . . . . . . . . . . . .191 Logging In . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191 Manage Users and Roles . . . . . . . . . . . . . . . . . .192 Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .192 Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .193 Searching ChemOffice Enterprise Applications 194
Accessing a ChemOffice Enterprise Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .194 The Query Input Form User Interface . . . . . . .195
The Navigation Toolbar . . . . . . . . . . . . . . . . .195 Search Input Form . . . . . . . . . . . . . . . . . . . . .197 Performing a Simple Search . . . . . . . . . . . . . . . .197 Searching by Different Query Methods . . . . . .198 Searching With Text . . . . . . . . . . . . . . . . . . . .198 Searching With Structures . . . . . . . . . . . . . . . .199 Searching With Molecular Formulas . . . . . . . .201 Searching With Numerical Ranges . . . . . . . . . .202 Combination Searching . . . . . . . . . . . . . . . . . .202 Search Results . . . . . . . . . . . . . . . . . . . . . . . . . . . .203 Viewing Search Results . . . . . . . . . . . . . . . . . . .203 Viewing Results in List View . . . . . . . . . . . . . .203
Contents
CambridgeSoft
Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . 232 Checking for the Presence of the Cartridge . . . 232 Checking the Version of the Cartridge . . . . . . . 232 Checking for fields indexed by the cartridge . . 232 What to do if Creating an Index Fails . . . . . . . 233 What to do if a Client Program Fails . . . . . . . . 233 Setup Problems . . . . . . . . . . . . . . . . . . . . . . . . . 234 ORA-28575 unable to open RPC connection to external procedure agent . . . . . . . . . . . . . . . . . . . . . . 234 ORA-06520 PL/SQL: Error loading external library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235 Dependencies. . . . . . . . . . . . . . . . . . . . . . . . . . . . 236 Using ADO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236 Example of passing large queries . . . . . . . . . . . 237 Custom Screening . . . . . . . . . . . . . . . . . . . . . . . . 237 Optimizing client programs for version 9 . . . . . 238 Bulk Loading . . . . . . . . . . . . . . . . . . . . . . . . . . . 239 Data Structures . . . . . . . . . . . . . . . . . . . . . . . . . . 240 Schema Overview . . . . . . . . . . . . . . . . . . . . . . . 240 Tables Related to an Index . . . . . . . . . . . . . . . . 240 The sch_ix Table . . . . . . . . . . . . . . . . . . . . . . 240 The sch_ix_NR Table . . . . . . . . . . . . . . . . . . . 241 The sch_ix_NC Table . . . . . . . . . . . . . . . . . . . 242 The sch_ix_NX Table . . . . . . . . . . . . . . . . . . 242 The sch_ix_SR, sch_ix_SC, sch_ix_SX Tables 242 The sch_ix_FR, sch_ix_FC, sch_ix_FX Tables 242 The sch_ix_KR, sch_ix_KC, sch_ix_KX Tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242 The sch_ix_E Table . . . . . . . . . . . . . . . . . . . . 242 The sch_ix_3 Table . . . . . . . . . . . . . . . . . . . . 242 The sch_ix_O Table . . . . . . . . . . . . . . . . . . . . 242 Administrative Tables . . . . . . . . . . . . . . . . . . . . 243 ALL_CSC_INDEXES Table . . . . . . . . . . . . . 243 CUSTOM_SCREENS Table . . . . . . . . . . . . . 243 GLOBALS Table . . . . . . . . . . . . . . . . . . . . . . 243 Data stored outside of Oracle. . . . . . . . . . . . . . 244 The CsCartridgeData file . . . . . . . . . . . . . . . . 245 Program files . . . . . . . . . . . . . . . . . . . . . . . . . 245
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . .248 Using Scientific Databases . . . . . . . . . . . . . . . .248
Section V: Reference Data . . . . . . . . .251

Chapter 9: The Merck Index . . . . . . . . . . 253
How Is It Useful? . . . . . . . . . . . . . . . . . . . . . . . . .253 About The Merck Index. . . . . . . . . . . . . . . . . . . .253 Using The Merck Index Online . . . . . . . . . . . . .254 Compound Searching . . . . . . . . . . . . . . . . . . . . .254 Organic Name Reactions . . . . . . . . . . . . . . . . . .255 Additional Tables . . . . . . . . . . . . . . . . . . . . . . . .256 Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . .256
Chapter 10: MediChem . . . . . . . . . . . . . . 257

About Medichem . . . . . . . . . . . . . . . . . . . . . . . . .257 Using MediChem Online. . . . . . . . . . . . . . . . . . .257
Chapter 11: Traditional Chinese Medicines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

About TCM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .259 Using TCM with ChemOffice Enterprise . . . . .259
Chapter 12: Ashgate Drugs . . . . . . . . . . . 263

About Ashgate Drugs . . . . . . . . . . . . . . . . . . . . . .263 Using Ashgate Drugs on CD-ROM . . . . . . . . . .263 Using Ashgate Drugs Online or with ChemOffice Enterprise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .264 Compound Searching . . . . . . . . . . . . . . . . . . . . .264 Browse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .265
Chapter 13: ChemINDEX . . . . . . . . . . . . 267

How Is It Useful? . . . . . . . . . . . . . . . . . . . . . . . . .267 About ChemIndex . . . . . . . . . . . . . . . . . . . . . . . .267 Using ChemINDEX Ultra on DVD-. . . . . . . . . .267 BuckyBase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .268 ChemFinder.Com . . . . . . . . . . . . . . . . . . . . . . . . .268 Using ChemINDEX With ChemOffice Enterprise or Online . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .268
Chapter 14: NCI . . . . . . . . . . . . . . . . . . . . 271

Using NCI on CD. . . . . . . . . . . . . . . . . . . . . . . . .271 Using the NCI Forms . . . . . . . . . . . . . . . . . . . .271
Chapter 15: AIDS . . . . . . . . . . . . . . . . . . . 273

Using AIDS on CD . . . . . . . . . . . . . . . . . . . . . . . .273 Using AIDS Online . . . . . . . . . . . . . . . . . . . . . .273
Scientific Databases . . . . . . . . . . . . . 247

ChemFinder.Com Gateway. . . . . . . . . . . . . . . . . 247 Database Offerings . . . . . . . . . . . . . . . . . . . . . . . 247 Available Formats . . . . . . . . . . . . . . . . . . . . . . . . 247
Section VI: Sourcing & Safety Data . 275

Chapter 16: ChemACX . . . . . . . . . . . . . . . 277
ChemACX Database. . . . . . . . . . . . . . . . . . . . . . .277 How Is It Useful? . . . . . . . . . . . . . . . . . . . . . . . . .277
Subscriptions and ChemOffice Enterprise Based Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247 CD Based Databases . . . . . . . . . . . . . . . . . . . . . 248
Contents
Using ChemACX with ChemOffice Enterprise .277 Opening ChemACX . . . . . . . . . . . . . . . . . . . . . .278 Searching ChemACX Catalogs . . . . . . . . . . . . .278 Searching Without the Plug-in . . . . . . . . . . . . .279 Creating and Editing A List of Favorite Vendors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .279 Viewing Search Results . . . . . . . . . . . . . . . . . . .279 Viewing Search Results in List View . . . . . . . .280 Viewing Search Results in Details View . . . . . .281 Accessing MSDX Data . . . . . . . . . . . . . . . . . .282 Using the Shopping Cart . . . . . . . . . . . . . . . . . .283 Viewing Your Shopping Cart . . . . . . . . . . . . . .283 Removing Items from Your Shopping Cart . . .283 Ordering The Chemicals in the ChemACX Shopping Cart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .283 Registering and Creating Inventory Containers 284 Registering Products in Registration Enterprise. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .284 Creating Inventory Containers in Inventory for Products. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .285 Saving Hitlists and Exporting SD Files . . . . . . .286 Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . .286 Using the ChemACX Ultra DVD-ROM . . . . . . .286 What If My Favorite Supplier Isnt Listed Here?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287
Using ChemSynth on CD-ROM. . . . . . . . . . . . . 301 Using ChemSynth Online or with ChemOffice Enterprise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301 Searching ChemSynth . . . . . . . . . . . . . . . . . . . . 301
Chapter 22: ChemReact . . . . . . . . . . . . . . 305

About ChemReact . . . . . . . . . . . . . . . . . . . . . . . . 305 Using ChemReact68 on CD-ROM . . . . . . . . . . . 305 Using ChemReact Online or with ChemOffice Enterprise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306 Searching ChemReact . . . . . . . . . . . . . . . . . . . . 306
Administrator
Section VIII: Appendices . . . . . . . . .309

Appendix A: . DocManager Enterprise Free Text Searching . . . . . . . . . . . . . . . . . . . 311
Understanding Basic Text Searching. . . . . . . . . 311 Exact Phrase Matching . . . . . . . . . . . . . . . . . . . 311 Wildcard Searching . . . . . . . . . . . . . . . . . . . . . . 311 Understanding Advanced Text Searching . . . . . 312 ABOUT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312 AND (&) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313 EQUIValence (=) . . . . . . . . . . . . . . . . . . . . . . . 313 Fuzzy (?). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314 MINUS (-) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314 NEAR (;) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315 NOT (~) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316 OR (|) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316 Soundex (!) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317 Stem ($) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
Chapter 17: ChemMSDX . . . . . . . . . . . . . 289

How is it Useful?. . . . . . . . . . . . . . . . . . . . . . . . . .289 Using ChemMSDX from ChemACX Ultra DVD. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .289 Using ChemMSDX from ChemOffice Enterprise. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .289
Chapter 18: Sigma-Aldrich MSDS Collection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

About the Sigma-Aldrich MSDS Collection . . . .291
Appendix B: BioAssay Actions Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 319

Viewing Commands . . . . . . . . . . . . . . . . . . . . . . 319 View Details . . . . . . . . . . . . . . . . . . . . . . . . . . . 319 View Picklist . . . . . . . . . . . . . . . . . . . . . . . . . . . 319 View Plate Format . . . . . . . . . . . . . . . . . . . . . . . 319 View (from the plates grid) . . . . . . . . . . . . . . . . 319 View (from the plate formats grid) . . . . . . . . . . 319 Other Commands . . . . . . . . . . . . . . . . . . . . . . . . 319 Autofit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319 AutoFit On . . . . . . . . . . . . . . . . . . . . . . . . . . . 320 AutoFit Off . . . . . . . . . . . . . . . . . . . . . . . . . . 320 Change Validity . . . . . . . . . . . . . . . . . . . . . . . . . 320 Coloring Options . . . . . . . . . . . . . . . . . . . . . . . 321 Copy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Cut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Import Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
Chapter 19: EH&S Enterprise . . . . . . . . . 293

How Is It Useful? . . . . . . . . . . . . . . . . . . . . . . . . .293 Key Benefits: . . . . . . . . . . . . . . . . . . . . . . . . . . . . .293
Section VII: Reaction & Synthesis Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295

Chapter 20: ChemRXN . . . . . . . . . . . . . . 297
How Is It Useful? . . . . . . . . . . . . . . . . . . . . . . . . .297 ChemPrep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .297 ChemSelect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .298 Selection Criteria . . . . . . . . . . . . . . . . . . . . . . . .299
Chapter 21: ChemSynth . . . . . . . . . . . . . . 301

About ChemSynth. . . . . . . . . . . . . . . . . . . . . . . . .301
Contents
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Paste . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Recalculate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Save Compound List . . . . . . . . . . . . . . . . . . . . . 321 Select All . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Show Coloring . . . . . . . . . . . . . . . . . . . . . . . . . . 322 Show Only Valid Data. . . . . . . . . . . . . . . . . . . . 322
Browsing a Database . . . . . . . . . . . . . . . . . . . . . .328 The Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . .328 The Data Table . . . . . . . . . . . . . . . . . . . . . . . . . .329 Closing a Form . . . . . . . . . . . . . . . . . . . . . . . . . .330 Performing a Text Search. . . . . . . . . . . . . . . . . . .331 Searching by Formula . . . . . . . . . . . . . . . . . . . . .331 Searching by name . . . . . . . . . . . . . . . . . . . . . . .332 Searching by Molecular Weight . . . . . . . . . . . . .332 Performing a Structure Search . . . . . . . . . . . . . .332 Using the ChemDraw ActiveX Control . . . . . .332 Searching for the Structure in ChemFinder . . .334 Performing a Combined Search . . . . . . . . . . . . .336
Appendix C: BioAssay Plate Block Data Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323 Appendix D: Oracle Cartridge Dependencies by Operating System . . . . . . . . . . . . . . . 325 Appendix E: Scientific Databases First Search Tutorial . . . . . . . . . . . . . . . . . . . 327
Opening a Form in ChemFinder . . . . . . . . . . . 327 Switching Between Open Documents . . . . . . . 327
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . .i
Contents
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Contents CambridgeSoft
About the Manual

The ChemOffice Enterprise Workgroup & Databases Manual is a collection of instructions for CambridgeSoft products not including ChemDraw, ChemFinder, E-Notebook, and Chem3D. Because the ChemOffice Enterprise Workgroup & Databases Manual is a comprehensive collection, every user may not have access to all of the products represented. This guide assumes familiarity with your computers operating system and in some cases, a web browser. For details about using your operating system, refer to the user documentation provided with that system. For information about ChemDraw, please see the ChemDraw Manual. For information about Chem3D, ChemFinder, and/or E-Notebook please see the ChemOffice: Chem3D, ChemFinder and E-Notebook Manual.
Section V: Reference Data Section VI: Sourcing and Safety Data Section VII: Reaction and Synthesis Data
Helpful CambridgeSoft Links

The following table contains the addresses of ChemDraw and ChemOffice-related web pages.
Help For ... Technical Support Software Developers kit Access http://www.cambridgesoft.com/ services/ http://sdk.cambridgesoft.com/
Active X control http://sdk.cambridgesoft.com/ Purchasing CambridgeSoft products and chemicals ChemOffice Enterprise updated help files http://store.cambridgesoft.com/
Manual Organization
The ChemOffice Enterprise Workgroup & Databases Manual is divided into 7 sections:
Enterprise and Workgroup Solutions Section I: Knowledge Management Section II: Biological Informatics Section III: Chemical Informatics Section IV: ChemOffice Enterprise Scientific Databases
http://www.cambridgesoft.com/ services/documentation/manuals _enterprise.cfm
About the Manual 1 Manual Organization
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2About the Manual CambridgeSoft
ChemOffice Enterprise and Workgroup Solutions

Enterprise and Workgroup Solutions
ChemOffice Enterprise Solutions are designed to assist in the storage and workflow challenges arising from sharing and manipulating chemical and biological data. Enterprise Solutions offer flexibility, security, and a friendly web based user interface to encourage organization wide collaboration. These applications are mainly webbased and combine to form an integrated suite of products through one security interface. Enterprise Offerings include:
E-Notebook Enterprise DocManager Enterprise BioAssay Enterprise BioSAR Enterprise Inventory Enterprise Registration Enterprise
ChemOffice Workgroup Solutions are designed for organizations who want to organize and search over their inventory, purchase reagents, as well as manipulate and store chemical and biological data. ChemOffice Workgroup is compatible with SQL Server and is accessed through a client side application. Workgroup Offerings include:
E-Notebook Workgroup BioAssay Workgroup Inventory Workgroup
Installation
Installation instructions and requirements are contained in the Read Me document for each application. Software Requirements and installation instructions differ between applications.
Chem & Bio Office Enterprise, Workgroup & Databases 2006 ChemOffice Enterprise and Workgroup Solutions 3 Enterprise and Workgroup Solutions
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4ChemOffice Enterprise and Workgroup Solutions CambridgeSoft Installation
Section I: Knowledge Management

This section provides information about CambridgeSofts Knowledge Management Solutions. The following applications comprise CambridgeSofts Enterprise Solutions:
E-Notebook Enterprise (see the Chem3D,
ChemFinder, and E-Notebook manual for more details) DocManager Enterprise
Research organizations thrive when information is easily captured, well organized, and available to those who need it. E-Notebook Enterprise streamlines daily record keeping with rigorous security and efficient archiving, and facilitates searches by text and structure. DocManager Enterprise organizes procedures and reports for archiving and chemically-intelligent data mining. Discovery LIMS tracks laboratory requests, and 21CFR11 Compliance implements an organizations regulatory compliance processes.
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Chapter 1: E-Notebook Enterprise

E-Notebook streamlines the daily record-keeping of research scientists. Notebook pages consist of Excel spreadsheets, Word documents, ChemDraw drawings, and spectral data, and can be searched by text and structure. Oracle or SQL support allows organizations to share data, as well as maintain rigorous security and efficient archiving. E-Notebook Enterprise provides a user friendly interface designed to replace paper laboratory notebooks. E-Notebook pages contain Excel spreadsheets, Word documents, ChemDraw drawings and reactions and spectral data. ENotebook can be searched by text, structure or reaction. For additional information about E-Notebook Enterprise and E-Notebook Workgroup, please see the CambridgeSoft manual titled ChemOffice: Chem3D, ChemFinder, and E-Notebook.
E-Notebook Enterprise 7
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Chapter 2: DocManager Enterprise

Overview
The DocManager Enterprise utilizes the ChemOffice Enterprise to store and search through documents. The ChemOffice DocManager Enterprise will allow you to:
Create a central area, or repository, for
chemical documents in .doc, .txt, .ppt, .xls, and .pdf formats for your entire organization, over the web. Search .doc, .txt, .ppt, .xls, and .pdf* documents in the repository. A Boolean search can be performed over the web by chemical structure or text. * PDF documents can not be searched by structure. Furthermore, full text searching is only available for PDF documents on systems with: Oracle 9i OR Oracle 8i and PDF documents are version 4 and below Add, or submit, documents to the system over the web. The document submitted is securely stored in a database, indexed by both structure and text for DocManager Enterprise users to search and view. Remove documents that are no longer shared. Manage users as the system administrator.
Hostname is the name of the server that the DocManager Enterprise application is installed on. To obtain this name, please contact your system administrator. The Log In window appears in your browser. 2. Enter a valid username and password. 3. Click Login. The Global login page appears. DocManager Enterprise is in the bottom right.
4. Click on one of the links to enter DocManager
Enterprise
.
Logging In
To log in to DocManager Enterprise: 1. Enter http://hostname into your web browser.
DocManager Enterprise 9 Overview
Submitting Documents
Documents can be submitted through the DocManager Enterprise web interface. To submit a document: 1. From the Main Menu, click Submit Documents. The Submit Document page appears.
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Batch Submission
2. In the Document box, use the Browse button to
find the document you would like to submit. If you would like to view the document from within your web browser, click Add Document Details. The document will appear in the browser window. If you would like to submit the document, click Submit Now The submit documents page appears with a message that the document was submitted successfully.
The Batch Submission tool allows application administrators to schedule the submission of documents in a specified directory. Because batch submission often decreases the performance of the server, it is recommended that administrators schedule the submission during a low use period.
NOTE: Only one scheduled batch submission is recognized at once. In other words, if a new batch submission is scheduled, it will overwrite the previous submission schedule.
Add Document Details

When submitting a document, you have the option to add document details. To add details, click Add Document Details instead of Submit Now on the Add Document page. The Add Document Details window allows you to enter a title, author, and comments for the document being submitted as well as preview the document layout in a web browser. Click Submit This Document after you have entered your details.
To schedule a batch submission: 1. Click Batch Submission from the DocManager Enterprise homepage. or click Batch Submission from the Global Login page
The batch submission page appears.
10DocManager Enterprise
CambridgeSoft Submitting Documents
2. Enter sorting information.
2. Enter the directory which contains the
documents to be submitted. 3. Select a checkbox pertaining to a time of day when the submission should take place. 4. Uncheck the Index automatically checkbox if you want to shut off indexing while uploading the documents.
NOTE: Turning full-text index off will significantly improve the loading performance. If you turn it off, you must turn it back on after the loading finishes, otherwise the documents will not be text searchable.
5. Click OK.
3. Click Show Activities.
The results appears
Searching for Documents

DocManager Enterprise supports Basic and Advanced Text searching characters and operators as well as structure searching. When performing a text search, type search criteria or parameters into the search textbox. When performing a structure search, draw a structure in the Structure box. For more information about drawing structures, please see Drawing Chemical Structures in the ChemDraw Users Manual. After entering search criteria, start the search by clicking on Search button. For more information about Free Text Searching, see DocManager Enterprise Free Text Searching on page 311.
Recent Activities
The Recent Activities tool allows administrators to view and sort recent document submissions. To view recent activities performed by the user: 1. Click Recent Activities. The Recent activities page appears.
DocManager Enterprise 11 Recent Activities
For more information about search features, such as Retrieve All and New Query, see the ChemOffice Enterprise Users Guide.
The Search Results form appears
Performing a Search
To search documents for specific information: 1. From the Main Menu page, click Search Documents. The Search Documents page appears.
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The search results form displays all documents retrieved as a result of a search in table format. The table includes two columns: Document information and Download Options.
To view one of the files in the Results form
2. Enter the appropriate information. The Full
text textbox allows full text searching. Form more information about full text searching, please see DocManager Enterprise Free Text Searching on page 311. For more information about drawing structures, please see Drawing Chemical Structures in the ChemDraw Users Manual. 3. Click Search.
inside your web browser, click on the title of the appropriate document. To save a file to disk in order to view later, click on the download button to the right of the documents information.
Manage Users and Roles

The DocManager Enterprise application uses the global ChemOffice Enterprise User Management interface. Please see Manage Users and Roles on page 192 for more information.
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CambridgeSoft Manage Users and Roles
Section II: Biological Informatics

This section provides information about CambridgeSofts Biological Informatics Solutions. The following applications comprise CambridgeSofts BioInformatics Solutions:
BioAssay BioSAR Enterprise
Finding structural determinants of biological activity requires processing masses of biological assay data. Scientists use BioAssay and BioSAR Enterprise to set up biological models and visualize information, to generate spreadsheets correlating structure and activity, as well as to search by chemical structure.
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Chapter 3: BioAssay
Overview
BioAssay helps research biologists store, analyze, and report on biological protocol data. It is optimized for high-throughput screening data, but it can also be effectively used for low-throughput and in vivo studies. The system allows the user to define protocols as sets of tables holding raw data, summary data and aggregate data. In addition to storing data, the system also allows for curve fitting and data manipulation. The Login window appears.
2. The username and password used should be a
valid BioAssay username and password. For more information about valid usernames and passwords, please see your system administrator. 3. Select a connection type:
Direct Connection - BioAssay clients connect directly to Oracle via Oracle client software. Best for high-speed LANs.
Logging in to BioAssay
To start the BioAssay client application: 1. Go to START > Programs > BioAssay > BioAssay OR Double-click the desktop icon
.
Oracle Service The Oracle service where the bioassayhts schema is installed Schema - The name of the BioAssay schema by default bioassayhts
BioAssay 15 Overview
Proxy Connection - BioAssay clients use a
LTS - Low Throughput Screening - more in
HTTP server to communicate with Oracle. Fastest on lower-speed WANs, or on machines where Oracle client software is unavailable
Server - the name of the server where the BioAssay server is installed
If a valid username and password are entered for the appropriate server, BioAssay opens with the Start Page visible:
Options available from the BioAssay application could differ from user to user depending on permissions. If you do not see something you feel you should have access to, please see your system administrator.
Terminology
HTS -High Throughput Screening - testing
thousands of compounds in a short period of time.
depth screening of fewer compounds. Protocol - In BioAssay, a collection of database fields and calculations that hold data about a given biological experiment. Plate - A means of holding multiple samples in an easily transportable unit. Plate Format - The layout of the wells on a plate. Well Format - The type of contents in a well compound, control, empty, etc. Aggregate - A calculation that summarizes multiple results in one number, e.g. Average, Maximum, Minimum, Standard Deviation, Curve Fits. Grouping - Used in conjunction with aggregate calculations to summarize data. Primary Protocol Tables - The collection of tables that are automatically filled and calculated. Summary Tables - Summary tables provide alternate ways of summarizing primary data. File Import Template - A template which indicates how to take data from a file or files and place it into a HTS protocol Graph Template - Information that tells HTS how to place data in a 2-D graph. Browse Table - A table allowing the user to interact with data and perform Quality Control tasks. Search Table - A table allowing the user to search all protocol data. % Inhibition - A basic measure of potency normalizing raw data to a positive and negative control. IC50,EC50, LD50 - Measures of compound potency - the concentration in a protocol at which a compound is effective at the 50% level.
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16BioAssay
CambridgeSoft Terminology
Valid, Invalid, Not Validated - measures of
confidence in data. Generally, data that has less confidence assigned is less visible. Curve Fitting - Using an algorithm to determine the line that best fits a set of points. The parameters of this equation can then be used in further calculations. Direct Connection - BioAssay clients connect directly to Oracle via Oracle client software. Best for high-speed LANs. Proxy Connection - BioAssay clients use a HTTP server to communicate with Oracle. Fastest on lower-speed WANs, or on machines where Oracle client software is unavailable. Picklist - A defined list of items a user may pick from in a protocol.
Filter, and Edit, depending upon the table displayed. The Actions button in the Content Frame makes data specific tasks available to the user.
Resizing and Moving Columns

Columns in tables in the Content Frame are resized by the click and drag method often used in table/spreadsheet interfaces. To resize the columns in a table in the Content Frame: 1. Move the mouse over the border between two columns in the table header row, until the mouse turns into a double sided arrow.
Navigation
The user interface for BioAssay is split into two major frames: The Navigator and the Content Frame.
2. Click with the mouse and hold it down while
dragging the mouse. The column will resize as you drag the mouse. Release the mouse when the column is the appropriate size.
In some cases (e.g. protocol data tables) the columns can also be moved within the table. To move a column within a table:
1. Move the mouse over the column header to be
The Navigator (found in the left frame) acts much like a tree in Microsoft Explorer. Protocols and plates are organized into folders in the tree. Expand folders in the tree to find what you are looking for. The Content Frame displays the contents of the open folder in the Data Browser. The content frame can be used in 3 different modes: Browse,
moved and click. 2. Hold the mouse button down and drag the column to its new location.
NOTE: A column line appears when you have
dragged the column to a new column location.
BioAssay 17 Navigation
3. Release the mouse button when you have
2. Enter criteria into the new row.
dragged the column to the proper location.
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NOTE: This new column arrangement is saved for the
next time the table is opened.
Sorting Data
Data in any table can be sorted by any of the columns in the table. If you sort the data, the data will be sorted accordingly the next time the table is opened. To sort the data by a particular column, click on the column header.
Sorted by Barcode Sorted by GroupID
Criteria can be entered using drop down lists, if applicable, ranges for numerical columns, or the appropriate characters for text columns. 3. Click Apply. The data is sorted accordingly.
Tips
Searching in BioAssay is similar to searching in other ChemOffice Enterprise products: 1. Access the search form. 2. Enter search criteria. 3. Search results, made up of records matching the entered criteria, are returned. Numeric search criteria can be entered as a range using > (greater then), < (less then), and - (between one value and the next). The following table shows some examples of range searching:
Entered search criteria Really means...
To invert the sort, that is filter the data in descending order instead of ascending order, click the column header a second time.
Filtering Data
When the Filter button is available in the toolbar of the Content Frame, the table is available in Filter Mode. In Filter Mode, you are able to filter the data by any criterion in the table. When data is filtered, only the data matching the entered criteria is displayed. To filter the data in a table:
1. Click Filter.
3-11
Between 3 and 11 (not including 3 or 11) Greater then 100 (not including 100)
>100
A row with a green background appears at the top of the table.
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CambridgeSoft Navigation
Entered search criteria
Really means...
Table View
<200
Less then 200 (not including 200)
Form View
Refreshing the Data View

It is necessary to refresh the data view. Unless windows in the Content Frame are closed after you are finished, when the window is opened again, the data will not be refreshed. To refresh the view, click Get Data.
Getting Help
The BioAssay Users Guide, provided in a Windows Help File (a compiled HTML format), is available from the Content Frame by clicking Help.
Printing
Any table in BioAssay can be printed. To print a table:
1. Click Print.
Protocols
The BioAssay application makes it possible for users to store and analyze assay data. The interface to the data is similar to that of Microsoft Access. Fields contained in tables are defined as simple text, a piece of numerical data, a calculation, or an attachment such as a picture or document. After the table structure is defined, data can be imported into data tables from files through the use of a user defined file import template.
The Print Dialog appears. 2. Select your printing options and click OK.
Exporting Data to Excel

Any table in BioAssay can be exported to Excel. To open a table in Excel, click Excel.
Viewing Protocols in the Navigator Table and Form View

Any data table in BioAssay can be viewed in either Table or Form view. By default, all data is shown in table view. Switch between these views by clicking on the appropriate icon. The Protocols section of the BioAssay application allows the user to design a protocol and then import sets of data into the system to be analyzed by that assay. This makes it possible to analyze different sets of data with minimal amounts of subjectivity. The protocols folder in the Navigator contains any number of protocols accessed through a folder in the Protocols folder in the Navigator.
BioAssay 19 Protocols
2. Select Move Protocol (or Project)
The move project dialog appears.
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Right-clicking on the projects and/or folders in
the Navigator exposes a menu which allows users to create new projects/folders/protocols, rename the project/folder, or remove a project/folder. Right-clicking on a protocol in the Navigator exposes a menu which allows users to create new, or remove a protocol as well as: Move the Protocol Duplicate a Protocol View Protocol Properties (Renaming) The unclassified folder cannot be deleted because: When a project is deleted, the contained Protocols are moved to the Unclassified folder When a duplicate protocol is created, that duplicated protocol is placed, by default, in the Unclassified folder.
3. Highlight the folder or project to move the
project or protocol to. 4. Click OK.
Duplicating a Protocol
To duplicate a protocol:
1. Right-click on the protocol to duplicate. 2. Select Duplicate Protocol.
A copy of the selected protocol is added to the Unclassified project. Users can rename and/or move the protocol as desired.
Viewing a Protocols Properties (Renaming)

The protocol property dialog contains a name and description for the selected protocol along with the date and time the protocol was created. To view the properties of a protocol and change the name and/or description:
1. Right-click on the protocol. 2. Select Properties.
Moving a Protocol or Project

To move a protocol or a project: 1. Right-click on the project or protocol to move.
20BioAssay
CambridgeSoft Protocols
The Properties dialog appears.
Create Plates from Templates
This tool allows users to create plates for use within BioAssay. Plate templates are used to create plates. To create a plate:
1. Select Create Plates from a Template.
Protocol Data and Definitions

Protocol data and definitions are accessed by selecting (clicking) the appropriate protocol in the Navigator. The protocol opens in the right frame (the Data Viewer) exposing 3 tabs:
Tasks Data Definition
The plates dialog appears. 2. Select the template to use when creating your plates in the Plate Templates box. 3. Click Add. 4. Change the name of the plates to be added if desired.
NOTE: By default, the plates are given the same name as the templates they originate from. To change the names, edit the name in the second column of the middle table.
5. Enter other data that pertains to the batch of
plates in the Other Data box. 6. Click OK

Manage Plate Template
This tool is directly linked to Inventory Enterprise. It creates and edits plate templates according to input parameters. Plates can be created from these templates.
Tasks
The tasks tab gives users access to tools related to the selected protocol.
Import a Data File
This task allows users to import data into the protocol. See Importing Data on page 47 for more information.
The Manage Plate Template tool allows a user to map a compound ID to well formats specified in a given plate format. In other words, if a plate template contains well formats Compound 1, Compound 2, Compound 3, and Compound 4, you can map a particular compound ID (e.g. AB110293) to each well format (e.g. Compound 1). For more information about creating Compound Lists, seeCompound Lists on page 54.
To create a plate template:

1. Click Create plates from templates on the
c. Select how to import the list.
Protocol Tasks Tab.
NOTE: This link is only visible when the opened protocol is a plated based protocol, not linked to Inventory.
The Create Plates dialog appears. 2. Click the Manage Templates button. The Manage Plate Templates dialog appears.
Replace Current List - replace the current list with the new list Append to Current List - add the select list to the end of the current list. d. Click OK. By adding compound IDs manually a. Enter a compound ID in the Available Compounds textbox. b. Click Add.
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3. Enter a name for the template in the Plate
Templates textbox. 4. Click New.
7. Drag-and-drop the compounds in the
Compound List to the plate view, and the blocks of similarly-formatted wells will be highlighted. Drop a compound, and it will be assigned to those wells.
5. Select a plate format in the Based on: listbox. 6. Add compound IDs to the Available
Compounds list: By importing a Compound List a. Click Open Compound List. b. Highlight a compound list to use.
8. Click Save.
Create Plates from Templates
This tool allows users to create plates for use within BioAssay.
22BioAssay
Plate templates are used to create plates. To create or edit a plate template, click the Manage Templates button in the Create Plates dialog. For more information, see Manage Plate Template on page 21. To create a plate:
1. Select Create Plates from a Template.
5. Enter other data that pertains to the batch of
plates in the Other Data box.
NOTE: This link is only visible when the opened protocol is a plated based protocol, not linked to Inventory.
The plates dialog appears.
6. Click OK.
Protocol Data
Stored data for a protocol is accessed by clicking on the Data tab in the data viewer. This opens the Data Source Search Dialog.
2. Select the template to use when creating your
plates in the Plate Templates box. 3. Click Add. 4. Change the name of the plates to be added if desired.
NOTE: By default, the plates are given the same
name as the templates they originate from.
Primary Data tables are identified throughout the application with the blue data table icon. Summary tables are denoted by a similar green icon. The tables are defined under Protocol Definitions. To view your data, perform a search, or click Retrieve All. For more information about searching protocol data, see Searching Data on page 23.
Searching Data
The Protocol Search Dialog gives you the ability to search over protocol data according to your enter criteria. To search over the data:
1. Click the Data tab or click the Datasource
button under the Data tab if the Data tab is already open. The Search Dialog Appears. 2. Select the table to search over by highlighting a table under Select Data Source. 3. Enter you search criteria.
NOTE: The search fields vary depending on the data
displayed lower. If the number of tables displayed exceeds 4, a button allows you to bring the hidden tables back into view. Changing the selection to a table higher in the hierarchy cascades the change through the child tables. Thus, to see data for plate 2 instead of plate 1, we click plate 1s row in the Plates table, and that information is loaded into the Wells table.
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table selected.
4. Click Search.
Browsing Protocol Data
The data is arranged in tables, as defined by the Protocol Definition. Double-clicking a row in a table exposes the data related to that row in the next table in the hierarchy. For example, your protocol may contain 2 tables, a plates and a wells table. Clicking on a row in the plates table exposes the well data associated with the selected plate.
NOTE: Data is only editable, and most actions are only available, from the main grid (by default the most detailed table open (found at the bottom of the data viewer)). To bring a table from the top into the main grid, double click on its title bar. Related Plate Data
If a plate tab appears in the data view, a plate view is available for the open table.
Tables are arranged in the data viewer by the hierarchy defined in the assay definition. That is, tables which are higher in the hierarchy are found at the top of the data browser and nested tables are
To view data for a single plate:

Click the Plate Tab.
24BioAssay
The Plate viewer appears.
The Graph viewer appears.
To view data for multiple plates on one screen:

Click the MultiPlate Tab.
The MultiPlate viewer appears.
NOTE: In order to view the data for more than one row at once, hold down the CTRL or Shift keys when selecting rows. This will select multiple rows and display the results for the data on one plot.
Related Graphical Data
If a graph tab appears in the data view, a graph view is available for the open table.
Lookup Structure
To view the graph:

Click the Graph Tab.
If a protocol contains compound IDs which correspond to Registration IDs in Registration Enterprise, those compound records can be opened in the Registration Enterprise interface by selecting Lookup Structure in BioAssay.
To open a compound record in Registration Enterprise:

1. Select the row corresponding to the compound
For more information about defining tables for a protocol, please see Defining Tables and Fields on page 30. When a Protocol Definition folder is opened, the protocol structure is displayed in the right frame. The tree in the protocol definition frame groups information in five ways:
Primary Tables Calculation Tables Summary Tables Additional Tables File Import Templates Graph Templates
of interest in BioAssay. 2. Right-click or click Action and select Lookup Structure.

NOTE: The user logged in must have the appropriate privileges to browse Registration data in order to view compound details. View Wells in Inventory
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If a protocol is linked to Inventory Enterprise, users are able to view well details stored in the inventory schema by selecting View Wells in Inventory Actions menu option. To view well details:
1. Highlight the wells of interest in BioAssay by
holding the SHIFT or CTRL keys down during row selection. 2. Right-click or click Action and select View Wells in Inventory.
NOTE: The user logged in must have the appropriate privileges to browse Inventory data in order to view well details.
Primary Tables
Protocol Definitions
The Protocol Definition is accessed by clicking on the Definition tab in the data viewer. This is where the protocol's structure and calculations are defined. The protocol tables must be defined before importing data.
Tables are arranged in levels. A table situated lower in the tree contains rows which hold aggregate data of one row in a higher table. For example, a plate based assay has at least two tables: Plates and Wells. The Plates table is higher on the tree than the Wells table. This makes sense because each plate contains several wells. The Plates table defines plate attributes such as the barcode while the Wells table holds data associated with a particular well, such as the well ID.
26BioAssay
Each field falls under the appropriate table in the tree. Clicking on a table name or field name prompts the application to display details about the table or field under the appropriate tab to the right of the tree.
Child Tables always contain at least one field which is identical to a field with the same name in the Parent table. This field is the grouping field. This field allows the user to indicate to the application which data in the wells table belongs to the corresponding row in the parent table (e.g. Plate ID).
Calculation Tables
Calculation tables in BioAssay are used to calculate data for a protocol, in ways that may not fit into the standard hierarchy. For example, the primary data hierarchy may be Plates->Wells, but you would like to run some calculations over the same compound that is plated on multiple plates. Parent Tables Every primary table in an assay, except the table at the top of the hierarchy, has a parent. The parent table is the table found in the next highest level in the protocol tree. For example, in the image above, the Summary Table is a parent of the WELLS table. Because the Summary table is at the very top of the hierarchy, the Summary table does not have a parent. In this example, and in any parent table example, the parent table holds information summarizing the data in tables below it. For example, the Summary table contains a Compound ID field because all of the data in the WELLS table have a common Compound ID. Child Tables Every table in a protocol, except the table at the bottom of the hierarchy, has a child. Child tables are named as such because their data is summarized in some way by its parent. For example, the WELLS table in the above image is a child of the Summary table. There are many wells which are summarized (with various statistics) in the Summary table.
Summary Tables
Calculation tables contain one or more grouping fields in addition to calculation fields. The grouping fields indicate which data should be used in a calculation. For example, if the compound ID is used as the grouping field, calculations are made for each compound ID. Without the grouping field, calculations would be based on all valid data recorded for the protocol.
Summary tables in BioAssay are used to summarize data for a single protocol. Calculations in the standard data tables are usually based on grouped data. That is, data for an individual plate or run. Taking averages and standard deviations of data in more then one plate or run helps to visualize the overall picture.
Summary tables contain one or more grouping fields in addition to calculation fields. The grouping fields indicate which data should be used in a calculation. For example, if the compound ID is used as the grouping field, calculations are made for each compound ID. Without the grouping field, calculations would be based on all valid data recorded for the assay.
For more information about using the File Import Template wizard, please see File Import Templates on page 43. For more information about importing data, using a defined File Import Template, please seeImporting Data on page 47.
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Graph Templates
Additional Tables
Additional tables are tables which contain data related, but not linked, to the rest of the data in the protocol. These tables can contain any number of fields. These tables allow the user to enter additional data which is mapped to the protocol but does not belong in any other fields.
File Import Templates
Graph templates are used to plot data. After a graph template is made, you can plot data by clicking on the appropriate Graph tab in Data View. Please see Related Graphical Data on page 25 for more information. Graph templates include information related to both the data and the display of that data. For more information about creating Graph Templates, please see Creating a Graph Template on page 49.
BioAssay includes a wizard which aides in designing templates called File Import Templates. These templates define how data should be imported into tables. The advantage of creating a template is to indicate the format of a data file once, and not have to enter the same information when using a file with the same format again. File Import Templates tell the system the format of the file (i.e. what kind of delimiter is used, if there are header lines in the file) as well as where to put the data, once it is imported, in the assay data tables of the assay. There must be at least one File Import Template defined for any file being imported.
Protocol Security
Protocol security in BioAssay is mostly centered around permissions to view, change data related to, and change definitions for protocols. The user who creates a protocol is automatically given the
28BioAssay
appropriate permissions for the protocol, but all other users must be explicitly added to the protocol security list. There are three levels of protocol security for users:
Security Description
To steps involved in creating a new protocol include:

1. Right-click a project in the Navigator. 2. Select New Protocol.
Change Data Validate Data Change Protocol Definition
edit, add new, and delete protocol data validate data already in protocol data tables edit, add new, and delete table definitions, file import templates, graph templates and protocol security
3. Enter a name for your protocol and click OK.
The Protocol Wizard appears.
For information about granting users permissions to a particular protocol, please see Defining Security on page 43.
Designing a New Protocol

The first step in designing a new protocol is knowing what kind of data is going to be provided, what the overall result should be, and finding all of the steps necessary to move from the data to the result.
Protocol Template Description
4. Select the template you would like to use from
the Protocol Templates list.
Plate Based?
InventoryLinked?
Blank
Blank protocol definition Blank protocol definition with 2 tables
Simple 2-Tier
Protocol Template Description
Plate Based?
InventoryLinked?
Initial Screen
one-dose, singlenumber-percompound protocol
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Confirmation Screen multi-dose, multiple- Y number-percompound protocol IC50 Initial Screen (Inventory Linked) IC50 protocol one-dose, singlenumber-percompound protocol Y Y
N Y
Confirmation Screen multi-dose, multiple- Y (Inventory Linked) number-percompound protocol IC50 (Inventory Linked)
5. Click OK.
IC50 protocol
The protocol is inserted in the Navigator under the select project. The protocol definition must be defined, and at least one file import template must be added before you can import data.
Any number of tables can be defined. If a table's data depends on the data in another table, the dependent table must be higher in the structure than the other table. The table structure will be defined most efficiently by, defining the lowest level table first, and working up to the highest level table. There are protocol templates that will help you to get your protocol started. Please see Designing a New Protocol on page 29 for more information.
NOTE: After importing data, the user will be limited to
Defining Tables and Fields

How tables are arranged, depends on the data and the desired result. Typically, raw data values are found in a table at the lowest level. It might be helpful to make a sketch of the table structure ahead of time.
adding new fields and adjusting calculation definitions.
30BioAssay
Defining a Primary Protocol Table
2. Perform the appropriate action:
If you have used a template, or if you have started with a duplicate protocol, your table may already exist. To start defining tables:
1. Open the protocol and click on the Definition
If you would like to...
Then...
tab.
Rename the table or edit the table comments Add a parent table
Click on the table and edit the fields in the far right frame. Right-click on the table name and select Create parent table Right-click on the table name and select Create child table Right-click on the table name and select Remove table
Add a child table
The Protocol Definition appears in the right frame.
Remove a table
3. Click Save Changes, if necessary.
Defining Fields in a Table
If you have used a template, or if you have started with a duplicate protocol, some fields may already exist.
NOTE: Templates do not define calculations, they only
insert a field with type calculation. After tables are created, the table fields must be defined before data can populate them. Depending upon the template chosen, the contents of the frame will differ. To start defining fields:
1. Open the protocol and click on the Definitions
Tab. The Protocol Definition appears in the right frame.
Depending upon the template chosen, the contents of the frame will differ. 2. Do one of the following: To add a new field: a. Right-click the name of the table you would like to add a field to. b. Select New Field.
Then...
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Move a field from a Right-click on the higher table to a lower appropriate field table name and select Move Down To... Move a field from a Right-click on the lower table to a higher appropriate field table name and select Move Up To... Move a field up within a table Right-click on the appropriate field name and select Move Up Right-click on the appropriate field name and select Move Down
c. Go on to edit the field data.
To edit the data for an existing field:

a. Click on the appropriate field in the tree.
Field data appears in the right frame.
Move a field down within a table
Field Types
b. Edit the appropriate data in the right frame. 3. Click Save Changes, if necessary.:
The field options available to be defined vary according to the field type chosen. When defining a field, after entering a name and comment, select a field type. Enter the appropriate information.
Field Type Field Options Display in Scientific notation? (yes if selected) Number of decimal places
Then...
Remove a field
Right-click on the appropriate field name and select Remove Field
Number (Real)
Number (Integer)
Display in Scientific notation? (yes if selected)
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Field Type
Field Options
Field Type
Field Options
Text Date Elapsed Time (hh:mm:ss format) Yes/No Picklist Value Calculation (Numeric Output) Calculation (Text Output)
None None
Display in Scientific notation? (yes if selected) Units of Time
Attachment None (Data Storage) Attachment (External Storage)

Indexed Fields
None
None
Which Picklist? Display in Scientific notation? (yes if selected) Defined calculation Defined calculation
Indexed fields have the following characteristics:

Fields which will be used to search data often
(searching speeds improve when a field is indexed) Importing data into an indexed field is slightly slower than importing data into a field which is not indexed. Examples of fields to index: Compound ID Protocol data fields which are often search over To index a field:
1. Open the field definition (click on the field in
Compound ID None Well Index Inventoried Plate Barcode None None
the protocol definition tree). 2. Select the Indexed checkbox.

Key Fields
Key fields in a table accomplish two things:

Limits the data returned to the user to only data
Plate Identifier None Plate Format Well Format Concentration None None
Display in Scientific notation? (yes if selected)
related to the row selected in the previous table. Groups data for calculations - only data with the same value in the key field are used to determine calculations.
NOTE: Every table must contain at least one key field.
To make a field a key field:

the protocol definition tree). 2. Select the Key Field checkbox.

Required Fields
application will then be able to link your new view to other tables in Oracle and make the view available to users for reporting. To Expose the table in BioSAR Enterprise:
1. Click Expose Table In BioSAR Browser.
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If a field is required, a value must be given to the field before a data import is complete. To make a field required:
the protocol definition tree). 2. Select the Value checkbox.

Allow Editing
2. Select which views to publish on the right side
Any data table field can be made read-only by unselecting the Allow Editing checkbox in the field definition. By default, Allow Editing is selected. If this checkbox is unchecked, users will not be able the manually edit this field in the data table in Edit Mode.
(valid data only, and/or all data) by selecting the appropriate checkbox. 3. Select the Link to base table indicated on right checkbox if the protocol table can be linked to another schema in BioSAR Enterprise. The application will try to pick a field which is most likely to be linked. This field can be changed by selecting a different field from the Field listbox.
Show Field
Assigning a Calculation to a Field

When a user clicks Edit Calculation in a Calculation field definition, the Calculations Wizard appears.
Users defining a field in a protocol have the option of hiding that field in the data table display. This may be useful for fields necessary for certain calculations, but not relevant to the user browsing the data. By default, all fields are visible. To hide a field from the data table display, unselect the Show Field checkbox in the field definition.
Expose Table in BioSAR Browser

Clicking the Expose Table In BioSAR Browser button makes the table visible in the BioSAR Enterprise administrator interface. Note that in BioSAR Enterprise, BioAssay tables will appear in the Views section, as they are actually Oracle views. Administrators of the BioSAR Enterprise
This wizard helps to define the calculation, and the data used to compute the calculation.
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To start using the Calculation Wizard:

1. Select the tab for the appropriate calculation.
The default aggregate calculations are:

Mean - takes an average of all aggregate data Standard Deviation - finds the standard
Three types of calculations are available: Aggregate - calculations made on a rows aggregate data found in a lower table Mathematical - calculations dependent upon a user defined equation Curve Fit - calculations made to fit a set of data to a particular curve Conditional - calculations that fill a field based on a set of user-defined conditions For more information about defining calculations and assigning values, please click on the type of calculation in the above list. 2. Highlight the calculation to be used, and click Next. While defining a calculation, you must select the fields that you want to use for variables in the calculation. The fields listed depend on the type of calculation you are creating and the field type of field.
Except for Conditional calculations, only fields
deviation of all aggregate data

Sum - computes the sum of all aggregate data Maximum - returns the maximum value in the
aggregate data
Minimum - returns the minimum value in the
aggregate data When a user clicks Edit Calculation, the calculation wizard appears. Click on the Aggregate Tab to define an aggregate calculation. To insert a aggregate calculation:
1. Highlight which calculation you would like
inserted into the cell.

2. Click Next.
The Input Values screen appears.
with a field type of Number (Real), Number (Integer), or Calculation will be options. For Aggregate Calculations Only fields in tables below the current table are displayed For Mathematical, Conditional, and Curve Fit Calculations Only fields in the current table or tables higher then the current table are displayed
Aggregate Calculations
3. Select the table where the data that will be used
Aggregate calculations are calculations performed on a data set resulting in one figure that is representative of the whole group. Therefore, aggregate calculations must be included in a table higher than the location of the aggregate data.
for the calculation is located, from the Table listbox. 4. Select the field where the data that will be used for the calculation is located, from the Values listbox. 5. Click Next.
The Define Conditions screen appears.
Mathematical Calculations
Mathematical calculations are any calculations performed using a defined equation. Therefore, calculations must be made on data in the same table as the table where the calculation is inserted or any table higher than that table. There are some already defined calculations which can be used including:
% Inhibition - returns the % inhibition (100 *
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6. If you would like to only use data points if
certain conditions are met, add a condition: a. Click on Add. b. Select a field where the data must fulfill the condition. c. Select a mathematical equality symbol. d. Finish the condition by entering the value that the data must fulfill. 7. Click Next.
The Finished screen appears.
((Value - LowControlAverage) / (HighControlAverage - LowControlAverage))) Log(x) - returns the log (base 10) of a value 10^x - returns the inverse log of a value Addition Subtraction Multiplication Division Percentage Half Life - (Time * ln(2)) / (ln(100 / PctRemaining)) Z' Factor - 1 - ((3*SDPosCtl + 3*SDNegCtl) / abs(AvgPosCtl - AvgNegCtl)) When a user clicks Edit Calculation, the calculation wizard appears. Click on the Aggregate Tab to define an aggregate calculation.
8. Select the number of decimal places that the
result should be limited to, from the listbox. 9. Click Finish.
36BioAssay
There are two options in using a mathematical calculation:

Use a default equation Define a new equation Use a Default Mathematical Calculation
To use a default calculation: 1. Click on the Mathematical Tab. 2. Highlight which calculation you would like inserted into the cell. 3. Click Next. The Calculation Parameters screen appears.
result should be limited to, from the listbox. 8. Click Finish.

Define a New Mathematical Calculation
To define a new calculation:

1. Click on the Mathematical Tab. 2. Click New.
The Edit Custom Function window, a window allowing the definition of a new equation, appears.
4. The equation used to compute the chosen
value is displayed. Select, in the table at the bottom of the window, what values should be used for the variables in the equation. This involves first selecting a Table, and then a field in that table from listboxes. 5. Repeat step 4 for all of the variables listed in the table. 6. Click Next.
3. Enter a name for the calculation in Function 4.
5. 6. 7.
listbox. Enter an equation for the calculation in the Equation textarea. General information about defining an equation is provided in the help section of this window. Supported operators are found under the Operators Tab and predefined functions are listed under the Functions Tab. Click OK. Highlight the function, just defined, and click Next. Continue with step 4 in Use a Default Mathematical Calculation on page 37.
have been defined for those graphs. If the list does not contain any values, go back to the Graph Templates section and set up the graphs and curve fits that you wish to perform first.
1. Select the curve parameter to be used for the
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calculation in the listbox (these options will be limited to curve parameters which make sense with the highlighted curve fit calculation).
NOTE: If no predicted values were defined in the Curve Fit calculation definition, there will be no options in the listbox (when Predicted value is selected).
2. Click Next.
The Input Values screen appears
Curve Fit Calculations
Curve Fit calculations are calculations obtained from fitting data to a curve equation. Therefore, calculations must be made on data in the same table as the table where the calculation is inserted or any table higher than that table. When a user clicks Edit Calculation, the calculation wizard appears. Click on the Curve Fit Tab to access the Curve Fit calculations.
3. Select the table where the data that will be used
The list will contain the curve fits that are applicable for the given table, based on the graph templates that have been set up and the curve equations that
for the calculation is located, from the Table listbox. 4. Select the field where the data that will be used for the x-values in the curve is located, from the X-Values listbox. 5. Select the field where the data that will be used for the y-values in the curve is located, from the Y-Values listbox. 6. Click Next.
38BioAssay
The Define Conditions screen appears
Define a New Curve Fit Calculation

1. Click New.
The Curve Fit Template window, a window allowing the definition of a new curve fit calculation, appears.
7. If you would like to only use data points if
certain conditions are met, add a condition: a. Click on Add. b. Select a field where the data must fulfill the condition. c. Select a mathematical equality symbol. d. Finish the condition by entering the value that the data must fulfill.
8. Click Next.
For more information about creating new models, please see Defining a New Model on page 40.
2. Enter a name for the calculation in the
Template textbox.
3. Highlight the Model to be used. 4. Enter Parameter information under the
Parameters Tab.
a. Select Variable or Constant, in the Type
result should be limited to from the listbox.

10.Click Finish.
column, for each parameter. b. Enter a numerical value, or select a value from the drop-down menu in the Value column.
5. Enter additional calculation options under the
Defining a New Model
Advanced Tab.
Models are, in general, equations used to calculate curve fit parameters. New models can be defined under the User-Defined Tab in the Curvefit Template dialog box. To define a new model:
1. Click New under the User-Defined Tab in the
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6. Enter the desired predicted values for
variables under the Predicted Tab For more information about creating new models, please see Defining a New Model on page 40.
Curvefit Template dialog box. The User-Defined Model dialog box appears.
a. Click Add to add parameters for a predicted
2. Enter a name for your model in the Name
value.
b. Enter a name for the result. c. Select which value is given (X or Y).
textbox. 3. Enter an equation in the Equation textbox. Equation definition tips and conventions can be found in the lower half of the window. 4. Click Validate Equation to make sure the equation entered is written in the correct syntax. 5. Click OK. The new model is listed under the UserDefined Tab.
Editing a Curve Fit Calculation
NOTE: The value not provided is the value which is
predicted.
d. Enter a value for the variable. e. Click OK. 7. Click OK.
To edit a curve fit calculation:

1. Highlight the calculation to be edited. 2. Click Edit.
40BioAssay
The CurveFit Template window, populated with the definition of the selected calculation, appears.
6. Edit additional calculation options under the
Advanced Tab.
7. Edit the desired predicted values for variables
under the Predicted Tab.
For more information about creating new models, please see Defining a New Model on page 40.
3. Edit the name for the calculation in the Name
a. Click Add to add parameters for a predicted
value.
textbox, if necessary. 4. Highlight the Model to be used, if it is not selected correctly. 5. Edit Parameter information under the Parameters Tab.
b. Enter a name for the result. c. Select which value is given (X or Y). Note:
a. Select Variable or Constant, in the Type
column, for each parameter.

b. Enter a numerical value, or select a value
The value not provided is the value which is predicted. d. Enter a value for the variable. e. Click OK. 8. Click OK.
Conditional Calculations
from the drop-down menu in the Value column
Conditional calculations allow the user to fill a field based on the contents of other fields in the protocol. Conditional calculations are the only calculations that may output a text value or a numeric value. In order for a conditional calculation to hold a text value, it must be defined as a Calculation (Text Output) in the Field Type section of the field definition.
When a user clicks Edit Calculation, the calculation wizard appears. Click on the Conditional Tab to define a conditional calculation.
2. Choose a value that will be placed in the field
when none of the conditions are met (the default value). 3. Add as many conditions and output values as you need by clicking the Add button and filling in the table. In the example above, the field will contain "In Range" if the value the Successful Curves field is between 1 and 5, and will contain the appropriate out of range message if it is high or low. 4. Click Next, and Finish.
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To insert a conditional calculation:
1. Click Next.
Summary Tables
Summary tables are treated like primary tables in BioAssay, but they only contain a grouping field and calculation fields. They are used to group data by a different parameter to allow for additional analysis (calculations). Summary Tables include:
One grouping field As many calculation fields as desired
For example, this summary table is grouped by Compound ID:

Compound ID The grouping field. Calculations are made according to the grouping field. Count of >3 SDs above - this calculation counts how many instances are found for each compound ID with standard deviations greater than 3
The Output Values screen appears.
42BioAssay
Defining Security
Users, other then the creator, must be given the appropriate permissions to access and edit protocols. To give a user or group permissions to a protocol:
1. Open the appropriate protocol's protocol
b. Click Remove. 7. Click OK.
Importing and Viewing Data

In order to import data, the assay tables must first be defined. If there are no tables listed in the Assay Definitions, the protocol tables have not been defined. The only way to import protocol data into BioAssay is to use the File Import Wizard. The File Import Wizard uses user defined file import templates. Therefore, a file import template compatible with the data being imported must also be defined before importing data.
definition. 2. Click on the Security Tab. 3. Check the box that says Lock valid data if you want to disallow editing of data that has been validated. 4. Click the Edit Protocol Security button. The Protocol Security window opens.
File Import Templates

File Import Templates are used to import data from a file and populate user-defined tables with that data. To define a File Import Template:
5. Select either the Users or Groups radiobutton 1. Open the protocol definition. 2. Right-click the File Import Templates folder
(depending on who you would like to add to the security). 6. Choose the appropriate action: To add a user or group to the protocol's security: a. Highlight the user or group in the list. b. Click Add. c. Select the checkboxes corresponding to the permissions you would like to give the user or group. For more information about your options, please see Protocol Security. To remove a user or group from the protocol's security: a. Highlight the user or group in the table (on the right).
in the tree.
3. Select New Template.
The File Import Template Wizard appears. 4. Enter the a name and description for your file import template in the Select Data File window. 5. Click Next. The File Format Information screen appears. 6. Select a file delimiter. Commas Tabs Spaces Tecan (used for importing files created with certain Tecan instruments)
Other (enter the delimiter in the textbox
which appears to the right) 7. Select the type of file you are importing:
File Type
Description
Even though all the results above apply to compound AB-00001, the compound name is not repeated for clarity. When you import, you should choose Fill field with last non-empty value encountered. The data in BioAssay will then look like this:
Administrator
Columnar (ExcelType)
a series of columns; each column contains the values for one variable.
Compound ID AB-00001 AB-00001 AB-00001
Result 34.5 56.4 67.8
Plate Block raw data is arranged in a block; the block is arranged to coincide with plate arrangement See BioAssay Plate Block Data Files on page 323 for more information.
8. Complete the details related to your file type.
Columnar:
All results are properly associated with the correct compound id. Your data may include legitimate empty spaces, where a result is not available, for instance:
Indicate if your data file has header lines (lines not containing actual data). If there are header lines, enter how many in the textbox. Indicate how you want to treat empty values in your data. You can either leave those fields blank, or fill them with the last non-blank value encountered in the file. For example, your Excel data may look like this:
Compound ID AB-00001 AB-00001 AB-00001
Result 34.5
67.8
Compound ID AB-00001
Result 34.5 56.4 67.8
In this case, you should choose Leave field blank. Plate Block: Check the boxes to indicate which sections are present in your plate block file. Enter the number of rows in each category. For more information about the parts of a plate block file, see BioAssay Plate Block Data Files on page 323. 9. Click Next.
44BioAssay
If you have selected a plate block file, the Well Options screen appears. (If you have selected a Columnar file, go on to step 10). Here you can select how many values appear for each well in your file. The options are detailed below:
Option Description
Option
Description
Multiple values for each well columnar format, same field.
A kinetic protocol where multiple values are measured for each well at different timepoints, and the data goes into the same field.
A single A standard protocol which value for each measures a single value for well. each well. There may be data for multiple plates in a single file, but each well has just one number associated with it. Multiple values for each well separate data blocks, separate fields. Multiple values for each well separate data blocks, same field. Multiple values for each well columnar format, separate fields. A protocol where multiple values are measured for each well. In the most common case, a reader reads at 2 different wavelengths and outputs a data block for each wavelength. A kinetic protocol where multiple values are measured for each well at different timepoints. All the values will go in the same field, but there are many for each well. A protocol where multiple values are measured for each well, and the data is arranged in a columnar format similar to an Excel file.
10.Click Next
The Map Fields screen appears. 11. Assign values to the fields in the selected table by: a. Selecting what type of value to populate the field with: Choices depend on the type of file you have chosen and the type of file being imported.
Data Source File Type Description
Leave Blank
Columnar (Excel) or Plate Block Columnar (Excel)
No data is imported into this field Data is found in a column in a data file enter the column number to the right Data is part of the filename -
Data in File Column Number
Use Filename Data
Columnar (Excel) or Plate Block
Data Source
File Type
Description
Data Source
File Type
Description
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Use Default
A default value should be entered for this field enter the default value to the right During import, the user will be prompted for the value of this field For attachment fields only. The file itself will be uploaded to the database, into the field.
Fill From Plate Inventory
Prompt Me
For platelinked assays only. The field will be filled with the corresponding data from the plate inventory field. Select which field will be used as the data source to the right. Data is the data found in the plate block Data is in a particular cell in the File Header Block - enter the cell to the right Data is in a particular cell in the Block Header Cell enter the cell to the right
Upload File
Plate Block Data
Plate Block
File Header Cell
Plate Block
Block Header Cell
Plate Block
46BioAssay
Data Source
File Type
Description
12.Repeat this for each field listed. 13.Click Finish.
Block Footer Plate Block Cell
Data is in a particular feel in the File Block Footer Cell - enter the cell to the right Data is in a particular feel in the Block Column Cell enter the cell to the right Uses time on user's machine when file is imported Uses username of user who imports file
The new File Import Template is defined and ready for use.
Importing Data
If the protocol tables and a File Import Template compatible with the data file being imported have been defined, data can be imported through the use of the File Import Wizard. To import data:
1. Open the protocol (select the protocol in the
Block Plate Block Column Cell
Navigator). 2. Click on the Tasks Tab. 3. Click Import a Data File. The File Import Wizard appears.
Use Import Time
Use Current Columnar User (Excel) or Plate Block
4. Select an import template. 5. Click Next. 6. 7. 8.
b. Entering the appropriate information in the
right most column, if applicable: for Use Default - a default value for Data in File Column - enter the column number for Block Header Cell - enter the cell (as entered in an application like Excel) in the plate block header lines.
9.
The second window appears. Use the browse button to browse to the data files you would like to import. Click Next. Enter the appropriate information, if the wizard asks. This window will differ depending on the File Import Template being used. Click Next.
The Import File screen appears.
See Protocol Data on page 23 for more information about searching and browsing protocol data.
Validating Protocol Data

When protocol data is first imported, a not validated icon appears in the left most column in the data table. This indicates to users that nobody has made a decision about the validation of the data yet. Invalid data is not used in calculations or curve fits. To validate your data:
1. Open the data tables that contains the data to
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10.Select the checkbox if you would like to view
the data in the data tables before importing. 11. Click Finish. The appropriate table is populated with data. If any fields in the protocol tables are calculations, those calculations are made.
Searching for and Viewing Data in Tables

Stored data for a protocol is accessed by clicking on the Data tab in the data viewer. This opens the Data Source Search Dialog.
be validated. 2. Highlight the data to be validated. 3. Select Change Validity under the Actions Menu. The validation dialog appers.
4. Select the validity you would like to assign to
the highlighted data. Primary Data tables are identified throughout the application with the blue data table icon. Summary tables are denoted by a similar green icon. The tables are defined under Protocol Definitions. To view your data, perform a search, or click Retrieve All.
Validity Option Icon Description Used in Calculations?
Not I Validated
no validation Yes decision has been made
48BioAssay
Validity Option
Icon Description Used in Calculations?
Creating a Graph Template
Graph templates are used to plot data in a protocol. These templates define properties such as:
Which data is to be plotted Physical properties of the graph - e.g. error
Valid
data is found Yes to be valid data is found No to be invalid data must be Yes reviewed before making a validation decision
Invalid
Request Review
bars, gridlines, graph type, data point markers Where the graph template can be accessed from What curve equations will be fit to the data by default To create a new graph template, browse to the definition of your protocol and right-click the Summary Table for the Graph Template and select is New Graph Template. A new template is listed. To begin defining a template:
1. Click the graph template name in the Protocol
5. Select the appropriate cascading options.
Cascade validity change to detail records
- apply the same validity decision to records summarized by the highlighted record Override current invalid records - change invalid records summarized by the highlighted data to the new validation 6. Click OK.
Definition tree. The graph template details open in the right frame.
Data Manipulation and Curve Fitting

Any set of data can be plotted and fit to a curve if desired. The only constraint is that both fields being plotted are found in the same table. In order to plot your data, you must first have a graph template designed for your assay. Graph templates define not only what data is plotted, but where the graph template is accessed from, and the physical properties of the graph.
NOTE: If the opened template is new, the above frame
is populated with default information.

2. Enter the desired information:
Template Name - a name for the template Comment - additional comments for the
template.
Summary Table - The table in the protocol
where the graph images will be stored. For instance, if you are preparing a graph of activity vs. concentration for each compound, you would select the Compounds table as the Summary Table, and the Data Table would contain the activity at each concentration. Data Table - The table the plotted data is taken from. This will typically be the direct child table of the Summary Table. X-Axis - The field from which the application should populate the X-Axis. Y-Axis - The field from which the application should populate the Y-Axis.
3. Click Conditions to limit the points that are
If image fields are not found for your graph template, they will be created in the Summary Table. You will see 2 new fields appear, one named as <Graph Template Name> and one as <Graph Template Name> (Small). These fields are where graph images will be stored when calculations are run.
Administrator
4. 5. 6. 7.
Plotting Data using a Graph Template

There are 2 ways to show the graphs that have been defined using the graph templates - graph images and interactive graphs.
Graph Images
included in your graph. For instance, you may wish to include only points where the Y-axis value is above 0. Click Graph Storage to define how to store images of the graphs in your data table. You can store the full image, or strip the titles and legends from the stored image. These stored images are recreated when the data is recalculated. Click Curve Fits to change the list of curve equations that are fit to the data by default when calculations are done. The set of curves that you define here will be available for use when you set up Curve Fit calculations. You can use the default equations, or create your own. See Define a New Curve Fit Calculation on page 39 for more information. Click Display Options to define the graph display options. The Display Options dialog appears. Please see Graphing Options on page 53 for more information. Click Save Changes.
When defining a graph template, the user must indicate which table is the summary table for the graph. Image fields are added to this table, and when calculations are performed, a small and a large image of the graph are stored in these fields. By default, the graphs are shown as blue links that say (Graph), and they may be opened by double clicking or shown in place by right-clicking and choosing Show Pictures.
Interactive Graphs
When defining a graph template, the user must indicate where the data for the graph template should come from. If a graph template is defined to be available from a table, a button for that graph will appear in the Display Bar:
Clicking this button switches to a plotting window with the specified data plotted according to the graph template.
50BioAssay
Fitting Data to a Curve

The graphing interface will fit any data to any curve as long as the curve is defined in the system. Two default curves are defined:
Sigmoidal-dose response One Phase exponential decay
After fitting the data to a curve, the Data Tab will display equation parameter values, and fit statistics.
Curve Fit Templates
For more information about how to define a new curve fit equation, please see Define a New Curve Fit Calculation on page 39. If the correct curve is already defined, do the following to fit plotted data to a curve:
1. After plotting data, click Curve. 2. Highlight the name of the curve in the
Curve Fit Templates are listed in the Available Curves box found in the Add or Remove Curve window. To access this window, click Curve from any plot. For more information about using a template that is already listed, please see Fitting Data to a Curve on page 51.
Creating a New Template
To create a new curve fit template:

1. From the Add or Remove Curve window,
Available Curves box. 3. Click Graph Selected Curve. The name of the curve appears in the Graphed Curve box. 4. Repeat this process until all of the curves you wanted plotted are listed in the Graphed Curve box. 5. Click OK. All curves listed in the Graphed Curve box are added to the plot, fitting the equation as close as possible to the data points.
2. 3.
4.
5. 6.
click New. The Curvefit Template window opens. Enter a name for the template in the Name textbox. Highlight the Model to be used. For more information about creating new models, please see Defining a New Model on page 40. Enter Parameter information under the Parameters Tab. a. Select Variable or Constant, in the Type column, for each parameter. b. Enter a numerical value, or select a value from the drop-down menu in the Value column. Enter additional information under the Advanced Tab. Click OK. The name or your new template will be listed in the Available Curves box.
The graph characteristics, such as the type of scaling on the axes and how far the fitted curve is extended from the data, are defined in the Graph Options dialog box.
Editing a Template
The edit template interface behaves just like the new template interface. If you would like to edit a template:
From the Add or Remove Curve window,
Data Statistics
click Edit. The Curvefit Template window opens with the current template settings populating the fields in the window. See Creating a New Template on page 51 for more details.
Various statistics defining the data are found under the Data Statistics Tab. Statistics for both the X and Y values are recorded.
Administrator
Viewing the Plotted Data

The Data Tab found on any plot frame displays the data plotted along with information about any curve fits made.
Equation
The Equation Tab displays the equation that the data is fit to under Parameterized Equation. The x and y variables define the x and y coordinates for the fit curve. The values for other parameters in the equation are assigned to fit the data the best. The final values are recorded in the Parameter Values table.
Fit Statistics
The Fit Statistics Tab records statistics defining how well the Equation, found under the Equation Tab, fits the data found under the Values Tab. The information found under this tab will give the user information to determine if the data has a meaningful fit to the curve.
Values
The Values Tab displays the actual data point values to which the equation found under the Equation Tab is fit.
Invalidating Data Points

Any data point plotted can be removed from the plot. This may be useful in removing outliers in order to produce a better curve fit.
52BioAssay
When viewing a plot (for more information please see Plotting Data using a Graph Template on page 50), you can exclude and include data points. By default, active data points appear in blue, inactive data points in red. All data points are active by default. To exclude an active datapoint from the fit or include an inactive data point in the fit:
1. Find the point in the plot and right-click. 2. Select the appropriate options (Exclude from
Selecting a checkbox next to a Show option will show that option. Unchecking the box will hide the item.
Fit or Include in Fit).

NOTE: Points invalidated from the graphing interface are also marked as invalid in the data tables, therefore excluding them from calculations.
Graphing Options
There are three tabs in the Graph Options dialog:
General - define general plotting
Scaling
characteristics such as error bars, grid lines, and graph extensions Title - give the plot and its axes titles Plots - define display characteristics such as data point markers and the plot type To access the Graph options dialog: Click Options from a plotting window OR Click Graph Options from a Graph Template definition.
Graph Options General Tab
By default, the graph window will fit itself to the data being plotted. This means that the maximum and minimum numbers shown on the scales may change from graph to graph. To prevent this, you can lock either or both axes to a maximum and minimum value.
Graph Extension
Most of the options under the general tab will remove and add particular parts of the plot such as the legend, the axes labels, or the data itself.
The graph extension listbox determines how much the fitted curve should extend from the data points. The default is 10%. This means the fitted curve will extend 10% more from the data points at the two ends of the curve. Making this value larger will extend the curve farther, as seen in the following images:
Graph Extension =10%
3. Select a color from the drop-down box.
Administrator
Graph Extension = 40%
Graph Options Plots Tab
The graph options Plots Tab allows you to control the display characteristics of the graph. From this
Error Bars
tab, select a plot type, color and point style.
Error bars can be added to any plot. To add error bars to a plot:
1. Click Options. 2. Select an error bar option (found in the right
column of the Graph Options dialog box). Only one error bar option can be chosen at one time. Error bars can be calculated from individual data or aggregated data. 3. Click OK.
Graph Options Title Tab
The graph options Title Tab allows you to label the graph and its axes. To make a label:
1. Enter text in the appropriate textbox. 2. Click Font to select a font, style, and size.
Compound Lists
Compound Lists are lists of compounds for use in plate templates. To create a new list:
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CambridgeSoft Compound Lists
1. From any data table with a Compound ID
field, select the rows containing the Compound IDs to be saved. 2. Right-click and select Save Compound List. Lists appear in the Navigator under the Lists folder.
NOTE: If the list contains the same compound ID more than once, that compound ID will only be saved once.
The following settings can be defined from BioAssay:

Plate Formats Well Formats Picklists NOTE: All settings defined in BioAssay are reflected in
Inventory and vice versa.
Manipulating Compound Lists

Compound Lists are lists of compounds for use in plate templates. These lists can be added together, subtracted, etc. To manipulate your compound list:
1. Open a list by clicking on it in the Navigator. 1. Click on the Actions Button and select the
Editing the settings tables

All of the settings tables have the same basic interface. Data is stored in a table. By default the table opens in Browse Mode (as seen by the active browse button). While in Browse mode, the user can view the settings listed, but cannot make any changes. To make changes to a settings table, click Edit. When in Edit Mode, the Add, Delete, and Cancel buttons are visible.
appropriate option: Merge a List - produce a new list which is the result of both lists together. Intersect a List - produce a list of only the Compound IDs which are included in both the original list and the selected list. Subtract a List - produce a list of only the Compound IDs which appear in one of the lists (are not common to both lists) 2. Select a list to perform the operation on. 3. Click OK. The new list appears.
Adding an entry
To add an entry to a settings table: 1. While in Edit Mode, click Add. An empty column is inserted. 2. Enter information in the appropriate columns of the new row. 3. Click Save.
Deleting an entry
To delete an entry in a settings table: 1. While in Edit Mode, click in the row to be deleted. 2. Click Delete. 3. Click Save.
Settings
Plate settings are defined through the lists found under the Settings heading in BioAssay. These lists define what options are available when defining a plate.
BioAssay 55 Settings
Canceling/Discarding Changes
If you have made changes to a settings table, but have not saved those changes, changes can be canceled. To cancel changes: 1. While in Edit Mode (after making changes, but before saving), click Cancel. A dialog box appears asking if you want to discard changes.
format (by double-clicking on the appropriate row). The plate opens with the number of wells defined in the Physical Plate Format. The default is all wells contain the default well format Compound. The default well format options are:
Compound - a compound can be inserted in
Administrator
2. Click Yes.
Plate Formats
Plate Formats are defined as a format indicating the layout in a plate of the general contents of each well. For this reason, the Plate Format setting needs a Physical Plate Type defined in order to have a general idea of the layout and capacity of the wells in the plate first. There are two steps in defining a plate format.
the well Empty - the well remains empty Positive Control - this well is reserved for a positive control Negative Control - this well is reserved for a negative control More well formats can be defined by the user. For more information about editing the entries in the Plate Formats table, please see Editing the settings tables on page 55. To define the general contents of the plate's wells:
1. Enter edit mode (by clicking Edit). 2. Highlight the appropriate wells. 3. Click on the arrow in the well to display your
Defining a Plate Format

Plate Formats are defined as a format indicating the layout in a plate of the general contents of each well. There are two steps in defining a plate format.
Defining a Plate Format
options for the well format for a particular well. 4. Select a contents option. The well label is updated.
Well Formats
Well Formats define the general contents of a well. The well format is used when defining Plate Formats. The default Well Formats are:
Compound - a compound can be inserted in
The following attributes can be defined for a Plate Format:

Name - the name of the plate format Physical Plate Format - the physical plate
format to be used for the plate's layout

Defining Attributes of the Plate
After entering values for the above attributes, it is necessary to define the general contents of each well. This is accomplished by opening the Plate
the well Empty - the well remain empty Positive Control - this well is reserved for a positive control Negative Control - this well is reserved for a negative control
56BioAssay
CambridgeSoft Settings
It is important to note that the only well that the system recognizes as a well in which a compound from a database can be inserted, is a well with the Compound Well Format. For more information about editing the entries in the Well Formats table, please see Editing the settings tables on page 55.
Protocol Picklist
Items listed in the Protocol Picklist table are items that can be used to limit the entries that may be made in a field to a controlled list. For example, a default picklist category is Scientist. There are four picklist options defined.
A table defining the entries in the picklist appears. 9. Click Edit. 10.Click Add. 11. Enter an entry for the picklist. 12.Click Save. 13.Repeat steps 10-12 until all of the entries you choose to define have been entered.
Adding Picklist Options

To edit the entries in an existing picklist:
1. In the left frame, browse to 2.
3.
Adding a Picklist to the Picklist Table

To define a new picklist:
1. In the left frame, browse to 2. 4. 5.
3. 4. 5. 6. 7. 8.
Settings>Protocol Picklist Click on Protocol Picklist. The Protocol Picklist table appears in the right frame. Click Edit. Click Add. An empty row is inserted. Enter a name for the new picklist in the empty row. Click Save. Click Browse. Double-click on the row with the name of the new picklist.
6. 7. 8.
Settings>Protocol Picklist Click on Protocol Picklist. The Protocol Picklist table appears in the right frame. Double-click on the row containing the name of the picklist. A table defining the entries in the picklist appears. Click Edit. Do one of the following: Click Add. Double click on the entry you would like to edit. Enter the desired information. Click Save. Repeat steps 5-7 until all of the entries you choose to define have been entered.
Using a Picklist
To use a picklist in a protocol's table:
1. Define a table (or choose a defined table). 2. Open the table by double clicking on its row in
the Table Definitions table. 3. Click Edit.
BioAssay 57 Settings
4. Do one of the following:
Click Add to add a new field. Find the appropriate row.

5. Select a picklist name in the picklist column. 6. Click Save.
BioAssay uses the ChemOffice Enterprises global security to add and edit the properties of users. To access the Manage Users interface:
1. Open a browser and go to the ChemOffice
Administrator
Security
BioAssay applies two levels of security. The first level controls access to certain parts of the software, such as plate setup, editing inventory, and user management. The second level is more granular, managing users' abilities to view and edit protocol data on a protocol by protocol basis.
Enterprise homepage (http://<servername>, where <servername> is your server's name). 2. Click Global Login. 3. Enter a username and password and click OK.
4. From the Global Login homepage, click
Manage Users. The Manage Users interface appears.
Managing Users
A list of ChemOffice Enterprise users (including but not limited to BioAssay users) can be found under Settings > Users.
To make changes to the users in the system:

1. Select the application in which the user exists
from the View Users From drop down menu.

NOTE: Selecting All CS Applications will list all
users.
2. Click Refresh. 3. Click Add User (to add a new user) or
highlight a user name and click Update User (to edit an existing user). A page allowing you to enter user details appears. 4. Enter user details as desired. Fields highlighted in red are required.
58BioAssay
CambridgeSoft Security
5. Select the roles for the user. To select more
then one role at once, hold down the CTRL key while highlighting. 6. Click OK.
Creating New Groups

To create a new group:
1. Click Edit. 2. Click Add
Managing Groups
A list of BioAssay groups can be found under Settings > Groups.
A new row appears. 3. Enter the appropriate information. 4. Click Save.
Adding a User to a Group

To add a user to a group:
1. Highlight the group you would like to add a 2. 3. 4. 5. 6.
Each group contains a number of users. Applying a role to a group applies that role to all users in the group.
user to, and click Actions. Select View Group. A list of the users in the group appears. Click Edit. Click Add A new row appears. Enter the appropriate information. Click Save.
BioAssay 59 Security
Administrator
60BioAssay CambridgeSoft Security
Chapter 4: BioSAR Enterprise

Overview
The BioSAR Enterprise application allows the user to combine data from multiple applications including the CambridgeSoft Enterprise applications and subsequently search through, and view that data in one screen. The application is fully customizable allowing users to create their own search forms and decide how data will be displayed. For example, one schema may have a table defining a person (with fields like person id, last name and first name) while another table might define an order (with fields like customer id, product, and order date).
View
View refers to a database view that exists in a schema in the Oracle instance. Views are created by assigning the results of a query to a new table in the database. For example, a view could be made from the person and order table mentioned above (under Table). This view could include the last name and first name of the person as well as order date. Now, the view can be accessed much like a table eliminating the need for longer, more complicated SQL statements to access the information. In most respects, a view is dealt with in the same way a table is dealt with in the BioSAR application.
Terminology
Schema
A schema details the structure of a particular database which can be accessed from the BioSAR Enterprise application. Each schema is made up of several tables. Each table contains a number of fields. In addition to describing the contents of each table, the schema also defines any relationships between tables and fields in that schema. These relationships are automatically generated for you when you enable a schema for use in BioSAR. Relationships that cross schemas can also be applied. For example, if a registration id number in the REGDB schema is the same id number included in the CHMINVDB2 schema, these two fields can be linked within the application.
Formgroup
Each from created with the Manage Your Forms function actually contains 3 forms: a search form, a list view form, and a details view form. The 3 forms are linked. A formgroup refers to the group of 3 forms. When creating formgroups, users are able to give other users access. If users, other than the creator is given access to a formgroup, the formgroup is considered public.
Table
Table refers to a database table that exists in a schema in the Oracle instance. Tables define entities in the schema.
BioSAR Enterprise 61 Overview
Login to BioSAR Enterprise

Administrator
To login and start using BioSAR Enterprise: 1. Enter http://<servername>/ into your web browser. <servername> should be substituted for your ChemOffice Enterprise name. To find the name of your ChemOffice Enterprise, please see your system administrator. 2. Click on the BioSAR Enterprise link. The BioSAR login screen appears.
Schema Management
BioSAR Enterprise's Schema Management allows administrators to control what is visible to the users. That is, Schema Management gives administrators the tools to control what schemas, tables, views, and fields can be used in forms. Schema Management can be accessed by:
Clicking on Schema Management from the
Global Login page OR
Selecting Manage > Schema from the
BioSAR Enterprise Admin menu.
3. Enter a username and password and click Log
in. The ChemOffice Enterprise Global Login page appears. 4. Select the part of the application you wish to access:
From this page, administrators can control all aspects of schema configurations for the application. Any schema can be viewed from BioSAR Enterprise. For more information, please see the BioSAR Enterprise Admin Guide.
BioSAR Enterprise opens. The forms displayed depend on the option selected. Use the toolbar to navigate through the software.
Refreshing Tables
Users with the appropriate privileges may see a button called Refresh All Tables or Refresh Table in Schema Management. Clicking on this button will wipe out any links set up between schemas and there is no undo operations. Please be sure you are aware of the consequences before refreshing a table.
62BioSAR Enterprise
CambridgeSoft Login to BioSAR Enterprise
Add/Remove Schemas
The administrator decides which schemas are available to the users of the system. If a schema is not visible, none of the tables or views can be seen or used by the users of the system. Any schema which exists on the Oracle instance of the server can be included in the BioSAR Enterprise application.
4. Click Save Changes to save your changes
before returning to the previous page.
Remove a Schema
To remove a schema from the list of available schemas:
1. From the main menu, click on Schema
Add a Schema
To add a schema to the list of available schemas: 1. From the main menu, click on Schema Management. 2. Click on Add/Remove Schema. A table containing all of the schemas which exist on the Oracle instance appears.
Management. 2. Click Add/Remove Schema. A table containing all of the schemas which exist on the Oracle instance appears.
3. Uncheck the checkbox in the Exposed
column to the right of the names of schemas you would like to remove. 4. Click Save Changes to save your changes before returning to the previous page.
3. Select the checkbox in the Exposed column to
the right of the names of schemas you would like to make visible.
BioSAR Enterprise 63 Schema Management
Edit Schema Description/Password

To edit the description or password for a schema:
1. Select a schema from the Schema Listbox on
Administrator
the Schema Management page.
Schema Display Name

2. Expand the schema you would like to rename
by clicking on the arrowhead next to the schema name in the tree control.
The display name for the schema is the name a user will see to identify the schema. The default display name is the name of the schema, but it is sometimes more convenient to enter a more descriptive name for the schema. If you would like to change the display name:
Enter the new name in the textbox next to
Display Name.
Schema Password
The password for the schema is assigned when the schema is created. For information about schema passwords for CambridgeSoft schemas, please contact esupport@cambridgesoft.com. If you would like to change the password (in BioSAR Enterprise only, it still must be the actual schema password):
Enter the password for the schema in the
3. Click Edit Schema Description/Password.
The Edit Schema page appears.
textbox next to Schema Password
Edit Exposed Tables

Users are able to decide which tables in a schema are visible when creating forms. To edit which tables are visible to users creating forms:
64BioSAR Enterprise
CambridgeSoft Schema Management
1. Expand the schema which you would like to
The selected table's page appears.
edit by clicking on the arrowhead next to the schema name in the tree control. 2. Click Edit Exposed Tables. 3. Select the checkbox in the Visible column next to any tables you would like to see visible when users are creating forms. 4. Click Save Changes.
Edit Table Details

To specify which fields in an exposed table or view should be visible to users:
1. Select a schema from the Schema Listbox on
The following things can be defined for a table:

Table Properties The display name for the table The primary key for the table The default column order Field Properties Which fields in the table are visible to the
the Schema Management page.
users
The display name for each field The description for each field
2. Expand the schema which contains the table by
A lookup table for each field A parent column for each field The Index Type The Content Type
clicking on the arrowhead next to the schema name in the tree control.
After making changes to the table, be sure to click Save Changes to save your changes.
Edit a Table's Primary Key

The primary key of a table is a column which contains a unique value for each row. This field is usually an ID_number of some kind. The ChemOffice Enterprise requires every table have a primary key, even if a table doesn't have a primary key defined in the database. Each table can only have one primary key, and the primary key must be an integer field. To choose the primary key for a table:
Select the radio button in the primary key
3. Click the Edit Table Fields arrowhead to
expand (if not yet expanded). 4. Click on the name of the table.
column to the left of the field name.
Table Fields
Specify the Visible Fields in a Table
If you would like to make a field available to users, select the checkbox in the Visible? column, to the left of the field name. If the checkbox is not selected, users will not be able to use it in any forms.
Administrator
Edit a Table's Default Column Order

The default column order column orders the fields in a table. If the fields are selected to be used in a form, the default order they will appear in the form is indicated by the Default Column Order (the order is chronological).
Edit the Display Name for a Field
The display name for a field is the name a user uses to identify the field. The default display name is the name of the field in the database. to change the display name for the field:
Enter the new name in the textbox in the
Display Name column.
Edit Table Display Name

The display name for the table is the name a user uses to identify the table. The default display name is the name of the table, but it is sometimes more convenient to enter a more descriptive name for the table. If you would like to change the display name:
Enter the new name in the textbox next to Edit the Description for a Field
Display Name
The display name for a field is the name a user will see to identify the field. The default display name is the name of the field, but it is sometimes more convenient to enter a more descriptive name for the field. If you would like to change the display name:
Enter the new description in the textbox in the
Description column.
66BioSAR Enterprise
CambridgeSoft Schema Management
4. Select the Linking Column and Display Name. 5. Click Save Changes.
Linking Column The linking column is the column in the lookup table with the same value as the field whose lookup table is being defined.
Specify a Lookup Table for a Field
A lookup table for a field defines where a field's display value can be found. Many times a lookup table is defined for an ID field so that instead of displaying the ID to the user when the information is viewed, a value more useful to the user is displayed. During installation, lookup tables are automatically recorded for ChemOffice Enterprise schemas. To define a lookup table for a field,
1. Click on the link in the Lookup Table column
For example, there is a field called EXPERIMENT_TYPE_ID in the EXPERIMENTS table in the REGDB schema. this ID, to a user, doesn't give much information, but the EXPERIEMTNTYPE table in the REGDB schema defines the relationship between the ID and an experiment's name. For this reason, the linking column for regdb.experiments.experiment_type_id is regdb.experimenttype.experiment_type_id. Display Column The display column is the value that should be used in place of the actual field value in forms. In our example above, we have linked two tables together. The EXPERIEMENTS table contains a field called EXPERIMENT_TYPE_NAME (in addition to the EXPERIMENT_TYPE_ID). This field contains a name for each ID. Therefore, experimenttype.experiment_type_name is the Display Column for regdb.experiments.experiment_type_id.
Specify a Parent Column for a Field
to the right of the field name. The Lookup Table page appears.
2. Select the schema where the lookup table exists
from the Lookup Schema listbox. The Lookup Table listbox is populated. 3. Select the lookup table from the Lookup Table listbox. The Linking Column and Display Column listboxes are populated.
A parent column defines a table which is related to many tables in the same way. As opposed to a lookup table Specify a Lookup Table for a Field on page 67, which has a one to one relationship with its related table, a parent table has a one to many relationship. During installation, parent columns are automatically recorded for ChemOffice Enterprise schemas.
To specify a parent column for a field:

1. Click on the link in the Parent Column
Parent Column - REG_INTERNAL_ID Specify an Index Type for a Field
column to the right of the field name. The Parent Column page appears.
The index type for a field is for a field containing a LOB that is indexed. Currently the only supported index type is the Oracle Cartridge. Most other fields containing LOBs (such as GIFs, JPEGs, etc.) are not indexed and should be assigned the index type "no index".
Specify a Content Type for a Field
Administrator
The content type for a field is the HTTP MIME_TYPE for a particular LOB. The current options are:
Type of LOB in field
2. Select the schema where the lookup table exists
Content Type
from the Parent Schema listbox. The Parent Table listbox is populated. 3. Select the parent table from the Parent Table listbox. The Parent Column listbox is populated. 4. Select the Parent Column. 5. Click Save Changes. For example, the REG_NUMBERS table is a parent of the BATCHES table because one compound can contain many batches. For each REGDB.REG_NUMBERS.REG_ID, there are one or more matching records in BATCHES. BATCHES.REG_INTERNAL_ID contains the same value as REGDB.REG_NUMBERS.REG_ID. So, if we would select the following when defining the Parent Column for REGDB.BATCHES.REG_INTERNAL_ID:
Parent Schema - REGDB Parent Table - REG_NUMBERS
Oracle Cartridge GIF
ichemical/x-cdx IMAGE/gif
Manage Your Forms

BioSAR Enterprise allows users to search through and view data in multiple application databases all at once. In order to accomplish this, the user must define how information will be searched and what will be returned. BioSAR Enterprise's Form Management gives you the tools to create and customize search and results forms. Not all users are entitled to make their own forms. If you are able to access Manage Your Forms, please see your system administrator about gaining the privileges to make new forms. Manage Your Forms can be accessed by:
Clicking on Manage Your Forms from the
Global Login page OR
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CambridgeSoft Manage Your Forms
Selecting a Base Table

The base table is the table which your form is built around. Not only is it the first table in any form, all additional tables included must be linked to the base table in some way. The base table for a form can be any of the tables contained in the visible schemas on the system. Only one base table can be chosen, and the list of child tables to choose from will change depending on the base table chosen. To select a base table:
1. Click on [Select Base Table].
Selecting Manage > Forms from the BioSAR
Enterprise Forms menu.
Create a New Form

To create a new form: 1. From the Manage Your Forms page, click Create New Form. A page allowing the definition of a new form appears.
A page allowing you to select a table appears.
2. Select a schema from the Schema listbox.
2. Enter a name and description for the new form
is the appropriate textboxes. 3. Click Save Changes.

NOTE: To continue defining the form, select the new
form from the listbox and click Edit.
The Base Table listbox is populated. 3. Select the base table from the Base Table listbox. 4. Click Save Changes. You are returned to the Edit Form page and the name of the table chosen will be listed under Base Table.
BioSAR Enterprise 69 Manage Your Forms
Selecting Fields in a Table
After selecting a base or child table, it is necessary to indicate which fields should be visible to the form user, and when. To do this:
1. Click Edit in the Fields column.
Administrator
A page listing all fields available in the table is listed.
2. Select a format for the field to be displayed in,
for each view, from the Format drop down menu. For more information about the field formats, see the table below.
NOTE: Some fields have only one way of being
2. Three columns are shown to the right of field
displayed. In this case, there is no choice given.

3. Enter the desired dimensions of each field in
names and descriptions in the table, representing different views, entitled Query - visible in the query form used to search List - visible in the results list form (multiple records viewed at one time) Detail - visible when one record is viewed alone Select the checkboxes in the appropriate columns to indicate the field should be visible in that view. 3. Click Save Changes.
How Fields are Displayed in Forms
each view. 4. Select the Show checkbox if you would like that field to be visible to users in the specified view. 5. Click Save Changes.
Display Type Description Option in which View
Structure
A structure window appears A CDX file is displayed (can be edited with ChemDraw toolbar).
Search
It is also possible to indicate how fields should be displayed in a form. To do this:

1. Click Edit in the Field Options column.
ChemDraw PlugIn
List, Detail
A list of all available fields appears.
70BioSAR Enterprise
Display Type
Description
Option in which View
Display Type
Description
Option in which View
Graphic
A graphic is List, displayed. INDetail LINE means the graphic appears in the current window, NEW WINDOW means a link to the graphic will be displayed and clicking on the link will open the graphic in a new window. A GIF (showing List, an image of the Detail structure) is displayed. Cannot be edited. A textbox. A larger area allowing multiple lines of text to be entered. Search Search
TextBoxAllow Allows users to: List
Search
1. Browse to a list
of files and use that as the entry OR

2. Enter multiple
values delimited by commas, tabs, or linefeeds. These values can be pasted from Excel, or a text file.
Static GIF
DatePicker
Validated as a text Search field, includes a calendar icon allowing easier input of dates. Validated as a date. Search
TextBox TextArea
Date
Display Order of Fields
A user can also decide the order in which fields are shown in a form. To do this:
1. Click the appropriate view name in the Field
Order column. A page listing all chosen fields are listed.
Edit Integration Options

Users can allow forms to be integrated with the Export to Excel feature. This feature allows users to export the data displayed in the form to an Excel spreadsheet. To allow the Export to Excel feature in your form:
2. Click on the arrows to the right of a field name
Administrator
to move a field higher or lower on the form. 3. Click Save Changes.
To enable Microsoft Excel:

1. Click on the Integration Tab.
Integration window appears:
Selecting Child Tables

Child table options for a form will change depending on the base table Selecting a Base Table on page 69 chosen. To select a child table:
1. Click on [Select Child Tables]. 2. Select the Enable Export to Microsoft Excel
A page listing all child tables, compatible with the chosen base table, appears. 2. Select the checkbox next to any table you would like visible on the form. 3. Click Save Changes. You are returned to the New Form page and the names of the tables chosen are listed under Child Tables.
checkbox.
Form Roles and Users

Some users are given the option to choose specific roles or users that should have access to a form. If this is the case, a table like the one below will be visible:
4. Select the appropriate fields for each table.
Fields are selected in the same way as for the base table. Please see Selecting Fields in a Table on page 70 for more information. 5. Indicate the order you would like the tables to be displayed in the form by clicking on the arrows in the Table Order column. 6. Click Save Changes.
To add users or roles for the form, highlight the appropriate listing in the listbox below All Users and Roles and click Add. This will move the listing into the Permitted Users and Roles listbox to the right. To remove a listing from the Permitted Users and Roles listbox, highlight the appropriate listing in the listbox below Permitted Users and Roles and click Remove.
72BioSAR Enterprise
If roles or users are chosen, even if an individual user is missing a role (for example, one to view a specific table in the form), this role is granted to the user for the use of the form automatically.
Editing a Form
After a form has been created, the information can be edited at anytime as long as you are logged in as the user who made the form in the first place, or you are assigned the appropriate privileges to edit other users forms. To edit a form:
1. From the Manage Your Forms page, select
Assign the Form to Project(s)

Forms can be assigned to any number of projects in the system.
the form from the listbox. 2. Click Edit. A page allowing the definition of a form appears.
To assign the form to a project:

1. Click Add to Project Category (or Add to
Public Category for a public project group). 2. Browse to the project using the tree control. 3. Select the project to add the form to by clicking on the project name. To change the project assignment to a different project:
1. Click Move to the right of the project name. 2. Browse to a project using the tree control. 3. Select the project to add the form to by clicking 3. Enter/Select the appropriate information.
on the project name. To delete a project assignment:

Click Delete to the right of the project name.
There are four parts of a form's setup: Edit the name and description for the form (cannot be changed from this page). Select users and roles entitling access. Select a Base Table for the form and define which fields will be visible to the user. Select Child Tables for the form and define which fields will be visible to the user. 4. Click Save Changes.
Renaming a Form
The name and description of a form are used to identify the form when it is restored to search.
Delete an Existing Form

To delete a form listed on the Manage Your Forms page:
1. From the Form Management page, select the
Administrator
To rename or change the description of a form:

form from the listbox. 2. Click Rename. A page allowing you to rename the form appears.
form from the listbox. 2. Click Delete. The following warning appears:
3. Click the appropriate link. 3. Edit the name and description in the textboxes. 4. Click Save Changes.
Opening a Form/Searching Using a Form

One way to retrieve search results is to perform a search with the use of a search form. For more information about defining search forms, please see Manage Your Forms on page 68. To search using a search form:
1. Select Open Forms from the Forms Menu.
Duplicating a Form
Duplicating a form is often useful if there is a form, that already exists, which has many of the properties that you would like in a new form. For example, if you are creating a new form with the same base table and field properties of an old form, duplicating a form can save time in defining the new form. To duplicate a form:
form to be duplicated from the listbox. 2. Click Duplicate. The form is duplicated and can now be accessed from the listbox. The name of the new form is the name of the old form preceded by "Copy of".
2. Select a search form to use, from the list of
forms. The search form you chose appears.
74BioSAR Enterprise
Searching
There are three different ways to retrieve search results from the main menu under the heading Search Using:
Using a Form Group Opening a
The form you see will depend on the form group chosen and will most likely not have all of the same fields as the above form. 3. Enter the desired information in the form. 4. Select a Sort by field, from the Search Sort By drop down menu, if desired. 5. Select one of the following radiobuttson: Show All Child Data - show all child data for matching records (if one set of child data matches the entered criteria, but another set for the same base record doesnt, this option allows you to view all data) Show Only Child Data Matching Entered Criteria - show only the child data which matches the entered criteria 6. Click Search. Your search results are displayed. For tips in using ChemOffice Enterprise search forms, please see Performing Searches in the ChemOffice Enterprise Chapter.
Form/Searching Using a Form on page 74. Retrieving a Saved Query Search Using a Saved Query on page 75. Retrieving a Query in the History Searching Using the History on page 76. After performing a search, search results are always displayed in the same format. For more information about viewing search results, please see Viewing Search Results on page 76.
Search Using a Saved Query

It is possible to save a query after it has been entered. Saving queries might be helpful if it is necessary to repeat a query a number of times. With this feature, it would, for example, allow you to save a query which searches for batch information for a particular compound. Since batches are not all made at once, one day the results may be one set, but the next day (after another batch was made), more results would be retrieved. To save a query:
Select Save from the Queries menu.
To use a saved query: 1. Select Restore from the Queries menu.
BioSAR Enterprise 75 Searching
To access a query in the history:

1. Select Queries from the History menu.
Administrator
2. Select either Saved or Last depending on the
query you wish to restore. If you select Saved, a dialog box opens.
The history dialog box opens.
3. Select the appropriate form, and the query
2. Select the appropriate search from the listbox. 3. Add more information, if desired, and click
associated with that form. 4. Click Restore. 5. Add more information, if desired, and click Search. For tips in using ChemOffice Enterprise search forms, please see Performing Searches in the ChemOffice Enterprise User's Guide.
Search. For tips in using ChemOffice Enterprise search forms, please see Performing Searches in the ChemOffice Enterprise User's Guide.
Viewing Search Results

After a search is performed, the results are displayed in a list form allowing the user to view some of the contents from each record retrieved.
Searching Using the History

A history of searches performed is automatically saved for each session. Once a session is ended, the history is erased. If you would like to save a query after an individual session with BioSAR Enterprise ends, please see Search Using a Saved Query on page 75. Queries saved in the history are saved under names of the following format: HISTORY-<date><time>
where <date> is the date the query was
entered and <time> is the time at which the query was entered
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CambridgeSoft Searching
To show all retrieved information for a particular record, click on Show Details. What information is displayed at the different view levels is defined when creating a new formCreate a New Form on page 69. For more information about manipulating search results, please see Search Results in the ChemOffice Enterprise User's Guide. After clicking on Show Details, the Results Form View appears. Here, it is possible to view your results in different formats. The information displayed in each of the formats is the same and the screen differs only in its layout. The view options are: Frame View Tab View Report View
indicated integration with Excel should be available see Edit Integration Options on page 72 for more information about integrating with Excel To create view your data in a spreadsheet: Click Display in Excel. Your data appears in a spreadsheet in a new window.
List View Options

List view allows two layout options:
Columns Down - arranges fields in columns
spaced horizontally.
Columns Across - arranges fields in columns
Sorting Results
Search results can be sorted by clicking on the table header of one of the columns.
spaced vertically. Click Toggle Layout to switch between the two views.
Columns Down
Dynamically Editing a Form

Often, once a form is opened, a user would like to edit the layout or content. To edit the form which is currently open:
1. Select Edit this Form from the Forms menu. 2. Make your changes. 3. Click Save Changes.
You are returned to the open form, reflecting the changes made.
Columns Across
Displaying Search Results in MS Excel

When in list view, users have the option to view search results in a MS Excel spreadsheet. This option is only available in forms whose creator
Details View Options

Frame View
Report View
Frame View is the default search results details view. This view shows data in two frames, the base table in the left frame and the child tables in the right frame.
In the Report View, all data is displayed on one page, in one frame. Base table data is displayed at the top, and child table data appears below.
Administrator
Tab View
In Tab View, each table's or view's data is separated into tabs. Click on the tab to access the appropriate information.
Generating Reports
BioSAR Enterprise allows users to generate reports for any publicly defined formgroup. After performing a search using a public formgroup, a Generate Report link is found at the top of the page. To generate a report:
1. Perform a search See Searching on page 75.
using a public form group See Manage Your Forms on page 68. 2. Select Generate Report from the Reports menu. The Report window appears.
78BioSAR Enterprise
Report Setting
Description
Options
Table Layout Tables can be placed across (arranged horizontally next to each other) or down (arranged vertically).
3. Select the appropriate options for your report.
Tables Across Tables Down
Report Setting
Description
Options
Settings profile for the report
Data View
The data view is the cross-section of data you would like to see. When creating your forms, you defined a List and Details view. Usually the Details view has more information about each record in the list view. Select the data you would like the create the report for.
List Details
Profiles define the display settings for a report. This includes font size, color, and style as well as the inclusion or exclusion of logos. Use the links to the right of the listbox to view, edit, or delete the selected profile before creating the report.
List of all available profiles. Profiles can be made public.
Report Setting
Description
Options
Report Setting
Description
Options
Administrator
Page Reports can be Orientation forced to be created to fit a portrait of landscape format. If Auto is selected, the appropriate size (in the attempt to display as much information as possible) is chosen and implemented. Page Size The page size is implemented when the report is created to fit on the page you are using.
Auto Portrait Landscape
New page for each record
If you would like a page break to be inserted after each record, use this setting by selecting Yes. Select the format you would like the report displayed in
No Yes
Report Format
SNP (Microsof t Access reporting format) PDF
Letter (8.5 x 11 in.) Legal (8.5 x 14 in.) A3 (297 x 197 mm) A4 (210 x 297 mm) B4 (250 x 354mm) B5 (182 x 257mm) Tabloid ( 11 x17in.)
4. Click Run Report.
NOTE: If structures are not appearing in your reports, the schema may not be configured correctly. Please see your system administrator.
Create a New Profile

A Report Profile controls the font color, style, and size as well as the inclusion or exclusion of logos and header lines. To create a new profile:
1. Click the New link to the right of the profile
listbox. The Profile window appears. The defaults are the values in the default profile.
80BioSAR Enterprise
If you Then ... would like to ...
Set the margin width
Select the appropriate margin size in the margin listboxes.
2. Enter the appropriate settings:
Set the Select the color in the color of the appropriate listboxes header, footer, or detail in the report Adjust the font type, style, size, weight, or color of a particular part of your report Select the appropriate options from the listboxes to the right of the appropriate text block name.
Give the profile a name (*required)
Enter a name for your profile in the Profile Name textbox. This name is used as an identifier and is listed in the profile listbox in the Report window.
write a brief Enter a description in the description Description textbox. of the profile. Make the profile public Select Yes in the Public listbox. Note: Making a profile public makes it available to other user's use when generating reports. Only the owner of a profile can edit or delete a profile.
Insert Enter text into the header line header lines textboxes. to the top of the report Include a logo
3. Click OK.
Select the logo to include from the Logo listbox, or click Add to add a new logo.
Adding Logos
Logos can be used at the top of reports. To add a logo to the list of options:
Administrator
1. Click the Add link to the right of the Logo
listbox. The Add window appears.
2. Click Browse and browse to the file. Logos
must be of one of the following file types:

GIF (.gif) JPEG (.jpg) PNG (.png)
3. Click Add Logo when the file name appears in
3. Change the appropriate settings:
the textbox.
Edit a Profile
Profiles can only be edited by the user who created them, even if the profile is public. To edit an existing profile:
1. Select the profile to be edited from the listbox. 2. Click Edit.
The Profile window appears with the selected profile's values populating the fields.
82BioSAR Enterprise
View a Profile
BioSAR Enterprise allows users to generate reports for any publicly defined formgroup. After performing a search using a public formgroup, a Generate Report link is found at the top of the page. To view an existing profile:
1. Select the profile to be viewed from the listbox. 2. Click View.
The profile appears.
4. Click OK.
NOTE: Profiles can be edited, only by the creator of the profile. Select Duplicate to create a new profile using another profile's settings.
Duplicate a Profile
User can create a duplicate of an existing Profiles, even if the profile is public. To create a duplicate of an existing profile:
1. Select the profile to be duplicated from the
listbox. 2. Click Duplicate. The Profile window appears with the selected profile's values populating the fields.
Administrator
3. Change the appropriate settings:
4. Click OK.
Delete a Profile
Profiles can only be deleted by the user who created them, even if the profile is public. The default profile can not be deleted.
84BioSAR Enterprise
To delete an existing profile:

1. Select the profile to be deleted from the listbox. 2. Click Delete.
3. Click on the name of the form you would like
A confirmation message appears. 3. Click OK.
Ordering Fields and Changing Label Sizes in Reports

The order and size of fields in reports are a direct result of the form the report is generated from. Therefore, to change the order of fields, or the size of field labels in a report, you need to change the size of the field specified in the form. To change the order of fields:
1. Return to the Main Menu. 2. Click Mange Your Forms. 3. Click on the name of the form you would like 4. 5. 6. 7.
to adjust. 4. Click Edit. 5. Select the link for the appropriate table under Field Options. 6. Scroll to the appropriate field and set the width to the width you would like to see in your report.
7. Click Save Changes and return to your form. 8. Generate the report again.
Your new width will be reflected.
to adjust. Click Edit. Click on the link in the Field Order column. Use the Arrow buttons to move fields up and down. Click Save Changes.

The BioSAR Enterprise application uses the global ChemOffice Enterprise User Management interface. Please See Manage Users and Roles on page 192. in the ChemOffice Enterprise User's Guide for more information.
To change the field label size:

1. Return to the Main Menu. 2. Click Mange Your Forms.
BioSAR Enterprise 85 Manage Users and Roles
Administrator
86BioSAR Enterprise CambridgeSoft Manage Users and Roles
Section III: Chemical Informatics

This section provides information about CambridgeSofts Chemical Informatics Solutions. The following applications comprise CambridgeSofts Chemical Informatics Solutions:
Registration Enterprise Inventory Inventory Enterprise CS Inventory Desktop/Workgroup CombiChem Enterprise (see the Chem3D,
Managing the huge data streams of new lab technology is a key challenge. Registration Enterprise organizes information about new compounds according to an organizations business rules, while Inventory Enterprise works with Registration Enterprise and ChemACX for complete management of chemical inventories. CombiChem Enterprise and Formulations & Mixtures are also important parts of research data management.
ChemFinder, and E-Notebook manual for more details)
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Administrator
88 CambridgeSoft
Chapter 5: Inventory
Desktop / Workgroup
Inventory is an application designed to manage the chemical and reagent tracking needs of laboratories and research centers. The system manages data associated with both commercially procured and internally produced chemical substances from their procurement or initial production through their depletion and disposal. To meet the needs of institutions of all sizes, Inventory comes in two Desktop editions (Pro and Ultra), a Workgroup edition, and a web - based Enterprise edition. Inventory Workgroup is a thick-client SQLServerbased product. Suitable for larger organizations that dont have the ability (or dont want) to maintain an Oracle server, it requires, but does not include, a SQLServer license.
MSDE is optimized for 5 concurrent users. The word optimized is important here. With up to 5 concurrent users, MSDE will perform just like all other SQL Server editions. When more users are connected, and all query the server, MSDE will throttle the speed. If the clients are connected, but are not active, nothing will happen. MSDE will slow down only when more than 5 queries arrive at the server at the same time.
CS Inventory Desktop/Workgroup
Inventory Pro is an all-inclusive desktop product. It includes Microsoft SQL-Server Desktop Engine (MSDE), the redistributable database engine for SQLServer 2000. No additional licensing is required. Suitable for single-user installations, the inventory database can accept up to five simultaneous queries with no degradation of performance. The connection to the database is not live except when you actually process a query, so the only practical limit to the number of computers connected to an Inventory MSDE database is the probability of more than five users attempting simultaneous queries. Inventory Ultra is the same MSDE-based product, but includes the DVD version of ChemACX, CambridgeSofts catalog of chemical products and suppliers.
Inventory Enterprise
Inventory Enterprise is an Oracle-based, ChemOffice WebServer product. The rich feature set is designed for large organizations, it has a number of features not included in the Pro/Ultra/Workgroup versions. For more information about the Enterprise version of the product, see Inventory Enterprise on page 115.
Terminology
The three primary entities in an Inventory system are Locations, Substances, and Containers.
Location
An Inventory Location represents a physical location where one or more Containers may be stored. Locations can be nested within other locations to produce a hierarchy. The location hierarchy is
Inventory Terminology
89
represented as folders n a tree control analogous to that found in the Windows file explorer. The following is an example of a typical location tree:
Highly advanced duplicate checking is incorporated into the system. Only a single Substance may be associated with each Inventory Container. Aside from structure and name, substances can be identified via unique registry numbers such as CAS or ACX ID. Custom fields may also be defined. For information on defining mixtures as substances, see Mixtures on page 97.
Administrator
Container
An Inventory Container represents a physical container capable of storing chemical substances. While a Container may physically contain a complex mixture of chemical substances, Inventory is ideally suited for the assignment of a single (primary) chemical substance to each Container. Additional text fields are available to track other chemical contents such as the solvent. Typical container types include: bottle, vial, tube, cylinder, box, etc...
Substance
An Inventory Substance represents a single pure chemical entity which can be expressed as a two dimensional chemical structure drawing. The system maintains its own internal chemical structure database containing unique substances that can be associated with Inventory Containers.
90Inventory Terminology
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Inventory Desktop/Workgroup
Whats New in CS Inventory 10?
CS Inventory 10 new features include the following:
Role Based Security Audit Trail Managing EHS Data Duplicate Container Check-In/Check-Out Containers Change Quantity Change Status Multi Select Backup/Restore Database Logout
To facilitate administrators testing of new roles, CS Inventory now has a Logout feature. This allows an administrator to log out and log back in with a different username quickly and easily. The Logout command is on the File menu.
Desktop / Workgroup
The User Interface

The User Interface is divided into three main areas or frames:
Location tree. Container list. Substance details.
Login and Logout

The first screen you see when starting CS Inventory is a login screen.
These areas support browsing the inventory; that is, viewing locations, the containers present in them, and details of the substances in the containers.
Location Tree Menu Bar Container List
Enter your username and password to enter the database. Usernames are assigned Roles and Roles are defined by Privileges, which are specific tasks that a user with that role can perform. See Managing Roles on page 108 for more details.
Substance Details
The Location Tree shows all of the locations in the inventory. It is a collapsible hierarchical tree structure, like the Windows Explorer folders list.
Inventory Desktop/Workgroup The User Interface
91
The Container List displays the containers in the selected location. Use the scroll bar to view all of the containers in a location. The Substance Detail section is a tabbed frame that shows the details for the selected container. Five of the tabs are identical in all versions:
Summary Substance Supplier Quantities Comments
Format, and Description. In addition, the Enterprise version allows for defining reaction plate types. Required fields are indicated with color. The Edit Location form is the same as New Location, but without a Parent Location field. (You edit the parent location by using the Move Location command.) The Location forms are accessed from the Manage menu.
Administrator
Containers
New and Edit Container are tabbed forms with
The remaining tabs access features that are unique to the version or the way it is set up. For example, the Custom tab will only appear if you have defined custom fields.
many optional fields defining the container and the substance in it. The top-most tab contains the required fields.
Container forms are accessed from the Manage
Forms
In addition to the main Inventory GUI, there are a number of forms for creating and editing substances, containers, and locations, and for searching substances and containers. These are accessed from menus.
menu. The Search Container form is accessed from the Search menu. See Searching for Containers on page 101 for more information.
Substances
New substances are usually created along with new containers. For this reason, there is a link to the New Substance form on the New Container form. You can also create new substances from the Manage menu, but inserting them into containers then becomes a separate process. There are two options for inserting a substance into a container:
Locations
The New Location form has the same basic fields in all versions: Parent Location, Location, Location Name, Location Type, Location Owner, Grid
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create a new substance, or import from an existing database, such as ACX or the existing inventory database.
other data associated with any of these special locations, but may not delete them. Privileges associated with managing locations:
Desktop / Workgroup
Create
New Substance links
Delete Move
Edit
Location Tree
The location tree control allows navigation of the Location hierarchy. Click on the +/- symbols to expand/contract location folders. Click on the location name to display its contents in the container list frame. Right-click on a location to display a context menu of Location commands.
Figure 1 Select database
Additional fields
Creating a New Location
Managing Locations
A location is defined as any place that a container, plate, or another location can be stored. This includes a laboratory, a refrigerator, or even a particular shelf. Different facilities can decide how best to organize locations. Inventory comes with five special locations: Root, Disposed, Missing, On Order, and Trash Can. You may edit the names and
To add a new location: 1. Click the New Location command on the Manage menu. The Create New Location form appears.
NOTE: Plate types are not currently supported in the
Pro/Ultra or Workgroup versions.

2. Enter the parent location (the folder that is one
level up from your new folder). If you pointed to the parent folder before opening the dialog box, the correct location will be entered automatically. You may use the Browse button for one-click entry of the correct location.
93
3. Enter the remaining information. Location Name is the only required field. Inventory will fill in the Location barcode field automatically
unless you enter your own value. (In either case, it will assign an internal location ID number.) 4. When you have finished entering data, click OK. The new location appears in the tree under the parent, in alphabetical order.
Editing a Location
After a location is created, its properties may change. For example, when a particular laboratory was initially set up, a number of containers were placed on a shelf. As the laboratory grew, it was necessary to move the containers to a cabinet. The simplest way to reflect this change in Inventory is to change the location type. Rather than create a new location, you can edit the existing location. To change the properties of a location: 1. Browse to the location to be edited in the Location Tree. Click the Edit Location menu command.The Edit Location form appears. 2. Make sure the information listed in the window that opens is for the correct location. 3. Enter the desired new information in the window. 4. Click OK.
To move a location: 1. Browse to the location to be moved in the Location Tree. 2. Click the Move Location menu command. The Move Location form appears. 3. Make sure the information listed in the window that opens is for the correct location. 4. Enter the new parent location in the Destination Location text box. 5. Click OK. The location and all of its sublocations and containers is moved to the new parent location.
Administrator
Deleting a Location
If a location needs to be removed from the inventory system, you should use the delete location tool. If the location is merely being moved, see Moving a Location on page 94. To delete a location: 1. Browse to the location to be deleted in the Location Tree. 2. Click the Delete Location menu command. The Delete Location form appears.
NOTE: As a safety precaution, a location can only be deleted if it is empty. You can override this precaution by selecting the Recursively delete related locations and containers checkbox. Use this checkbox with caution. You cannot undo the deletion of a location.
Moving a Location
After a location is created, it may be necessary to move the location to somewhere else in the tree. For example, a refrigerator may have been located in a lab on the first floor, but is being moved to a lab on the third floor. Of course all of the containers inside the refrigerator are moved along with it. It is easy to move a location along with all of its contents in the Inventory system.
Refreshing the Location Tree

If Inventory is being used by more than one concurrent user, the Location Tree you see may not be the most current one. The refresh command repopulates the tree from the most recent available location data and returns it to its fully contracted position. If, however, you have a location open
CambridgeSoft
when you choose to refresh, that branch of the tree is not contracted: the location will remain open for you to work with. To refresh the Location Tree:
Click the Refresh menu command.
If you have the ACX database installed, search
ACX for the substance, then add it to the inventory database. To create a new substance: 1. Click New Substance on the Manage menu or create a new container, then click the New Substance link on the New Container Substance Tab.
Desktop / Workgroup
Managing Substances
Substance records store the chemical structure, formula, and molecular weight information of the compounds in your inventory. Each record is identified with a substance ID number, and may also contain a CAS number and/or ACX number for cross-reference purposes. If you have administrator privileges, you can also add up to five custom fields that connecting users can subsequently populate when defining a new substance. Privileges associated with managing substances are:
Create Edit delete MSDS Delete Create MSDS
new substance select substance
The New Substance form appears.
Each substance has only one record in the database. If you create a new substance that matches an existing one in any field (except supplier) a conflict resolution window appears, showing you which fields match (see Conflict Resolution on page 97). To avoid unnecessary conflicts, it is a good idea to perform a search before creating a new substance.
2. Fill in the fields. Substance Name is the only
required field.
NOTE: Custom fields may also be designated as
Creating a New Substance

There are three ways to create new a new substance.
Create directly, from the Manage menu Create a new container, then click the New
Substance link on the New Container form
required.
3. To add a structure, click in the Structure field.
The structure field box is outlined in blue, and the ChemDraw toolbar appears. 4. When you have finished filling in the fields, click OK.
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To create a new substance from the ACX database: 1. Search the ACX databasedo one of the following: Click Substances on the Search menu Click the Select Substance link on a New Container form. 2. On the search form, select the ChemACX radio button in the Databases section. 3. Select the search type (if you are doing a structure search).
TIP: The default Substructure is generally used for
automatically. If a conflict is found in the database with any field entry, the Conflict Resolution page appears. See Conflict Resolution on page 97.
Material Safety Data Sheets

When you have created a new substance, you can link a Material Safety Data Sheet (MSDS) to the substance. To attach a MSDS, have the CAS number of the substance and/or catalog number ready. 1. Point to MSDS on the Manage menu, and click Add. The Add MSDS dialog box appears.
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this type of search.

4. Enter data in at least one of the fields. Usually
either a name or formula or structure is used. 5. Click the Search button. In a few seconds, you will see the results in the Search Results form. Click the entry to see the detailed form shown in . 6. If you want to add a supplier from the ChemACX list, click the Show Suppliers link. The supplier list for that substance appears.
add link
2. Enter the required information. You may
insert
show suppliers link 7. Click the Insert button to add the substance to
the inventory database. When you create a new substance record, Inventory searches the database for duplicates, and gives you an opportunity to resolve any conflicts. Only if there are no conflicts will the substance be added
enter: a CAS number a CAS number plus supplier a CAS number plus supplier and catalog number a supplier and catalog number. 3. Browse to the file containing the MSDS data. 4. If you want to create a link to the file, select the Add link check box. If you do not select the Add link checkbox, the file will be copied into the database. While this is the safest way to make sure that the MSDS will be available, it also adds considerably to the size of the database. You may also enter a link to a web page or intranet page by using the link option.
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Once you have added one or more data sheets to the CAS number, you may view them by clicking the MSDS link on the container details window. The ability to define MSDS by CAS number, supplier, and catalog number allows you to view different data sheets from different containers of the same substance when this is appropriate. If you want to search in ChemACX for data sheets, point to Preferences on the File menu, point to MSDS, and select the Search ACX option.
NOTE: You must have the ACX database installed to do
fieldincluding reactions (with arrows) and labels. While this may not be particularly useful, and might cause problems when searching, it does give you the flexibility to draw multiple structures and define them as a single substance. Note that the Molecular Weight and Chemical Formula (which are generated automatically) will be for the total of all structures in the field.
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Conflict Resolution
Conflict Resolution flags and corrects duplicates in the system. When creating a new substance in Inventory, Conflict Resolution runs automatically. You may also search for duplicates at any time. If a conflict is found, a page like this one appears. The conflicting field(s) are highlighted in red.
this.
Using ACX
If you have installed and linked the ACX database, you may search in it for compounds.
Mixtures
Normally, a Substance is defined as a pure chemical compound. However, Inventory, with some customization, may be used to define mixtures. Depending on the approach that makes the most sense for your users, you could choose to use either the custom substance fields or the custom container fields. For example, to define solvent mixtures commonly used in reversed phase chromatography, each of which contain various percentages of methanol, acetonitrile and tetrahydrofuran, use the custom substance fields (of which there are five available). The Substance name would identify the mixture (e.g. Name = HPLC Mixture 10% Methanol), and the custom compound fields would identify the exact composition (e.g. Mixture Component 1 = 10% methanol, Mixture Component 2 = 6% acetonitrile, Mixture Component 3 = 4% THF). This is not, however, the only way to handle mixtures. Anything you can draw with the ChemDraw toolbar can be stored in a structure
Cl
Name conflict
Cl
Structure conflict
In the example above, the existing substance and the new substance share the same Substance name and structure. From here, the user has up to three options:
Select an existing substance (thus cancelling the
new substance). Edit the conflicting substance or the existing substance so there is no longer a conflict. Create a duplicate substance and resolve the conflict later.
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Conflict Resolution - Select
To select one of the existing substances rather then adding a new substance, click Select. You will be returned to the Create New Container form with the substance inserted.
Conflict Resolution - Edit
for more information. If there are no duplicate fields, Inventory saves the changes to the database.
Managing Containers
Containers are the main focus of Inventory. You track your use of chemicals, ordering, reordering, and disposal by tracking the containers. Privileges associated with managing containers are defined in
Create Edit Checkin Change status Print container label Delete Move Checkout Change quantity
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To edit the duplicate substance or an existing substance: 1. Click Edit for the appropriate substance. The substance record appears. 2. Edit the appropriate fields. 3. Click OK.
Conflict Resolution - Create Duplicate
To create the duplicate, click Create Duplicate. You will be returned to continue creating a new container with the substance inserted. Creating a duplicate is not recommended. You must have appropriate permissions to delete duplicate substances.
Creating a New Container

To create a new container: 1. Click the New Container menu command. A window with multiple tabs labeled Required, Substance, Supplier, Contents, Optional, Owner, Comments, and Other (name may vary) opens. 2. Enter information about the new container. Required fields are highlighted with color.
TIP: Substance is not a required field. This allows
Editing a Substance
To edit a substance: 1. Choose Substances... from the Search menu. The Substances search form appears. 2. Fill in the desired field(s) and click Search. A hit list of matching substances appears. 3. Select a substance. The substance details appear in the lower pane. 4. Click Edit. The Create/Edit Substance form appears. 5. Make the desired changes, and click Update. If a duplicate for any required field is found in the system, the conflict resolution page appears. See Conflict Resolution on page 97
you to enter supplies such as glassware or disposables into the inventory. If you dont enter a substance, you will get a warning when you try to create the new container. You may safely click OK and ignore the warning. If you dont want to see the warning, create a dummy Substance (such as a letter or word) for nonchemical supplies.
3. Click OK.
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Editing a Container
To edit a container: 1. Select a container to edit. 2. Click the Edit Container on the Manage menu. The Edit Container form appears. This form is identical to the Create Container form. 3. Enter new values and click OK.
From the File menu, point to Preferences and click Default Checkout Location. If you do not set a checkout location preference, the default will be Root. Since Root cannot hold containers, only locations, you will need to change the Destination Location every time you check out a container. Failure to do this will result in an error message, reminding you to change the location. To check out a container: 1. Select a container. 2. Click Check Out Container on the Manage menu.
TIP: You can also right-click on the container and use
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Moving a Container
To move a container to another location: 1. Select a container to move. 2. Click the Move Container on the Manage menu. 3. Enter the destination location in the Move Container form and click OK.
TIP: Right-click on a container icon to get a context menu
the context menu. The Checkout Container dialog box appears. 3. Review the default settings, change as required, then click OK.
NOTE: The default status is in use, the default
of Container commands. You can also drag-and-drop containers to move them from location to location.You may select multiple containers to move simultaneously. See Multi Select on page 100 for details.
user is the one checking the container out. The container is removed to the selected location, and its status is reset. Checking a container back in follows a similar process. The defaults on the Check In Container dialog box are to set the status to Available and to return the container to the location from which it was checked out. The default Current User does not revert to the previous user.
Deleting Containers
To delete a container, drag or move it to the Trash Can. To remove containers completely from the database, click the Empty Trash Can command on the Manage menu.
Check-in/out, Changing Quantities, and Other Shortcuts

CS Inventory offers several shortcuts for the most common operations, including checking chemicals in and out of a central storeroom, and updating quantities as compounds are used up.
Duplicate Container
A new command on the Manage menu allows you to duplicate an existing container. The duplicate contains an exact copy of all fields, except the Quantity Remaining field, which defaults to the container size, and the Container ID and Barcode
Check-In/Check-Out Containers
Containers can be checked in and out of locations. If you routinely work at a specific location, you can set a default Destination Location.
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fields, which gets new values. The command is useful when restocking chemicals from the same supplier.
Move Delete
TIP: All of the new Manage menu commands are also
available on the context menu displayed when you right-click in the Container Grid.
Change Quantity
If all you want to do is change the amount of material left in a container, CS Inventory gives you a simple way to do that. 1. Select a container. 2. Click Change Quantity on the Manage menu. A dialog box appears where you can enter either the amount remaining or the amount used. When you click OK, the quantity field in the container is updated.
To enable multi-select: 1. Check Multi-select Containers from the View menu. A row of checkboxes appears in the Container Grid. 2. Select the containers, then right-click in the Container Grid. From the context menu select Move Selected Containers or Delete Selected Containers. If you selected Move..., a browse window opens to help you navigate to the new location.
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Managing EHS Data

CS Inventory 10 has added forms for attaching Environmental Health and Safety (EHS) data to Substances and Containers. Privileges associated with managing EHS Data are defined in . The Edit
Edit EHS Data Edit SQL Report
Change Status
To change the Status of a selected container, click the Change Container Status command on the Manage menu and select a status from the dropdown list on the dialog box. There are 23 predefined statuses, including order statuses (backordered, requested, etc.). The list may be edited from the Edit submenu of the Data menu. Status is displayed in the Container Details, and can also be changed from the Edit Container dialog box. You may search by status by selecting Container Status on the Advanced Search tab of the container search dialog box.
EHS Data privilege is required for both creating and
editing forms. EHS data has two levels: Substance and Container. You begin by creating substance-level data. You may then modify it at the container level to allow for differences due to different suppliers or product IDs. To create EHS data: 1. Use the Search>Substances menu, or on the main page, browse to a container of a substance for which you want to create EHS data.
Multi Select
The Multi Select menu command places a checkbox next to each Container ID in the container list. This allows you to select more than one container and perform one action on all of those containers at once. The actions available to Multi Select are:
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2. Click the EHS tab on the Container Details
form.
supplier information will appear at the top of the form if you have entered it. If you have not entered supplier information, your modifications apply to the container you are modifying. To edit the EHS queries: 1. Select Edit EHS Report SQL from the SQL menu. 2. Select the report to edit from the drop down menu at the top of the form. 3. Click the Edit button. A duplicate window opens with an editable copy of the SQL. (The first window is only for viewing.) 4. Make your changes and click the Update button.
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EHS tab Add EHS link 3. Click the Add Substance EH&S link.
The EHS form appears. 4. Enter the EHS data. Note that the only required fields are automatically filled in.
TIP: The names of the three EHS groups can be
modified on the EHS tab of the Custom Fields preferences. You can also add up to ten Custom Fields. To modify EHS data in a container: Click the Edit EH&S link on the EHS tab of the container details form. The EHS tab of the Container form has a Help link that brings up a document explaining the EHS categories. The default glossary is a Word document with UN Numbers, NFPA categories, and ACGIH carcinogens. You can edit this document, or replace it. To replace the EHS glossary: 1. Point to Update on the Data menu and click EHS Glossary Doc. 2. Enter a path or Browse to a file. 3. If you do not select the link checkbox, the file will be added to the inventory database. 4. Click the Add button. Enter data in the EHS data form. If you have entered data for the supplier and catalog number, the edited EHS data will apply to every container from that supplier with that catalog number. The
Searching Inventory
Searching is the easiest way to find particular substances or containers in Inventory. The system allows for combined chemical and text searches of all attributes associated with a container or substance. Several search forms are available to accommodate the search preferences of different users. For example, the Substructure Search form, for searches based on chemical structure, substance name, CAS number and other attributes, is particularly well suited for use by chemists. Similarly, the Advanced Search form, which exposes fields such as container and location barcode, is particularly well suited for use by stock room or receiving room personnel.
Searching for Containers

To begin a search:
Click the Search Containers menu command.
This displays a tabbed search form for all search types. Click on the tab indicating the type of search you would like to perform, and enter your search parameters.
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Simple Search
The Simple Search option allows you to use any combination of basic criteria, such as CAS Registry number, Container Barcode, Location Barcode, Catalog Number, Substance Name, Substance Synonym, Container Name, Container Comments, and/or Location ID. How to search: 1. Enter the search criteria. 2. Select the Search Sublocations checkbox if you want to search all sublocations of the chosen location. 3. Click Search.
NOTE: Inventory always does substring searches on text queries. Thus, entering benz in Substance Name will return Benzene, Benzyne, Bromobenzene, and so forth.
Advanced Search
The Advanced Search option adds a number of categories to the basic Simple Search, such as Purity, Concentration, Grade, Container Size, Container Status, Unit of Measure, Quantity Remaining, and so forth. This search concentrates more on container properties as opposed to substance properties. How to search: 1. Enter the search criteria. Custom fields, if defined, will appear on this search form. Any additional fields have been defined for your site. Please see you system administrator for more details. 2. Select the Search Sublocations checkbox if you want to search all sublocations of the chosen location. 3. Click Search. A list of containers matching your search parameters is returned. Clicking on one of the containers will allow you to view, the location of the container (left frame), container information (upper right frame), and the contents of the container (lower right frame). See Managing Containers on page 98 for more information.
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A list of containers matching your search parameters is returned. Clicking one of the containers will allow you to view the location of the container (left frame), container information (upper right frame), and the contents of the container (lower right frame).
Substructure Search
The Substructure search option includes most of the criteria in the Advanced Search, in addition to Substance Name, Molecular Formula, MolWeight Range, and of course, Substructure.
location contents information
To draw a structure, double-click in the structure box. Use the ChemDraw toolbar to draw your substructure. For more information about using the ChemDraw toolbar, see Drawing Chemical Structures in the ChemDraw User's Manual.
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You may include generic atom types, such as X for any halogen, or R for an unspecified organic group, in your query structure. In fact, you can include any query specifications (except those specific to reactions) available in ChemDraw. For more information, see Drawing Query Structures in the ChemDraw User's Manual. You have a choice of how Inventory will match the structure you draw to the structures in the Inventory database. Select the correct type from the Search Type drop-down menu.
Substructure
nature, fuzzy. For this reason, similarity searches are useful if you have a general idea of the types of compounds you are looking for, but dont have a precise conception of the target compound.
Search Preferences
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You can set a number of defaults that affect how Inventory performs structure searches.
Click Preferences in the File menu (or on the
Search form.)
The Search Preferences form appears. How to search: 1. Enter the search criteria. 2. Select the Search Sublocations checkbox if you want to search all sublocations of the chosen location. 3. Click Search. A list of containers matching your search criteria is returned. For information about Searching for substances and their properties, see Searching for Substances on page 103.
Substructure searches find structures that contain the query, plus any additional attachments at the open positions. Use this search type to find classes of compounds.
Exact
Exact searches find structures that completely match the query. You may get more than one hit if there are stereo-isomers in the inventory and you did not specify a particular one to be matched, or if you included a generic atom type.
Identity
The Identity search type is intended for use in compound registration, when you must know if a perfectly identical copy of your query compound is already present in the database. It is similar to an exact search, except that generic atom and bond types in the query must match corresponding atom and bond types in the target exactly. Moreover, stereochemistry must match precisely between query and target.
Similarity
Searching for Substances

Searching for substances is the same as the Substructure search option for containers, except that you begin from a different place, and fewer fields are displayed. Perform a substance search to edit a substance record or search for duplicates. How to search for substances: Select Substances from the Search menu. The Search Substances form appears.
NOTE: Your form may not have the same number of fields,
A Similarity search finds structures that have structural features that generally correspond to those in the query. Similarity searches are, by their
depending on whether or not custom fields have been created.
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Entering search criteria and performing the search are exactly the same as with a Container search. See Substructure Search on page 102 for details. 1. Enter search criteria and click Search. If you are searching for duplicate substances, select the checkbox at the top of the form. Inventory will search for duplicates according to the fields you enter. For more information on resolving duplicates, see Conflict Resolution on page 97. A hit list appears. 2. Select a substance from the hit list. A details frame opens in the lower pane. 3. Click Edit to edit the substance details. For more information, see Editing a Substance on page 98. 4. When you have finished editing, click OK.
NOTE: Right-click on a substance icon to delete a
SQL queries. Once a user with SQL privileges defines a custom SQL query, it can be used by other users.
Help
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TIP: In the Reporting tab of the Application Configuration
dialog box, you can set the default format for Help to either PDF or MSWord doc. Privileges associated with managing printing are defined in
Print report Print container label
substance or locate its containers.
Printing Labels and Reports

Inventory Pro/Ultra/Workgroup uses the List & Label reporting utility from Combit GmbH. Detailed information on creating customized reports can be found in List & Labels Help, available from the Inventory Report dialog box. This document describes how to use the built-in templates to produce basic reports and barcode labels, as well as how to design more advanced reports. The Inventory Report dialog box is used for printing both labels and reports. Several sample label/report templates are provided, or you can design your own as described above. You can sort the generated reports by up to three fields (see figure below). More complex reporting, such as EHS reports, can be produced by defining custom
Labels
The standard Inventory installation includes the following sample templates:
eight barcode label four standard label four EHS-data label.
You may also design your own labels. To print labels with a standard template: 1. Select a location. 2. Choose Labels... from the Report menu. The Inventory Report dialog box appears, with Label selected as the Report Type. 3. Click the Print/Preview/Export... button. The Generating Labels window appears.
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4. Select a label template and click the Open
2. Click the Print Label link on the Summary tab
button.
TIP: If you click Open without selecting a file, you will activate the template Wizard to help you design a new template.
of the Substance Details section.

NH4
S S
Print label
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The Print Options dialog box appears. The Inventory Report dialog box appears, with Label selected as the Report Type. 3. Proceed as with multiple labels. The only difference is that the data for a single label only has been passed to the print utility. To create a new label template: 1. Select a location. 2. Choose Labels... from the Report menu.
NOTE: If there are no containers in the location you
5. Use the Direct to... drop down menu to select
Direct to
Start position
have selected, you will get an error message.

3. Click the Design... button on the Inventory
Preview mode, or to send the output to a file instead of printing. 6. When you have selected your options, click Start. Labels are printed for all of the containers in the selected location.
TIP: Note the Start Position option. It allows you
Report dialog box. 4. Enter a new file name in the File Name text box of the Generating Labels window. The List & Label Project Wizard appears to walk you through the new label creation process. To change the label style: 1. Select a location. 2. Choose Labels... from the Report menu. 3. Click the Design... button on the Inventory Report dialog box. 4. Select an existing label template and click the Open button. The List & Label design page appears. 5. Select Page Setup from the Project menu. 6. Select the Templates tab.
utilize partially used label sheets by adjusting the start position. To print a label for a single container: 1. Select a container, either by browsing or searching.
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7. Locate your label style on the list of Avery,
ERO, Herlitz, Herma, and Leitz standard labels, and double-click to select it, then click OK. 8. Adjust the label components to fit the new label size as necessary, then close and save your changes to the label file.
NOTE: You may want to test for the positioning of the printed labels by printing a a sample page and adjusting the dimensions in the designer as necessary.
3. Use one of the sample queries provided (for example, GenericEHSQuery1), or a custom 4. 5. 6. 7.
EHS Labels
You can produce EHS labels for one or more containers. 1. Select a location or a container. 2. From the Report menu, point to EHS and select the appropriate label option.
query created in-house Click the Print/Preview/Export button. A dialog opens to select the report template. Select the file GenericEHSQuery.lbl, or create your own custom template. Click the Open button. The Print Options dialog box appears. Select your print options and click the Start button.
TIP: You can preview the labels by selecting Preview
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in the Direct to... text window. If you are printing a large number of labels, Preview may take several seconds to produce results.
The Report dialog appears
Reports
Inventory can print reports in two basic styles: with structures and without. When you choose Location Report (include structures), Inventory creates graphic files (*.emf) from the structural data to import to the print utility. This can be a time-
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consuming process, especially for a large inventory. You should consider the time factor when deciding which report command to use.
NOTE: The names of all of the available report templates
2. From the Report menu, point to EHS and select
appear when you select either report type. If you select a template with structures, but are using the command that does not save images of the structures, the Structure column of the report will be blank. Printing reports is similar to printing labels: select a location, select the style of report to print from the Report menu, and step through the dialog boxes. As with printing labels, you can design your own template rather than selecting one of the existing ones.
TIP: The Print Preview option in the Print Options dialog
3.
4. 5.
6. 7.
box allows you to print, save to file, or send an email of the report in PDF, text, or graphic format.
the appropriate report option. You can get a report broken down by location and sub-location if you wish. The Report dialog appears Use the default SampleTotalQuantities_List query (or SampleTotalQuantities_Base Units_List) query, or create your own custom query. Click the Print/Preview/Export button. A dialog opens to select the report template. Select the file SampleEHSTotalQtys.lst (or SampleEHSTotalQtys_BaseUnits.lst), or create your own custom template. Click the Open button. The Print Options dialog box appears. Select your print options and click the Start button.
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CS Inventory 10 includes more sample report forms, including EHS report templates. When selecting a report template based on a user-defined SQL query (whether for design or printing) such as the EHS templates, you must choose one that matches the defined query. If the fields in the report template do not match the fields in the selected SQL query, you will get an error message.
EHS Reports
EHS reports are produced in a similar manner to EHS labels.
NOTE: You must select a query that matches the report
Inventory Tasks
The following tasks may be performed by users who have been assigned the privilege. If you do not have access to something you need access to, please see your system administrator:
Search (Browse) View Audit Trail
you wish to produce. If you do not, you will get an error message. A typical report for total quantities of EHS materials would be done as follows: 1. Select a location (Root, if you want the report to be for the entire database.)
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Create container Edit container Change container
Delete container Move container Change container
The Inv_Admin role cannot be deleted, though it can be modified. Other Roles and Users may be added, modified, or deleted only by the database owner, invadmin. Users can change only their own passwords.
NOTE: There is a difference between the role Inv_Admin and the user with the name invadmin. User invadmin is the database owner, and has security permissions in MSDE. Users with the Inv_Admin role can make changes in the Inventory database, but cannot administer Users and Roles.
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status
Checkin container Create location Edit location Create substance Edit substance Create MSDS Print labels Edit SQL report
quantity
Checkout container Delete location Move location Delete substance Edit EHS data Delete MSDS Print reports
Managing Roles
To create or edit a Role: 1. Click Manage Roles on the Security menu. 2. Click the appropriate button at the bottom of the Manage Roles dialog box. explains the options.
The tasks specifically limited to the Inventory Administrator are:

Manage Users Lock/unlock Manage Roles Define custom
Button
Function
Close Add Role
Closes the dialog box. Creates a new role.
records
Backup the database
fields
Managing Users and Roles

CS Inventory 10.0 introduces the concept of security levels based on Roles. Roles are lists of privileges that determine what a user can and cannot do in the database. When you create a new user, you must assign the user to at least one Role. The predefined roles in Inventory are:
Inv_Admin Inv_Browser Inv_Chemist
Update Role Edits the selected role. Users Adds users to the selected role. Used to populate new roles or change user assignments to existing roles.
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2. Select a role and click the Users button on the
Button
Function
Manage Roles dialog box. 3. Select users and Add or Remove them from the Role with the buttons.
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Roles
Assigns all of the privileges of one or more roles to the selected role in a single step. This nesting capability gives you a consistent way of assigning hierarchies of privileges. Deletes the selected role.
Managing Users
To create, modify, or delete a user account: 1. Click Manage Users on the Security menu.
NOTE: These options only appear when you log in as
the database owner (invadmin).

2. Click the appropriate button at the bottom of
Delete
When you add or edit a Role, you work with the same dialog box. The only difference is that you have to type in a Role Name when adding a new Role. When editing, the name is grayed out, and cannot be changed. Check the privileges that will define the Role.
NOTE: The INV_BROWSE_ALL privilege is, by
the Manage Users dialog box. You must select a User before clicking Update User.
default, assigned to all roles. It cannot be unchecked. To nest roles within other roles: 1. Click Manage Roles on the Security menu. 2. Select a Role, and click the Roles button on the Manage Roles dialog box. 3. Select a Role and Add or Remove it with the buttons. The Role named in the Role Name text box now includes all of the privileges of those Roles that appear in the Current Roles window.
NOTE: If you inspect the privileges list for that Role, you will not see additional boxes checked. The checked privileges are only those that have been assigned directly.
When adding or modifying users, the Edit User dialog box appears. When modifying a user, the Username and Password text boxes are grayed out and cannot be changed.
TIP: Normally, users maintain their own passwords.
Thus, the Password text box is blocked from editing to prevent accidental changes. You can, however, override this by checking the Change Password checkbox.
3. Enter appropriate data in the text boxes. User Name and Last Name are the only required
To assign Users to a Role: 1. Click Manage Roles on the Security menu.
fields. Blank passwords are acceptable. There is no specific requirement for a User Name or Last Name, but the text boxes cannot be left blank. Any alphanumeric or symbol may
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be used. A User Name, once created, cannot be modified. To change a User Name, you must delete the user and create a new name.
NOTE: Deleting a User Name in Inventory does not
Suppliers
The default Supplier list has over 300 entries. To make it easier to find the correct supplier from the list, an administrator can not only add new suppliers, but can abbreviate the displayed list. To abbreviate the supplier list: 1. Point to Abbreviate on the Data menu and click Supplier List. 2. Deselect suppliers that will not be used in the Show column.
NOTE: The deselected suppliers are not removed from the database. They are merely not displayed. They can be restored at any time by reselecting them on the list.
3. Click the Save Changes button when you have
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delete the corresponding SQLServer login.

4. Add or remove User Roles by selecting a Role and clicking the Add or Remove buttons. Every
user must have at least one Role assigned.
Managing Tables
Some fields in Inventory forms are entered from drop-down menus rather than by typing in text. Inventory stores these pre-set field entries in tables that can be edited by an administrator. If, for example, you want to specify a type of Container that is not on the container type menu, the new type can be added. You can also delete items from the tables, provided they are not being referenced by any records in the Inventory database. To edit a table: 1. Select the table to edit from the Data menu. 2. Fill in the attributes in the form that appears, and click OK. Inventory stores the changes to the table. To edit or delete a table entry: 1. In the Data menu, point to Edit and select the table to edit. The table is displayed. 2. Do one of the following: a. Edit the text as required. b. Select the entire row you wish to delete, and press the Delete key. 3. Click Save. Inventory stores the changes to the table.
completed the edit.
Custom Fields
If you have Inventory administrative privileges, that is, if you are logged in as invadmin, you can add custom fields to compound, container, and EHS records. Compounds can have up to five custom fields. Containers can have up to ten custom fields and five custom dates. You may also add up to ten custom fields for EHS data. Custom fields and dates can be designated as required fields. Custom compound fields can be marked for duplicate checking. To add custom fields: 1. From the File menu, point to Preferences and select Custom Fields. The Custom Fields dialog box appears. 2. The Custom Fields form has three tabs: one for compounds, one for containers, and one for EHS data. Click the appropriate tab, and enter the name of the new field(s).
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The fields will appear on the blank forms when you open them.
NOTE: The custom fields appear directly on the Compound form. For containers, they appear on the tab labeled Custom, and when applicable, on the tab labeled Substance. When browsing containers, the first custom field defined is displayed on the Summary tab.
The default names of custom fields in the Grid Display is as follows:
Desktop / Workgroup
Custom Field
Field Name
Field_1 etc. Date_1 etc. ALT_ID_1 etc.
Container Fields Container Dates Substance Fields
Record Locking
Administrators can turn record locking on or off. When record locking is turned on (the default), a record (that is, a container or a substance thats being edited) can only be accessed by one user at a time. An administrator can unlock records to allow immediate concurrent access. When records are locked, a second user attempting to edit an open record will receive a notification message that the record is currently open, and cannot be accessed. If a user leaves a record open, but inactive, for more than 10 minutes, the lock times-out, and other users can access the record. When the original user returns to the record, a message is displayed warning the user to resave any changes.
Backup/Restore Database
CS Inventory 10 includes a backup/restore utility for your database. The utility requires you to quit the application in order to run. To backup or restore a database: 1. Click Backup/Restore DB on the Data menu. A message appears telling you that you must quit the Inventory application to continue. 2. Click Yes to continue. The application quits and a Backup dialog box appears. 3. Click the Connect button to connect the utility to SQLServer. A message appears at the bottom of the dialog box, recommending that you back up both the CS Inventory (CHEMINVDB2) and CSSecurity databases. 4. Type in the path, or browse to the location of the backup Inventory database file. The default location is...\All Users\Application Data\CambridgeSoft\Backup\ CHEMINVDB2.bak. 5. Browse to the location of the backup MstFiles folder. The default location is in the ...\CambridgeSoft\Backup\ folder.
Managing the Container list display

Any user can adjust the display of fields in the Container list. Changes will be viewed by all users.
From the File menu, point to Preferences and
select Container Grid Display. The Grid Display form appears. You can change the Field Name, Column Order, and Column Width. You can also select which fields will be displayed. Clicking the name of a column in the grid form sorts the entries by that column. This is to facilitate rapid editing; it does not affect the display.
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6. Type in the path, or browse to the location of
the CSSecurity DB backup file. The default location is in the...\CambridgeSoft\Backup\ folder. 7. If you check the Append timestamp checkbox, you will create a new backup DB file with the date and time in the file name. If you deselect the checkbox, Backup will append data to the existing backup database file, if there is one. 8. Click Backup. After a brief delay, a message appears advising you of a successful backup. To restore a backed up database: 1. Repeat steps 1-3 of the backup procedure. 2. Click the Restore tab of the dialog box. 3. Type in the path, or browse to the previously created backup file. When you click the browse button, you will open the previous backup folder. You must select the correct file to restore. 4. Browse to the location of the backup MstFiles folder. 5. Browse to the folder to receive the restored MstFiles. 6. Type in the path, or browse to the backup CSSecurity DB file. 7. Click the Restore button to restore the database.
Viewing the Audit Trail

You must view the Audit Trail before printing. To view the audit trail: 1. Click Audit Trail on the Data menu.
Administrator
Audit trail
The Audit Trail window appears.
Output area
Filter settings
The filter settings both limit the data that appears in the report, and determine how it is presented. Each setting has a blank position that signifies no filtering on that parameter.
Audit Trail
CS Inventory logs all changes relating to Locations, Containers, and Substances. You can view this log and print out reports, filtering the data according to your needs. Output can be directed to a printer or to a file. Output file formats include PDF, Excel, text, HTML, and RTF. You must be assigned the View Audit Trail privilege in order to do this.
Use Filter...
if you want to...
Table
view changes for just Containers, Substances, or Locations.
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Results per Page and Use Filter... if you want to... Order Results By
These affect both the view and the printout.
Desktop / Workgroup
From Date To Date
view changes by date. Select filter dates from a calendar display or type in the text box. view changes by a specific user. view the changes for a specific container. view the changes for a location. view the changes for a specific substance. view a specific type of change: Insert, Update, or Delete
Printing an Audit Report

You must view the data before printing. When you click the Filter button to view a report, two more buttons appear: Design and Print.
Current User
Print buttons
Container Barcode Location
Structure code
View link
Compound ID
A new template, AuditTrailReport, has been added to the default report templates listed when you click the Design or Print buttons. When you are reviewing changes to Structures, the Audit report displays only a structure code. The View link in the last column on the right allows you to display the structures. See annotations in and
Action
Note that when you create a new Container, Substance, or Location, you insert data for every field. Every edit or move is logged as an update to the field(s) that have changed. When you delete a Location or Substance, or empty the Trash Can, each field in the item affected is deleted. When you have selected the filters you want to apply to the data, click the Filter button to view the results. You can reset the filters, or change them individually, to view a different data set. The filters also give you two controls over the output format:
For more information on designing and printing reports, see Printing Labels and Reports on page 104.
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114Inventory Desktop/Workgroup Inventory Tasks CambridgeSoft
Inventory Enterprise is a ChemOffice Enterprise based application designed to manage the reagent tracking needs of chemical and pharmaceutical research centers. The system manages data associated with both commercially procured and internally produced chemical substances from their procurement or initial production through their depletion and disposal. Inventory Enterprise is an Oracle-based, ChemOffice Enterprise product. Designed for large organizations, it has a number of features. This chapter introduces the terminology and the User Interface, describes the set-up and management of an inventory database, and discusses the search forms used to locate substances and containers in the inventory. The three primary entities in the system are Locations, Substances, Containers, and described below: Click the Browse link under Inventory Enterprise to view the Inventory database.
NOTE: Administrative tasks relating to login, such as adding users and changing passwords, are covered in other sections. For Enterprise versions, Manage Users and Roles on page 192.
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Searching Inventory Enterprise

Simple Search
The simple search option allows searching through the use of CAS number, Container barcode, Location Barcode, Catalog number, PO number, PO Line Number, Substance Name, Substance Synonym, Container Name, Container Comments, and Location ID.
Logging in
All versions of Inventory use a password based login. Logging in to Inventory Enterprise brings you to the ChemOffice Enterprise homepage.
How to search
1. Enter the desired information to search for. 2. Select the Search Sublocations checkbox if
you want to search all sublocations of the chosen location. 3. Select the Exclude Special Locations checkbox if you want to exclude special locations. 4. Click Search in the toolbar.
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A list of containers matching your search parameters is returned. Clicking on one of the containers will allow you to view, the location of the container (left frame), container information (upper right frame), and the contents of the container (lower right frame).
A list of containers matching your search parameters is returned. Clicking on one of the containers will allow you to view, the location of the container (left frame), container information (upper right frame), and the contents of the container (lower right frame).
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Advanced Search
The advanced search option allows searching through the use of CAS number, ACX number, Reg Number, Purity, Concentration, Density, Grade, Size, Container Cost, Location ID, Container ID (barcode), Container ID (internal), Container Name, Container Type, Container Status, Unit of Measure, Qty Remain, Qty Available, Location Barcode, Compound Type, Catalog number, Supplier, Lot Number, Expiration Date, Ordered By, Date Ordered, Date Received, PO Number, Owner ID and Current User ID.
Substructure Search
The substructure search option allows searching through the use of all of the attributes in the Advanced Search in addition to Substance Name, Molecular Formula, MolWeight Range, and of course, Substructure. To allow you to draw your substructure, a ChemDraw Plugin will open along with this search tab. For more information about using the ChemDraw Plugin, see Drawing Chemical Structures in the ChemDraw User's Guide. Additionally, the structure drawn can be searched for assuming it to be a Substructure, Full Structure, Exact Structure, or with Tanimoto Similarity. Select the correct type under Search Type.
How to search
How to search
you want to search all sublocations of the chosen location. 3. Select the Exclude Special Locations checkbox if you want to exclude special locations. 4. Click Search in the toolbar.
you want to search all sublocations of the chosen location. 3. Select the Exclude Special Locations checkbox if you want to exclude special locations.
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4. Select the Group results by chemical
How to search:
1. Select the checkboxes next to the applications
structure checkbox if you want results grouped by chemical structure. 5. Click Search in the toolbar. A list of substances matching your search parameters is returned. Clicking on the details button of one of the substances will allow you to view, all of the inventory containers that contain that substance. For information about Searching for substances and their properties, Searching for a Substance on page 120. Deselecting the "Group results by chemical structure search box" will lead directly to a list of containers matching the search criteria (bypassing the substance grouping).
Global Search
The Global Search form allows users to search over the Registration Enterprise, ChemACX, or both, simultaneously with an Inventory Enterprise search. When results are returned, Inventory, Registration, and ACX results remain separate, but the application indicates if the retrieved substance is found in any inventory containers. The global search option allows searching through the use of Substance Name, CAS number, ACX number, Catalog number, Molecular Formula, MolWeight Range, Registry Number, Registry Sequence, Reg Alternate IDs, and Substructure.
you would like to search over. 2. Enter the desired information to search for. For more information about entering search criteria, see Searching ChemOffice Enterprise Applications on page 194. Additional fields may appear on this search form. Any additional fields have been defined for your site. Please see you system administrator for more details. 3. Click Search in the toolbar. A list of substances matching your search parameters is returned. 4. Click on the radio button next to the appropriate application to see results retrieved from that application. For more information, please see Viewing Results for a Global Search.
Viewing Results from a Global Search
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Search results from a global search are split into three lists, one for each application. To access results from an application, select the radiobutton next to the application's name. Results are initially listed by substance. To view the results by container, click the Details button for a substance. The Details button is only active if there is an associated container.
Plate Search
The plate search option allows searching through the use of Substructure, Substance Name, CAS Number, ACX Number, Reg Number, Molecular Formula, MolWeight Range, Purity, Concentration, Solvent, Location ID, Plate Barcode, Plate Map, Plate ID (internal), Plate Name, Plate Type, Plate Status, Unit of Measure, Qty Remaining, Qty Initial, Molar Amount, Supplier Name, Supplier Shipment Code, Supplier Shipment Number, Supplier Shipment Date, Date Created, Plate Format, Library, Group Name, and Freeze/Thaw Cycles.
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add a new substance to the database. This option is available after entering the substance management area and clicking on Add Mode.
Creating a New Substance

The "New Substance" form is available in the Substance Management area of Inventory Enterprise. To reach this form, do the following: How to search:
1. Enter the desired information to search for. 2. Select the Search Sublocations checkbox if 1. From the homepage, click Manage Substances. 2. Click Add Mode.
Administrator
you want to search all sublocations of the chosen location. 3. Select the Exclude Special Locations checkbox if you want to exclude special locations. 4. Click Search in the toolbar. A list of plates matching your search parameters is returned. Clicking on one of the plates will allow you to view, the location of the plate (left frame), plate information (upper right frame), and the contents of the plate (lower right frame).
This form is also available from the New Container Substance Tab, Substance Tab on page 129. Following screenshot appears.
Substance Management
The substance management area of Inventory Enterprise is available in the uppermost toolbar of the homepage and search page. This area allows users to search for substances by substructure, registration numbers, and other physical properties. Although similar to the types of searches found on the homepage, this area concentrates on the searchable aspects of substances and returns a table of substances as opposed to containers. If you have the appropriate privileges, in addition to allowing you to search for substances previously entered, this area also gives you the opportunity to How to create a new substance:
1. Enter information about the new substance.
NOTE: More fields may appear in your form. These forms are customized for your site. Please see your system administrator for more details.
2. Click Add Record in the toolbar.
If a conflict is recognized in the system (i.e. the same structure or Substance Name), the Conflict Resolution page appears. Otherwise, the substance is added to the system.
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3. Click OK.
New Substance Conflict Resolution
The New Substance Conflict Resolution is used to flag and correct duplicates in the system. After creating a new substance in Inventory Enterprise, the Conflict Resolution page appears if there is a conflict in any unique fields. Unique fields are defined by the system administrator, but by default are substructure, Substance name, CAS number and ACX number. This only checks conflicts within Inventory Enterprise, not with Registration Enterprise and ChemACX. If a conflict is found, a page like this one appears:
To select one of the existing substances rather then adding a new substance, click Select in the grey header bar above the substance you would like to select. You will be returned to continue creating a new container with the substance inserted. Conflict Resolution - Edit To edit the duplicate substance or an existing substance:
1. Click Edit in the grey header bar above the
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appropriate substance. The substance record appears.
2. Edit the appropriate fields.
The conflicting field is highlighted in red. In the example above, the existing substance and the conflicting substance (which is being added) share the same substructure. From here, the user has three options: Conflict Resolution - Select The option to select an existing substance and abort the new substance creation, is only available if the user is currently creating a new container. This option is not available from the Substance Management area of the application.
3. Click OK.
Conflict Resolution - Create Duplicate The option to create a duplicate by adding the new substance regardless of the conflict, is only available if the user is currently creating a new container. This option is not available from the Substance Management area of the application. To create the duplicate, click Create Duplicate in the grey header bar above the conflicting substance. You will be returned to continue creating a new container with the substance inserted.
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Creating a duplicate is not recommended, but is an option. To later search for all duplicates in the system, select System Duplicates from the Compound Type listbox in the Advanced Search form.
Creating Inventory Substances from Registration Enterprise and ChemACX
How to search:
1. Enter the desired information to search for. 2. Click Search in the toolbar.
Administrator
Inventory substances can be created from both the Registration Enterprise and ChemACX. If this option is not available from your instance of the Registration Enterprise or ChemACX, please see your system administrator.
A list of substances matching your search parameters is returned. Clicking on the details button of one of the substances will allow you to view, all of the entered properties of the given substance. New Container Substance Tab Form If accessed through the New Container Substance Tab, the following bar appears at the top of the form
Searching for a Substance

A form made to make finding a substance easier is available in Substance Management on page 118. To reach this form, simply click Manage Substances from the homepage. This form is also available when clicking on the Select Substance Link in the New Container Substance Tab. For more information, please see New Container Substance Tab Form (below). This form is a simplified version of the Substructure Search form found on the homepage. The following attributes are available to search under from this page: Substructure, Substance Name, CAS number, ACX number, Molecular Formula, MolWeight Range, Compound ID, and Compound Type.
The bar allows the user to search over all three applications simultaneously. For more information about global searches, Global Search on page 117. After the search is performed, select the Details button for the correct substance, and click OK to insert the substance in your new container. Perform another type of search.See Searching Inventory Enterprise on page 115..
Editing a Substance's Details

To edit a substance:
1. Perform a search and click on the Details
button for the substance. A page appears displaying all retrieved details for the appropriate record.
2. Click Edit Mode.
The record appears in Edit Mode.
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To access this section, please take the following steps:

1. From the Substance Management area, access
3. Enter or edit the appropriate information. 4. Click OK.
the search form. 2. Perform a search for the appropriate substance. 3. While in list view, click the Details button for the substance. 4. Click on the View History link. The View History window opens.
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NOTE: If a duplicate for any required field is found in the system, the conflict resolution page appears. Please see Substance Conflict Resolution, page 119 for more information.
Delete a Substance
To delete a substance:
1. Perform a search and click on the Details
button for the substance. 2. Click Delete Record. A page appears asking for confirmation.
This area allows you to view an audit report of substances. User can filter the details according to Filter Criteria. User can view Audit details in two ways, Standard & Aggregate. Application displays Standard report by default: To view Aggregate report:
1. Click Aggregate.
3. Click OK.
Aggregate report opens.
View History
The view history area of Inventory Enterprise is available as part of substance management.
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User can view the audit details group by fields. User can also select radio button to view group by date. 2. Enter details in appropriate fields. 3. Click Filter.
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Synonym Management
The synonym management area of Inventory Enterprise is available as part of substance management. To access this section, please take the following steps:
2. Enter a synonym. 3. Click OK.
To edit a synonym:
1. Click Edit next to the synonym to be edited. 2. Edit the name of the synonym. 3. Click OK.
the search form. 2. Perform a search for the appropriate substance. 3. While in list view, click the Details button for the substance. 4. Click on the Manage Synonyms link. The Synonym Management window opens.
To delete a synonym:
1. Click Delete next to the appropriate synonym. 2. If you do want to delete this synonym from the
list, Click OK.
Link Management
The manage link area of Inventory Enterprise is available as part of substance management. To access this section, please take the following steps:
This area allows you to add new synonyms for a substance edit the synonyms which are already listed, or delete a synonym from the list. After accessing the Synonym Management window, to add a new synonym:
1. Click New.
the search form. 2. Perform a search for the appropriate substance. 3. While in list view, click the Details button for the substance. 4. Click on the Manage Link. The Manage Links window opens.
A text field allowing the addition for a synonym appears.
This area allows adding a link to the substance. 5. Click New to add link.
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The Add a Link window opens.
Location Tree Frame
Current Location Container list Frame Frame
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6. Enter the appropriate information.
Enter a URL in the URL list box. NOTE: You must enter http:// for the URL if applicable. Enter Text that you would like the link to be
Container Details Frame
displayed as in the Link Text textbox. 7. Click OK. To edit a link:

1. Click Edit next to the link to be edited. 2. Edit the appropriate information. 3. Click OK.
Location Management
A location is defined as any "place" that a container can be stored. This includes a shelf, a refrigerator, or even a particular laboratory. Different facilities can decide how best to organize locations. For more information about locations, please see Location Tree Frame on page 124..
To delete a link:
1. Click Delete next to the appropriate link. 2. If you do want to delete this link from the list,
Current Location Frame

The location text box indicates the currently selected inventory location. Actions performed via the links on this frame apply to the currently selected location. In addition, you may enter a location id value into the location box to rapidly access a location on the tree. A barcode reader may be used to enter a location id value into this box further expediting navigation to a given location.
click OK.
Container Management
The container management area of Inventory Enterprise is available in the uppermost toolbar of the homepage. This area is split into 4 frames, shown below: Current Location Frame (top), Location Tree Frame (left), Container List Frame (top right), Container Contents Frame (bottom right).
The following controls and functions are available within the current location frame:
Inventory Enterprise Container Management
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Available to all users:

New Search
Returns to Search Mode screen. The last search form selected by the user will be automatically preselected.
Search Results
Returns to last hit list viewed while on Search Mode. If no search has been performed the link brings up the search default search form.
Help
Type, Unit of Measure, Container Size, and Initial Amount. The container name and barcode fields will default to an auto generated container id value. Other container attributes can be completed by populating additional tabs on this dialog. In particular, a chemical structure can be assigned to the container by following the New Substance or Select Substance links from the Substance tab.
Order Container
Administrator
Allows the user to enter an order for a container not currently in the Inventory Enterprise.
Tasks
Opens the Inventory Enterprise User's Guide.

Home
Brings the user back to the global login homepage.

Log Off
Opens a new window listing administrative tasks available.
Location Tree Frame
Logs the current user off.

Available to only some users:
New Location
Creates a new inventory Location at the currently selected location.

Edit Location
Allows setting of the following Location attributes: location name, location type, location barcode and location description.
Move Location
Allows moving a location to a different node on the location tree. Enter a location id value or use the browse link to select the destination locations. All containers and sub locations will follow with the moved location.
Delete Location
The location tree control allows navigation of the Location hierarchy. Click on the +/- symbols to expand/contract location folders. Click on the location name to display its contents on the container list frame. The refresh link at the top right of the page repopulates the tree from the latest available location data and returns it to its fully contracted position.
New Search/Search Results
Deletes the currently selected location. A location must be empty before it can be deleted.
New Container
Creates a new container in the currently selected location. There are five required parameters to create a new container: Location ID, Container
Searching is the easiest way to find particular substances or containers in Inventory Enterprise. The system allows for combined chemical and text searches of all attributes associated with a Container. Several search forms are available to accommodate
124Inventory Enterprise Container Management
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the search preferences of different users. For example, the Substructure Search form which allows searches based on chemical structure, substance name, CAS number and other attributes is particularly well suited for use by chemists. Similarly, the Advanced Search form which exposes fields such as container and location barcode is particularly well suited for use by stock room or receiving room personnel. The Global Search form allows the user to search over the Inventory Enterprise, Registration Enterprise, and ChemACX databases simultaneously if all three applications are installed on the server. Four distinct search forms are available from the homepage of the Inventory Enterprise through the use of tabs. Click on the tab indicating the type of search you would like to perform, and enter your search parameters.
Multi Scan
2. Enter Container ID in the field, press Tab.
NOTE: User can scan multiple Container IDs.
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NOTE: User can also remove container by clicking the
Remove link.
New Location
Containers are located in different places throughout a facility. The types of locations necessary in your Inventory Enterprise is highly dependent upon your setup. In order to create a new location:
1. From the homepage, click Manage
Containers. 2. Use the location tree to select where the new location should be created. 3. Click New Location in the Current Location Frame. The New Location window opens.
The Multi Scan feature allows user to scan more than one container in the same list. User can perform few operations such as Check In, Check Out, Move Container, Retire Container, Delete Container and Clear List, on the scanned container(s). In order to scan new container:
1. From the Current Location Frame, click Multi
Scan. The Multi Scan window opens.
4. Enter the desired information in the window
that opens.
5. Click Add Address link.
The Add Address window opens.
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4. Make sure the information listed in the window
that opens is for the correct location. Enter the desired new information in the window. 5. Click Add Address link. The Add Address window opens.
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6. Enter the desired information about address in
the window.
7. Click OK.
Edit Location
After a location is created, its properties may change. For example, the user may need to rename the location or add an address for the location. In order to change the properties of a particular location:
6. Enter the desired information about address in
the window. 7. Click OK.

Move Location
Containers.
2. Browse to the location to be edited in the
Location Tree Frame. 3. Click Edit Location in the Current Location Frame. The Edit Location window opens.
After a location is created, it may be necessary to move the location to somewhere else in the tree. For example, a refrigerator may have been located in a lab on the first floor, but is being moved to a lab on the third floor. Of course all of the containers inside the fridge are moved along with it. It is easy to move a location along with all of it's contents in the Inventory Enterprise. In order to move a location:
Containers.
2. Browse to the location to be moved in the
Location Tree Frame.

3. Click Move Location in the Current Location
Frame. 4. Make sure the information listed in the window that opens is for the correct location. Enter the new destination for the location to be moved. 5. Click OK.
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To reach this form, do the following:

Delete Location
If a location needs to be removed from the inventory, you should use the delete location tool. If the location is merely being moved, Move Location on page 126. In order to delete a location:
Containers. 2. Click New Container in the Current Location Frame. A window with multiple tabs labeled Required, Substance, Supplier, Contents, Optional, Owner, Comments, and Other (name may vary) opens. How to create a new container:
1. Enter information about the new container. 2. Click OK in the toolbar.
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Order Container
Containers. 2. Click Delete Location in the Current Location Frame. The Delete Location window opens.
Users can enter an order for a container that has not yet been created as part of the inventory by clicking on the Order Container link. If the container is already in the inventory and you would like to reorder the same container, please see Reorder Container. The following window opens when the Order Container link is clicked:
3. Browse to the location to be deleted in the
Location Tree Frame. 4. A location can only be deleted if it is empty, so make sure there are no containers in the location to be deleted.
NOTE: You can not undo the deleting of a location.
5. Click OK.
New Container
The "New Container" form is available in the Container Management area of Inventory Enterprise.
The Substance, Contents, Owner, and Comments Tabs appear and react just as the tabs with the same name in the New Container window react. The Required Tab in the Order Container window is also very similar to the New Container window. The Order Container Required Tab does not include all of the fields in that of the New Container
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Window. Additionally, there are two location IDs: one for the delivery location and one for the on order location. To order a container:
1. Click Order Container from the Current
Default Location
To save a default location, please do the following:

1. From the Container Management section,
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Location Frame The Order Container window appears. 2. Enter the required information and any other information which is desired. 3. Click OK.
Tasks
browse to the location to be saved as the default in the Location Tree Frame. 2. Open that location by clicking on the folder icon next to the location name. The default location window opens.
The following tasks are available to users with the correct administrative privileges. If you do not have privilege to access something you need to access, please see your system administrator.
Search, see page 124 New Location, see page 125 Edit Location, see page 126 Move Location, see page 126 Reconcile Location, see page 133 Plate Settings, see page 150 Create Plate from Excel, see page 161 Create Plates from Text File, see page 161 Custom Reports, see page 161 Change Password, see page 153 Manage Users, see page 192 Manage Roles, see page 192 Manage Container Requests, see page 153 Manage Sample Requests, see page 154 Analyze Audit Trail, see page 159 Manage Approvals, see page 158 Manage Tables, see page 159
3. Click OK.
Creating a New Container

The "New Container" form is available in the Container Management area of Inventory Enterprise. To reach this form, do the following:
1. From the homepage, click Manage Containers. 2. Click New Container in the Current Location
Frame. A window with multiple tabs labeled Required, Substance, Supplier, Contents, Optional, Owner, Comments, and Other (name may vary) opens. How to create a new container:
1. Enter information about the new container. 2. Click OK in the toolbar.
Required Tab
The Required Tab of the New Container window includes all of the information required to create a new container. Truly required fields are noted as such with a red field name.
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Contents Tab
The Contents Tab of the New Container window includes information pertaining to the contents of the container. Because different batches of a substance can have slightly different properties, it is important to keep track of such information.
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Substance Tab
The Substance Tab of the New Container window holds information about the substance in the container. When the tab is first opened, the tab is empty except for two links, New Substance and Select Substance. In order to insert a substance into the record, click on New Substance, if you would like to insert a substance that is not registered yet, or Select Substance, if you would like to insert a substance that is already in the database. If New Substance was selected, a new window opens that allows you to input information about the substance. If Select Substance was selected, a new window opens that allows you to search for a substance. Do the following to search:
1. Enter the desired information. 2. Click Search. 3. A list of substances is returned. Click on the
Optional Tab
The Optional Tab of the New Container window includes information that does not fit under any other heading, but may be important to include.
Owner Tab
The Owner Tab of the New Container window includes information about the owner and current user of the container. The current user must be an actuveuser of the Inventory Enterprise system.
details button for the appropriate substance.

4. Click OK to insert the substance.
Supplier Tab
The Supplier Tab of the New Container window includes information pertaining to the supplier of the contents of the container.
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Comments Tab
The Comments Tab of the New Container window allows the inclusion of comments about the container, or the contents of the container. This tab makes a space available to enter information not covered anywhere else.
be reproduced as a printable report. For more information about these search forms, Searching Inventory Enterprise on page 115. If you know location of the container you are looking for, you can use the location tree to navigate through all inventory locations to find the container. The Location Tree is displayed in the Container Management area. For more information about the Location Tree and how to navigate it, see Location Management.
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Viewing the Contents of a Container

After performing a search, or navigating through the location tree, a list of containers is displayed. For more information about searching for containers, seeSearching for a Container on page 130.
Other Tab Container List Frame
The Other Tab of the Container window gives users access to optional customizable fields. This tab is fully customizable and will vary from site to site. To learn more about customizable fields, please see your system administrator.
Searching for a Container

There is more then one way to search for a particular container. If you have some information about the container, but don't know it's actual location, using the search forms is often the easiest way to locate one or more inventory Containers. The system allows for combined chemical and text searches of all attributes associated with a Container. A search form configured to return matching Containers will result in a hit list comprised of containers matching the search criteria. Containers matching the search criteria appear on screen as a tabular report which can also
Both the container list frame found in the upper right hand frame of the Container Management area, and the report displayed after container based search results show a list of containers with some summary information. Containers are sorted in descending order by Container ID, but can be resorted by clicking any of the column headers. The small triangle next to the column name indicates the sorting order. Sorting affects containers regardless of whether they are displayed on the current page. Each container ID is preceded by a small flask. If the container information is open, the flask tips to the side. Click on one of the containers in the list to see the container details on the frame below.
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Container Details Frame
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All container attributes are displayed within the Container Details Frame. Given the large number of attributes associated with a container, they are subdivided into tabs which group the attributes into more manageable subsets. The first tab includes a summary of the most essential container attributes including container name, container id, barcode, location etc.... Other notable tabs include the substance tab, which summarizes the substance attributes and the supplier tab which brings together data related to the purchase of a chemical substance such supplier name, catalog number, lot number, container cost and purchase order number.
2. Select the checkbox next to any container you
would like to move.

3. Click Move Containers in the Container
Details Frame.
Large Icons
The Large Icons link displays the container flasks in the Container List Frame as large icons, similar to the Large Icons folder viewing option in Windows.

Available Functions of Container List Frame
Multi Select
Small Icons
The Small Icons link displays the container flasks in the Container List Frame as small icons, similar to the Small Icons folder viewing option in Windows.
The Multi Select Link changes the container list frame to details view and places a checkbox next to each Container ID. This allows users to select more than one containers and performs one action on all of those containers at once. For example, if you would like to move 3 containers to a new location:
1. Click Multi Select.
Details
The Details link displays the container flasks in the Container List Frame as a list of details, similar to the Details folder viewing option in Windows.
The containers are listed in Details view with checkboxes next to each container ID.
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Column Chooser
The Column Chooser window allows the user to customize the appearance of result lists. It allows control over the selection, order, and width of columns to be displayed on screen as well as the number of containers displayed per page.
The Update Contents link opens a window which aids users in keeping the list of inventory containers in a particular location up to date. This tool is a casual way for users to confirm the existence of a particular container. If a particular container is not confirmed, no action is taken on that container. For a tool to correct any discrepancies in a location's contents, please use the Rectify Contents tool. Update contents accomplishes the following:
confirm that containers are still where the
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By clicking the Set Widths button, another window opens that allows the user to enter specific widths for each column.
system thought them to be. move containers unexpectedly found at that location to specific location. allow for unknown containers to be created at specific location. To update the contents of a location:
1. Open the appropriate location and click
Update Contents in the Container List Frame. The Update Contents window opens.
Custom column settings are saved by the user's browser and remembered even after the browser has been closed. The settings available via the Column Chooser affect only the screen report. The appearance of printed reports is controlled by report templates managed by the application administrator. Multiple report templates can be associated with the screen report. Please contact the administrator if you need additional report templates produced.
Update Contents
2. Using a barcode scanner, or by manual
selecting the checkboxes, select the container ID for each container that is being verified. 3. Click OK.
At times, containers are moved and this is not updated in the inventory. Update Containers helps users to easily update the system confirming that a container is actually where the system thinks it is.
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Rectify Contents
At times, containers are moved and this is not updated in the inventory. Rectify Containers help users to easily update the system confirming that a container is actually where the system thinks it is. The Rectify Contents link opens a window which aids users in keeping the list of inventory containers in a particular location up to date. This tool is a formal way to correct inventory discrepancies. That is, if a particular container is not confirmed, that container is moved to the Missing Location in Inventory Enterprise. Rectify Contents is meant to be used on a quarterly or biannual basis during official inventory reconciliation efforts. For a less formal tool which only verifies the existence of a container in a location, please use the Update Contents tool. Rectify contents accomplishes the following:
confirm that containers are still where the
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2. Using a barcode scanner, or by manually
selecting the checkboxes, select the container ID for each container that is being verified.
NOTE: Any container IDs entered that are not currently
in this inventory location, are listed in the upper frame.
system thought them to be. move containers unexpectedly found at that location to specific location.
allow for unknown containers to be created at
specific location. move any containers that are not explicitly found to a missing location. To rectify the contents of a location:
1. Open the appropriate location and click
Select the checkbox next to any containers you would like moved to this location. 3. Click OK. The following message is displayed if there are containers listed which have not been verified:
Rectify Contents in the Container List Frame. The Rectify Contents window opens.
4. Click OK if you would like containers which
have not been verified moved to the Missing Location.

Print Label/Report
Reports can be printed from three places in Inventory Enterprise: the container list frame, the container view frame, and the search results window. All three of these reports are generated in
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the same way, but can display different information. Reports are driven by report templates on the server. Typically, the system administrator creates report templates with the appropriate layout and content to be printed. Please contact the administrator if you need additional reports created to satisfy your need. You can choose different templates and formats from the list boxes at the top of the report. Once a report is created on the server it can be printed from the browser by using the print icon a the button of the report viewer. Because reports are printed according to previously created report templates, information in a report is not necessarily the same information displayed in the window or frame that you choose to print. For example, the Print Report link in the container list frame will generate a report about the containers listed in that frame, but the report template may not include the container's cost, while the container list frame displays the container cost.
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Available Functions of Container Details Frame

Change Qty
The Change Qty function allows the modification of the quantity of material remaining in the container. Quantities are measured in the predefined unit of measure associated with the container.
Change Status
The Change Status function allows user to change the status of the container. The status of container depends upon current situation, these situations may be Available, Empty, Missing, etc. All status options are configurational.
Container labels are printed via report writer as well. A label is considered a special kind of report which can include any of the attributes associated with a single container. The report writer is also able to encode any of the container attributes into a scan barcode.
Check Out
The Check Out function is typically used when a user removes a container from a central storage location for subsequent use at a different location. The act of checking involves a change in container location plus a change in the current user responsible for the container.
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Check In
After you click the Copy Container link a Create Container dialog opens with all the data from the copied container already filled in the appropriate fields. Proceed by editing any fields that should differ from the copied container and the click OK. For more information about the fields, see Creating a New Container.
Certify Container
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The Check In function performs the reverse of the Check Out process. It is typically performed when a user returns a chemical container to its central storage location. The system remembers the location and user under which the container was created and uses them as the default values during the check in process.
The Certify Containers function. To certify a container:

1. Open the container in Details view.
Container details view opens:
Copy Container
2. Click Certify Container.
The Copy Container function allows you to create one or more containers using a preexisting container as a starting template. Typically, attributes such as lot number, container cost, and expiration date, may need to be modified before the new container(s) are created.
NOTE: This link is only available if the certification date
is not yet set. The Certify Container dialog appears.
3. Enter the Purity. 4. Enter a Recertification Interval in months.
This value is used to calculate the recertification date (expiration date) for the container. The recertification date is set to the number of months entered from the current date. 5. Click OK.
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Reorder Container
Users can reorder any container in the inventory, if the container is not already on order. If the container that you would like to order is not currently in the inventory, please see Order Container on page 127. To reorder a container:
1. Click Reorder Container.
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The Reorder Container window appears. After the Edit Container window opens, proceed by editing any fields necessary and click OK. For more information about the fields, see Creating a New Container on page 128. The Move Container function moves the currently selected container to a new location. The destination location ID can be directly entered or scanned into the text box in the dialog, or the browse link can be used to select a location from the tree.
2. Enter the required information and any other
information which is desired.

3. Click OK. Edit Container
The Edit Container function allows editing of all container attributes. You may switch between the various tabs to access all container attributes. Changes to the container are only committed to the database once the Update Container button is clicked.
Delete Container
The Delete Container function deletes the currently selected container and moves it to the trash can. The only way items can be removed from the trash can is by using the Empty Trash function. Please see your system administrator for more information.
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Retire Container
The Retire Container function retires the currently selected container. When a container is retired, it is not deleted, but is no longer in use.
A quantity field for each new container appears.

NOTE: In the example below, the sum of Container
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Quantities must equal the total quantity.
Split Container
The Split Container function splits contents of the current container into new containers, adding the specified number of new containers. The parent container will be removed (the container is now empty). Quantities in the new containers are updated automatically. When splitting a container, all of the contents must be used so the sum of the quantities of the new containers must equal the quantity of the original container. To split a container:
1. Click Split Container.
4. Make any changes necessary. 5. Click OK. Merge Containers
The Merge Containers function merges two containers (which have the same parent ID) into one container. If a container has no parent ID, this function is not available. To merge two containers (with the same parent ID):
1. Open the first container in Details view.
The Split Container dialog appears.
Container details view opens:
2. Click Merge Containers. 2. Enter a value for each field. For more
information about a field, click on the image above. 3. Click OK.
NOTE: The Merge Containers function is only available if
the container has a Parent ID. The Merge Containers window appears.
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3. Click OK.
The request has been made, and a Requests Tab is added to the container in the Container Details Frame.
Create Samples
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3. Select the container to merge with the currently
selected container. Only the containers with the same parent ID are listed.
Request Containers
The Create Samples function samples the current container and creates additional containers from that container with a specified quantity. The parent container will remain intact with any remaining quantity. Quantities in the new containers and the parent container are updated automatically. To create samples of a container:
1. Click Create Samples.
The Request Container link is only available from containers in stock room locations. A request can not be made if a previous request is still open. To request a container:
1. Click Request Container in the Container
The Create Samples dialog appears.
details frame. The Request Container dialog box appears.
2. Enter a value for each field. 3. Click OK.
The quantity remaining field is automatically populated and a quantity field for each new container appears.
The window is automatically populated with information about the container that is currently open. 2. Select a delivery location, User ID, Amount Required, and Date Required. Please Note, field names shown in red are required.
4. Make any changes necessary. 5. Click OK.
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History
The Container History link uses the Audit Report, page 159 window to display a container's history. Clicking on the History link will bring up the audit window and filters information to show any activity involving the current container.
example, the Print Report link in the container list frame will generate a report about the containers listed in that frame, but the report template may not include the container's cost, while the container list frame displays the container cost.
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For more information regarding the Audit Reports, please see Analyze Audit Trail.
Print Label/Report
Reports can be printed from three places in Inventory Enterprise: the container list frame, the container view frame, and the search results window. All three of these reports are generated in the same way, but can display different information. Reports are driven by report templates on the server. Typically, the system administrator creates report templates with the appropriate layout and content to be printed. Please contact the administrator if you need additional reports created to satisfy your need. You can choose different templates and formats from the list boxes at the top of the report. Once a report is created on the server it can be printed from the browser by using the print icon a the button of the report viewer. Because reports are printed according to previously created report templates, information in a report is not necessarily the same information displayed in the window or frame that you choose to print. For
Container labels are printed via report writer as well. A label is considered a special kind of report which can include any of the attributes associated with a single container. The report writer is also able to encode any of the container attributes into a scan barcode.
Link Management
Click Manage Links from a container record to add a new link:

1. Click New.
A window allowing the addition of a link appears with current container information already populating the fields.
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Substance Tab
2. Enter the appropriate information.
The Substance Tab of the View Container frame provides information about the compound found in the container. It is possible to add synonyms for the substance from this tab by clicking on Synonyms.
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Enter URL in the URL listbox. NOTE: You must enter http:// for the URL if applicable. Enter Text that you would like the link to be
displayed as in the Link Text textbox. 3. Click OK. To edit a link:

1. Click Edit next to the link to be edited. 2. Edit the appropriate information. 3. Click OK.
Supplier Tab
The Supplier Tab of the View Container frame provides information about the supplier of the container and/or its contents.
To delete a link:
1. Click Delete next to the appropriate link. 2. If you do want to delete this link from the list,
Click OK.
Summary Tab Quantities Tab
The Summary Tab of the View Container frame provides a summary of important details about the container and its contents.
The Quantities Tab of the View Container frame provides information about the amount of stock necessary for the facility.
Comments Tab
The Comments Tab of the Container View frame allows you to enter comments about the container, the batch inside the container, the location, etc. This is a good place to record any information that does not fit in any other fields.
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The EH&S tab is customizable by the system administrator, so the fields found under this tab vary. For more information about the fields in the EH&S Tab, please see your system administrator.
Requests Tab
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Reservations Tab
The Requests Tab of the Container View frame displays the current requests on the container. If there is no active requests, the tab is not visible. A user can also edit and/or delete the current request if permissions allow it.
The Reservations Tab of the View Container frame provides information about any reservations made for the container's contents. This tab also provides the ability to enter a new reservation as well as edit or delete an existing reservation.
Plate Inventory
Other Tab
The Other Tab of the Container window gives users access to optional customizable fields. This table is fully customizable and will vary from site to site. To learn more about customizable fields, please see your system administrator.
EH&S Tab
Plates are held in locations, much like containers. For this reason, plates are browsed in the same way that any other container is browsed.
The EH&S Tab of the View Container frame provides Environmental Health and Safety Data for the container. EH&S information is linked to records on two levels:
Substance level - requires a valid CAS number
in the record.
Container level - requires a valid CAS number,
Supplier Name, and catalog number in the record. Container level EH&S information can not be added unless substance level information exists.
Plates are indicated as such in the Container List Frame with a plate icon. When a plate is opened, the Plate Contents Frame is displayed in the bottom right frame. Plates and Containers can exist in the same location.
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Creating New Plates

Inventory Enterprise does not contain the necessary tools to create new plates. Plates are created through the InvLoader. See Inventory Loader on page 147
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Searching for a Plate

Plates are searched for under the plates tab on the search page. See Plate Search on page 117 for more information about the Plate Search Tab.
All plate attributes are displayed within the Details Frame Summary Tab. It lists all attributes for the plate, common to all wells, including plate ID, Barcode, Plate Type, Plate Name, Plate Format, etc.... The Plate Viewer Tab allows you to view the contents of the plate in a grid. Click on one of the wells to view the details for that well.
After performing the search, users are given a list of matching plates:
Viewing the Contents of a Plate

After performing a search, or navigating through the location tree, a list of containers and/or plates is displayed. For more information about searching for plates, Searching for a Plate on page 142. The container list frame lists plates much like it does containers. Plates are distinguished from containers by the plate icon. Plates are sorted in descending order by plate ID, but can be resorted by clicking any of the column headers. The small triangle next to the column name indicates the sorting order. Sorting affects plates regardless of whether they are displayed on the current page. Click on one of the plates in the list to see the plate details on the frame below.
Available Functions from Plate Details Frame

Creating Daughter Plates
The Create Daughter Plates function allows a user to create any number of daughter plates from a parent as long as the parent plate contains enough contents to fulfill the request. That is, if you would like to create 6 daughter plates taking 10 ml of a substance from the source plate which only contains 10 ml, you will be denied. To create daughter plates:
1. Search for or browse to the source plate. 2. Open the plate in the Details Frame. 3. Click Create Daughter Plates.
The Create Daughter Plate dialog appears.
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The following screen appears:
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4. Click Next.
The following window appears.
6. Enter the appropriate information about the
new plates.
7. Select the Dry Source Plates after Reformat 5. Select Yes if a solvent will be added to the plate
during daughtering and click Next. if Yes: The following screen appears
checkbox if your source plates should return to their original state after the reformatting action is complete. 8. Click OK.
Create Plate Map
The Create Plate Map function allows a user to create a plate map based on the selected plate. Plate maps are virtual representations of plates that store the plate type, physical plate type, etc. of the plate, but most importantly the substance information for each well. Plate maps can only be stored in special plate map locations. New plates can be created from a plate map.
a. Enter information about the solvent added. b. Click Next.
To create a plate map:

1. Search for or browse the plate you wish to
create a plate map from. 2. Open the plate in the Details Frame. 3. Click Create Plate Map. The Create Plate Map dialog appears.
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4. Enter the location for the new plate map. 5. Click OK.
Create a Plate Map Location
Plate Maps are stored in special plate map locations. To create a plate map location:
1. Click New Location. 2. Enter the appropriate information. 3. Select Plate Map from the Location Type
NOTE: Well attributes changed under this interface are
applied to all of the wells in the plate. To edit a plate: 1. Search for or browse to the plate you wish to edit. 2. Open the plate in the Details Frame. 3. Click Edit Plate. 4. Make the appropriate edits to the given plate and well attributes. 5. Click OK.
Edit Well
listbox. 4. Click OK. This new location is now ready to store plate maps created.
Edit Plate
The Edit Plate function allows editing of plate and well attributes. Plates are initially created in BioAssay so any attributes which can not be changed are greyed out (e.g. plate format).
The contents of an individual well can be edited by clicking Edit Well (from the Plate Well View dialog). This gives users the option of editing the attributes of one well at a time. If you would like to edit all wells uniformly, please see Edit Plate To edit your well attributes:
1. Click Edit Well.
Edit well page appears:
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5. Click OK.
The plate is copied and a new plate is created in the specified location.
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Move Plate
The Move Plate function allows a user to move a plate from one location to another. To move a plate: 1. Search for or browse to the plate you wish to move. 2. Open the plate in the Details Frame. 3. Click Move Plate. The Move Plate dialog appears.
2. Enter the required information. 3. Enter any additional information. 4. Click OK.
Copy Plate
The Copy Plate function allows a user to make a copy of an existing plate. To copy a plate:
1. Search for or browse to the plate you wish to
copy. 2. Open the plate in the Details Frame. 3. Click Copy Plate. The Copy Plate dialog appears.
4. Enter the location you would like to move the
selected plate to. 5. Click OK. The plate is moved to the new location.
Dilute Plate
The Dilute Plate function allows a user to dilute an existing plate. To dilute a plate:
4. Confirm the entered information.
dilute. 2. Open the plate in the Details Frame. 3. Click Dilute Plate. The Dilute Plate dialog appears:
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Delete Plate
The Delete Plate function allows deleting of plate and well attributes. To delete a plate:
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4. Confirms the entered information. 5. Click OK.
delete. 2. Open the plate in the Details Frame. 3. Click Delete Plate. The Delete Plate dialog appears.
The plate is diluted.

Retire Plate
The Retire Plate function allows retiring of a plate. Retiring is different than deleting because when a plate is retired the data is preserved, and the plate is placed in the Disposed location (unless specified otherwise), while when it is deleted, the data is lost permanently. To retire a plate:
4.
Click OK to confirm you would like to delete the plate.
Plate Viewing Form Tabs

Summary Tab The Summary Tab of the View Plate Frame lists all of the recorded attributes of the selected plate.
retire. 2. Open the plate in the Details Frame. 3. Click Retire Plate. The Retire Plate dialog appears.
Plate Viewer Tab
4. Make any necessary changes. 5. Click OK to confirm you would like to retire
The Plate Viewer Tab of the View Plate Frame displays a plate, in grid format, where each cell represents a well in the plate. Click on a well to view its contents.
the plate.
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3. Enter the name of the ChemOffice Enterprise
application server, your username, and your password.

NOTE: The username you use here must have sufficient privileges to add compounds to and create plates in the Inventory Enterprise system. If you want to register those compounds, you must have sufficient privileges on the Registration System.
4. Click Next.
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Administration
Inventory provides an interface to some frequently used administrative tasks. This interface is not available to all users. If you feel you need access to this interface, please see your system administrator.

Please see Manage Users and Roles on page 192. for more information concerning managing users and roles.
NOTE: If an error message appears saying no plate locations or plate formats are defined, you will have to configure at least one location in Inventory Enterprise to hold plates, and/or create at least one valid plate format. Consult the documentation for Inventory Enterprise.
5. Browse to the ChemFinder database you want
Inventory Loader
Inventory Loader is an application to load information from ChemFinder databases into the Inventory Enterprise and Registration Enterprise databases. ChemFinder databases may be created from many sources, most commonly SDFiles. SDFiles are the common currency of chemical information exchange today. Inventory Loader may be run from any machine with access to the ChemOffice Enterprise application server. To start loading compounds into Inventory Loader: 1. Start the Inventory Loader application. An introduction screen appears.
NOTE: You must start the Inventory Enterprise
to load. 6. Select whether you wish to load compounds into plates, or just load compounds.
Loading Compounds into Plates

1. Click Next.
NOTE: If an error message appears saying "Cannot open database", you may need to upgrade the database to the current ChemFinder version. To do this, simply open the database within ChemFinder and follow the prompts.
2. If more than one table is defined in the
application before using InvLoader.

2. Click Next.
ChemFinder db then you will have see a drop down list of table names. Select the table that holds the data to be mapped. Typically, the table name is "MolTable". A table appears. The tables left column displays the fields in Inventory Enterprise.
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The tables second column lets you choose to either enter a default value, or to pick a field from your ChemFinder database to insert into that field. If you choose Use Default, you can enter that default value in the 3rd column. The default is to leave the field blank. 3. Enter information for one or more fields. The following is an explanation of the fields::
Field Name Field Description
Field Name
Field Description
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Barcode
Well the address of the well on the Coordinate plate, e.g. A02 or H12 Row the row of the well on the plate, either in letter or number format. the column of the well on the plate, in number format. the CambridgeSoft registration number of the compound. You will generally leave this blank unless you are importing data from the Registration System into Inventory Enterprise. the CambridgeSoft registration batch number of the compound. You will generally leave this blank unless you are importing data from the Registration System into Inventory Enterprise.
the barcode of the plate. This is the barcode that will be used in Inventory Enterprise. If you leave this blank, Inventory Enterprise will assign new barcodes to the plates according to a scheme which you set up in a later screen.
Compound an identifier for the Name compound. CAS Number the CAS number for the compound. Many screening libraries do not include CAS numbers.
Column
Reg Number
ChemACX the CambridgeSoft ID ChemACX id for the compound. Many screening libraries do not include ChemACX numbers. Supplier Supplier Barcode the supplier of the plate. the barcode assigned by the supplier to the plate. If you will be re-barcoding the plates upon import, you may assign the original supplier barcode to this field for tracking purposes.
Batch Number
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Field Name
Field Description
5. Choose the location where you want to create
Supplier suppliers identifier for the Compound compound ID

The remainder of the fields should be selfexplanatory.
NOTE: You do not have to fill in all fields.
Some notes on filling in this grid: a. Either Well Coordinate or Row AND Column may be mapped to ChemFinder fields. It is not necessary to map both, and you dont have to do either, but if you map Row, you must map Column. If you map Well Coordinate, you shouldnt map Row or Column. b. If your plates have identifiers, you should map that identifier to either Barcode, Supplier Barcode, or (if the plate identifier is numeric) to Supplier Plate Number. If you dont, you will receive a warning, and the compounds will probably not be plated according to your expectations. c. If you map only Supplier Barcode, Supplier Plate Number, or Barcode, and you do NOT map Well Coordinate or Row AND Column, the compounds will probably not be plated correctly. d. If you do not map ANY of: Supplier Barcode, Supplier Plate Number, or Barcode, Well Coordinate or Row AND Column, then the compounds will be put into plates in the order that they are encountered in the file. This is probably a rare scenario. 4. Click Next.
the plates. 6. Choose the plate format you wish to use. The plate format describes the size of the plate (96, 384 well), as well as the layout of the plates where compounds are located, which wells are empty. 7. Choose the plate type you wish to create. The Plate Types list is an arbitrary list of types. The number of compounds being imported and the number of plates to be created appears at the bottom of this screen. This is a good place to check if the results are what you expected. 8. Click Next. 9. Choose the library to assign the plates to. This is an arbitrary list of classifications. 10.Enter how you want Inventory Enterprise to barcode your plates.
NOTE: If you have mapped a ChemFinder field to Barcode in a previous screen, the Barcode section of this screen will be grayed out, indicating that the barcodes from your file will be used.
11. Assign a starting group number for your plates
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if desired. This is rarely used. 12.Click Next. 13.If you want to register these compounds into the Registration System, check the box. Inventory Loader will validate your login against the registration system. If it succeeds, a grid containing the options for registering the compounds appears. You can choose what project, prefix and sequence to register the compounds with, as well as other options. For more documentation on what these choices mean, consult the Registration System documentation. a. If you want to assign fields to be filled in for the compound when it is registered, click Registration Options
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b. A dialog appears, with a table similar to the
one you used to assign inventory fields. Here you can choose default values or SDFile fields to assign to registration system fields. NOTE: Please note that the fields here are named as they are in the database, not as they are in the Registration System interface. The mapping between display name and database name may be found in C:\inetpub\wwwroot\chemoffice\chem_r eg\config\cfserver.ini 14.Click Next. 15.If you would like to save a log of the plates that were created in XML format, check the box and specify a path. This is usually not necessary unless you are experiencing problems. 16.Click Next. 17.Click Finish and the plates are imported. Each plate may take a while, as compounds are duplicate-checked and indexed for searching.
New Location
For more details please New Location on page 125.
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Edit Location
For more details please Edit Location on page 126.
Move Location
For more details please Move Location on page 126.
Delete Location
For more details please Delete Location on page 127.
Plate Settings
The plate settings Admin Task allows you to create, edit, delete and copy plate settings for use when creating and reformatting plates. The settings include:
Grid Formats Physical Plate Types Plate Formats Plate Types Well Formats Create Reformatting Plates Plate Import Templates
Import Compounds Only

1. A screen of inventory fields that can be
mapped to ChemFinder fields appears. See Loading Compounds into Plates on page 147. 2. Click Next. 3. Click Finish.
Inventory Tasks
The following tasks are available to users with the correct administrative privileges. If you do not have access to something you need access to, please see your system administrator: Tasks on page 128..
Search
For more detail please Searching Inventory Enterprise on page 115.
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Create New
Grid Formats
To create a new plate setting (regardless of type):

1. Click the New link to the right of the plate
setting you would like to create.

2. Enter the desired information.
The grid format allows you to create a grid of plate. This plate settings allows user to create a grid of choices, user can enter following details in the interface.
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NOTE: Fields highlighted in Red are required.

3. Click OK.
Edit
To edit a plate setting (regardless of type):

1. Select the plate setting you want to edit from 2. 3. 4. 5.
the appropriate listbox. Click the Edit link to the right of the plate setting you would like to edit. Enter the desired information. Fields highlighted in Red are required. Click OK.
Physical Plate Types
Delete
Physical plate type allows you to create a plate type. This plate settings allows user to create a physical plate of different well capacities, user can enter following details in the interface.
To delete a plate setting (regardless of type):

1. Select the plate setting you want to delete from
the appropriate listbox.

2. Click the Delete link to the right of the plate
setting you would like to delete. 3. Click OK.

Copy
To copy a plate setting (regardless of type):

1. Select the plate setting you want to copy from
the appropriate listbox. 2. Click the Copy link to the right of the plate setting you would like to copy.
NOTE: Fields highlighted in Red are required.
3. Click OK.
Plate Formats
Plate format assigns a new attribute to an existing physical plate. User can enter following details in the interface.
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Administrator
Plate Types
Create Reformatting Map
It allows you to create/edit plate types. By default system provides following types:
Assay Plate Master Plate Replicate Plate Source Plate Working Plate NOTE: These default plate types are editable.
This feature allows you to select the positioning of plates in the well of the target plate. You can create reformat map of only those plates which has same plate formats and plate types. User can select either Stamped or Dithered from the Reformat Map Type drop down list. If Stamped selected following screen appears:
If Dithered selected following screen appears:

Well Formats
It allows you to create/edit well format. By default system provides following formats:
Compound Empty Negative Control Positive Control NOTE: These default well formats are editable.
CambridgeSoft
Plate Import Templates
To change your password:

1. From the Home page, click Change
This feature allows user to create an import template of any choices. As import template created, user can select this template to import the text file. For more information about the contents and format of the listed import templates. Upon clicking New link following page appears:
Password. The Change Password window opens.
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2. Enter the new password in the New Password
textbox. 3. Enter the new password again in the Confirm New Password textbox. 4. Click OK. Enter the details to create import template and click Next button.
Manage Users
For more details please Manage Users and Roles on page 192.
Manager Roles
For more details please Manage Users and Roles on page 192.
Manage Container Requests

The Manage Container Requests tool lists all container requests that have been made. Requests for samples can be viewed under the Manage Sample Requests link. Enter the details of Column Mapping and click OK button. This tool is helpful for the person on site responsible for fulfilling requests. The requests can be filtered in the upper frame. Results from the filter are displayed in the bottom frame. By default, the window opens with no filtering (displays all open requests).
Change Password
Users always have the option to change their password.
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Administrator
To close a request:
1. Select the checkbox in the Delivered? column
Sample requests have 6 states:

New Approved Declined Filled Closed Cancelled
for the request. 2. Click OK. To view all closed requests:

1. Click the Closed Requests link in the upper
frame. 2. All closed requests are listed. These requests can be filtered using the top frame. 3. If you would like to Undo the Delivered action and return a request to the open list, click Undo. 4. Click OK.
The links at the top of the Manage Sample Requests window allows you to easily view the type of requests you want to see. The actions which can be taken on a request is determined by the state that request is in.
New Sample Requests
Manage Sample Requests

The Manage Sample Requests tool lists all requests for samples that have been made. This tool is helpful for the person on site responsible for fulfilling requests. Requests for containers can be viewed under the Manage Container Requests link. The list of requests can be filtered in the upper frame. Results from the filter are displayed in the bottom frame. By default, the window opens with no filtering. Click the Filter button with no input criteria for a list of all requests.
New sample requests are requests which have been submitted by a user but not yet approved for disbursement by the appropriate personnel. The following actions can be taken on a request with the status New:
Review a Request:
A Review link found to the left of each request listed in the Sample Requests dialog allows users to review details and edit them if necessary.
CambridgeSoft
To review a sample request:

1. Click Review to the left of the request to
Accept a Request
review. The Edit Request dialog appears.
Accepting a request changes the status of that request to approved. This indicates the request will be fulfilled. To accept a request:
1. Select the Accept checkbox to the right of the
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appropriate request. 2. Click OK. The request details will now appear under the Approved Requests. Decline a Request
2. Change the number of samples, if desired, and
click Next.
Declining a request changes the status of that request to declined. This indicates the request will not be fulfilled as requested. To decline a request:
1. Select the Decline checkbox to the right of the
appropriate request. 2. Click OK. A dialog to enter a reason for decline appears.
3. Enter a reason for decline. 3. Edit additional details if necessary.
NOTE: If the Apply Reason to all checkbox is selected, the
NOTE: Addresses are linked to the Delivery Location
reason will be applied to all of the requests listed.

4. Click OK. 5. The request details will now appear under the
selected. Editing the address for that location will be a global change for all requests being delivered to that location.
4. Click OK.
Declined Requests.
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Approved Sample Requests
Approved sample requests are requests which have been submitted and approved, but not yet fulfilled. Users can fulfill these requests by clicking on the Create Samples link to the left of the request.
6. The preview screen displays a summary of the
Administrator
action to be taken. If the preview is correct, click OK. 7. The samples are created and the request status is changed to Filled.
Declined Sample Requests
To fulfill a request:
1. Click Create Samples to the left of the
appropriate request. The Create Batch Sample screen appears.
Declined sample requests are requests which have been submitted by a user but have been declined. These requests are, in a sense, closed but were never fulfilled. Users can view the reason for decline from the Manage Sample Requests dialog by clicking on the Reason link to the left of the request.
2. Order the container in the batch by the order
Filled Sample Requests
in which samples should be taken.

NOTE: If a sample cannot be fulfilled in the current
container that sample will be taken from the next container.

3. Select a location where the new container
Filled sample requests are requests which have been submitted and approved and the samples have been created. Users can create orders and ship those orders from this interface.
should be placed in the Sample Location ID field. 4. Enter the size of the new containers. 5. Click Next. The preview screen appears.
CambridgeSoft
The orders column lists all orders, which contains containers linked to the request.
Closed Sample Requests
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Closed sample requests are requests which have been approved by a user but have been closed. These requests are, in a sense, closed but were fulfilled by the user. User can only view closed request but not able to do any further operations on these requests. Click the Edit link to edit the order or click Create Order to create a new order. To ship an order:
1. Select the Ship checkbox to the right of the
order. 2. Click OK.

Create an Order Cancelled Sample Requests
Cancelled sample request are request which have been submitted by a user but have been cancelled. These request are, in a sense, closed but were never fulfilled. User can only view the details of the sample.
The Create Order link is accessed from the Filled Sample Requests screen or from the Manage Orders screen. To Create an Order:
1. Click Create Order.
The Create Order dialog appears.
Manage Orders
The Manage Orders screen allows you to view all of the orders in the system. Orders have 3 states: New, Shipped, and Closed. Toggle between the list of new and shipped orders using the new and shipped links at the top of the dialog.
2. Scan in the containers in the order. 3. Enter the delivery location. 4. Click Save Order.
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Receive an Order
Receiving an order will move the containers in the order to their destination location and update the container status. To receive an order:
1. Scan in one of the containers in the order.
Users can view the linked documents by clicking Manage Document:

1. Click Manage Documents to the left of the
A list of all of the containers in the order appears. 2. Continue to scan in all of the container in the order. 3. After all of the containers are scanned in, click Receive Containers.
appropriate container. The Manage Documents dialog appears. 2. Click the link for the document you would like to view. The document appears in a web browser for your review.
Approving a Container
Administrator
Approving a container changes the container's status to the designated approved status, making the container available to be used. To approve a container:
1. Select the Approve checkbox to the right of
Manage Approvals
The Manage Approvals tool lists all container which have been certified using the Certify Container function, but have not yet been approved. The listed containers can be filtered in the upper frame. Results from the filter are displayed in the bottom frame. By default, the window opens with no filtering (displays all containers to be approved).
the appropriate container. 2. Click OK. The status of the container is updated (removing the container from the Manage Approvals interface) and the approval date is stored in the database.
Rejecting a Container
If the paperwork or test results are not satisfactory, the certification of the container can be rejected. Rejecting a container sets the container status to the default container status and clears the certification date. To reject a container:
1. Select the Reject checkbox to the right of the
Viewing Linked Documents
Documents related to the container are linked to the container record.
appropriate container. 2. Click OK. 3. The status of the container is updated (removing the container from the Manage Approvals interface) and the certification date is cleared.
CambridgeSoft
Manage Tables
The Manage Tables interface allows administrators to add, edit, and delete the contents of any table in Inventory Enterprise. This is especially helpful to add/change the choices in pick lists throughout the Inventory Enterprise forms.
4. Click OK.
The row is updated in the table.

Delete
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To delete a row in one of the Inventory Enterprise tables:

1. Select the table which contains the row to be
deleted from the Select Table listbox. The table appears. 2. Click the Delete link to the right of the row to be deleted. 3. Enter the desired information. 4. Click OK. The row is deleted from the table.
Analyze Audit Trail

New Row
The Analyze Audit Trail tool allows users to filter and view actions taken on containers, locations, compounds, or links.
Standard Audit Report
To create a new row in one of the Inventory Enterprise tables:

1. Select the table to add to from the Select
Table listbox. The table appears. 2. Click the New Row link. 3. Enter the desired information. 4. Click OK. The row is added to the table.
Edit
The Standard Audit Report allows users to filter by Table, User, RID, LocationID, ContianerID, Date, Action, or CompoundID. To filter and display the report:
1. Click Analyze Audit Trail and make sure the
Standard Link, in the upper frame, is chosen.
To edit a row in one of the Inventory Enterprise tables:

1. Select the table which contains the row to be
edited from the Select Table listbox. The table appears. 2. Click the Edit link to the right of the row to be edited. 3. Enter the desired information.
2. Enter your filter criteria.
Table the name of table (Containers |
Locations | Compounds | Links)
159
User the user who performed the action RID the action ID number (entered as a
To filter and display the report:

1. Click Analyze Audit Trail and make sure the
range) LocationID the location ID ContainerID the container ID From Date actions made after this date To Date actions made before this date Action type of SQL action (Update | Delete | Insert) CompoundID the compound ID 3. Click Filter.
Aggregate Link, in the upper frame, is chosen.
Administrator
2. Enter your filter criteria.
Table the name of table (Containers |

3.
The results are displayed in the lower frame.

Aggregate Audit Report
4.
The Aggregate Audit Report allows users to filter by Table, User, Date, or Action. This report does not give every step in the audit trail, like the Standard Report, but instead provides a summary of actions.
5.
Locations | Compounds | Links) User the user who performed the action From Date actions made after this date To Date actions made before this date Action type of SQL action (Update | Delete | Insert) Select Fields to display and group by selecting the checkboxes next to Table Name, Modified By, an Action. Indicate how date dependant data should be grouped by selecting the appropriate radio button next to Hour, Day, Month or Year. Click Filter. The results are displayed in the lower frame.
CambridgeSoft
Create Plates from Excel

Excel files are a good way of clearly indicating in your inventory what has happened to the contents of plates. CambridgeSoft supports the facility to create plates from excel file. To import a excel file into Inventory Enterprise:
1. Click Create Plates from Excel on the Tasks
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menu. The Excel File Import dialog appears:

2. Select Target or Source Plate.
Target Plates Source Plates
Target plates are assumed to be created from the contents of existing plates in the inventory. Source Plates are new plates created with new contents not previously found in the inventory. You cannot insert structures into plates when selecting this option.
2. Browse to the excel file being imported. 3. Click OK.
The plates are created in the indicated location.
Create Plates from Text File

Text File are a good way of clearly indicating in your inventory what has happened to the contents of plates. CambridgeSoft supports the use of a number of formats. If your format is not currently an option for importing, it is necessary to either perform some post processing on your file to match one of the default formats or contact technical support for guidance. To import a text file into Inventory Enterprise:
1. Click Create Plates from Text File on the
3. Select an import template from the list
provided. 4. Browse to the text file being imported. 5. Enter additional information about the new plates. 6. Click OK. The plates are created in the indicated location
Custom Reports
System administrators have the option to create custom reports for Inventory Enterprise. These reports pull information from the Inventory Enterprise database and display it in a useful form.
Tasks menu. The Text File Import dialog appears.
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To run a custom report:

1. Click Custom Reports (from the Tasks
dialog). 2. Select the name of the report you would like to run form the Report Layout listbox. 3. Select a report format from the Report Format listbox. 4. Click Go.
Administrator
CambridgeSoft
Chapter 6: Registration Enterprise

Overview
Registration Enterprise is a powerful, web-based registration solution, part of the ChemOffice Enterprise suite. The system includes a robust data model for pure compounds, batches, salt management, automatic duplicate checking, and unique ID assignments. As chemicals enter a laboratory, either via synthesis or procurement, they need to be characterized and tracked. Since chemical names are cumbersome, and one compound typically has many names, the name becomes a difficult identifier. The chemical structure, while more exact and recognizable, cannot be verbalized, and inclusion in written reports is difficult. The chemical registration number, by contrast, is a simple, compact, and unique way of identifying a chemical substance. registry number. If this is a new compound, simply sketch the molecule in the box and complete the form. At some time, scheduled by a person designated as a scientific administrator, the compounds are formally "registered". Each compound or batch is checked against a list of existing entries for duplication. Duplicate checking is done using an advanced structure-matching algorithm, which checks the molecular drawing against the database. If no match is found, a new registry number is assigned. If a duplicate is found, the registrar is asked how to process the duplicate.
Chemical Registry Number Assignment

Registry numbers are drawn sequentially from a table. If a compound is ever removed from the database, its registry number will not be re-used.
Registration Enterprise Workflow

The Registration Enterprise process begins by adding a compound to a temporary table space in the database. This is done using the "Add Compound" button from the main menu. The user is taken to an "input" screen, and the ChemDraw plug-in starts on the client. The scientist should sketch the molecule and fill in all known information about that compound. If this is a new batch of an existing compound, click the "new batch" button and enter the existing compound's
Starting Registration Enterprise

When Registration Enterprise is opened, you must log in to start working. To open and log in to Registration Enterprise: 1. Type http://hostname into your web browser. The main ChemOffice Enterprise window appears.
Registration Enterprise163 Overview
From the Main Menu you can start using Registration Enterprise.
NOTE: Your Administrator may set different privileges for different users, so your Main Menu may not look like the previous illustration.
Administrator
NOTE: Hostname is the name of the ChemOffice Enterprise machine. Contact your server administrator to obtain the correct hostname.
2. Type your Username and Password, and then click Log In.
The Main Menu is split into 4 major areas: Add to Temporary, Registration, Query & Reporting, and Administration, some of which will be available to you, the user.
Add to Temporary
The temporary table holds all newly created records. New records can be added to the temporary table, or temporary database, as a Compound or a Batch of compounds. Salts at the Compound or Batch levels can also be added.
The Global Login page appears. 3. Click Main Menu link on Global Login page. The Registration Enterprise main menu appears.
Adding a Compound
A compound is one of the types of records that can be added to the temporary table. A compound record includes information about the compounds physical properties as well as information about the chemist who is recording the information. To add a Compound record to Registration Enterprise: 1. From the Main Menu, click Add Compound. The New Compound Submission Form appears
164Registration Enterprise
CambridgeSoft Add to Temporary
2. Enter the appropriate information into the
fields in the New Compound Submission Form.

NOTE: You may be required to complete particular fields of a record; such information is usually surrounded by a red box. For more information, see your system administrator.
3. Click Add Record.
The dialog box appears that confirms you have added a record to the temporary table. 4. Click OK. The New Compound Submission Form reappears.
Adding a Batch/Lot
It is possible to add a Batch record to the temporary table that contains information about a batch of a compound. The compound is assigned a suffix to its registration number that identifies it as part of a Batch. Batches of the same compound often become available if for example, you prepare a compound, then later repeat the preparation to make more of the compound; or the organization purchases a compound from two different suppliers. Batch information is important because different batches may contain different impurities or behave differently in tests. In order to add a new batch record, you must have available the Registry Number of the compound. The registry number is assigned to a record when the record is registered and is included in the record when viewed in the permanent database.
NOTE: More fields may appear in your form. These forms are customized for your site. Please see your system administrator for more details.
Registration Enterprise165 Add to Temporary
To add a Batch/Lot record to Registration Enterprise:

1. From the Main Menu, click Add Batch/Lot.
The Batch Registration Number page appears.
Administrator
2. Type a Registry Number of a registered compound and then click OK.
The New Batch Submission Form appears.
Common compound information for all the Batches is retained, as shown in the upper gray area of the screenshot above. 3. Enter the appropriate information into the fields in the form.
CambridgeSoft Add to Temporary
A dialog box appears that confirms you have added a record to the temporary table. 5. Click OK. The Batch Registration Number page reappears.
The Search Temporary Structures Form appears.
Registration
Compounds are placed in the temporary table after they are initially submitted. This allows the records to be reviewed for accuracy and completeness before being inserted into the permanent database of registered compounds and assigned a registration number. When the time comes for a record to be registered, the Registration section of the main menu is the place to make that happen. Unlike other fields, after a record is registered, it is possible to add certain identifier and analytics data to a record.
2. Take the appropriate action:
Searching and Viewing Records in the Temporary Table

As the number of records in the temporary table grows it becomes more difficult to locate a particular record. For this reason, Registration Enterprise includes a tool for searching the temporary table. For more information about general searching techniques, see Searching ChemOffice Enterprise Applications on page 194. To find specific records in the temporary table: 1. From the Main Menu, click Search Temporary.
NOTE: It is also possible to access a list of records in the Temporary Table by clicking Review/Register from the Registration Enterprise homepage.
If you want to
Then a. in the Search

Temporary Table, type or
search for records that have specific attributes
choose the attributes of the records you want to review. b. Click Search.
see all of the records in the temporary table
click Retrieve All.
A list of records appears reflecting the search. 3. After locating the correct record in the search results, click the Review/Register button located to the left of the record summary. The Compound Commit Form appears.
Registration Enterprise167 Registration
To edit records that are in the temporary table:

1. Go to a record that you want to edit.
Scrolling through the form allows you to view all of the details entered for the chosen record. The Compound Commit Form includes a number of new operations displayed at the top of the page in the form of buttons. The operations include: Register, Edit, and Delete Record.
For more information about finding a record, see Searching and Viewing Records in the Temporary Table on page 167. 2. Click Review/ Register next to the appropriate record. The Compound Commit form appears. 3. Click Edit, if it is available. The Registered Compounds Results Form changes to allow editing. 4. Make the necessary changes to the record and then click Update Record. The Registered Compounds Results Form returns to view-record mode.
Administrator
Registering Records in the Temporary Table

When a record in the temporary table is registered, the record is deleted from the temporary table and moved to the permanent database. For this reason it is important to review the record for accuracy and completeness before registering the record. For more information about registering a record see Registering a Record on page 169.
Deleting Records in the Temporary Table

Records in the temporary table can be deleted instead of being added to the permanent database.
NOTE: Once committed, a delete operation cannot be
undone. To delete a record from the temporary table:

1. From the Main Menu, choose Review/Register. 2. Go to a record you want to delete from the
Editing Records in the Temporary Table

Records in the temporary table can be edited before they are registered and inserted into the permanent database.
NOTE: Once committed, an edit operation cannot be
undone, a re-edit must occur.
temporary table. For more information about finding a record, see Searching and Viewing Records in the Temporary Table on page 167. 3. Click Review/ Register. The Compound Commit form appears. 4. Click Delete Record . A dialog box appears before the record is deleted to reconfirm the action.
CambridgeSoft Registration
1. From the Main Menu,
If you know the record number of the
5. Click OK.
The record is deleted from the temporary table.
Registering a Record
After a record in the temporary table is reviewed, it can be registered. Registering a record moves it from the temporary table to the permanent tables, and assigns the record a unique registry number. Anyone using Registration Enterprise can see all records in the permanent database, unless Row Level Security is enabled. If the record is for a compound a registry number is assigned and the information recorded is assumed to be the first batch of the compound. If the record is for a new batch of an existing compound, the registry number is simply the registry number assigned previously to the compound followed by batch. It is possible to change the format of assigned registry numbers and batch numbers. For more information about this, please see Defining Sequences on page 174. Before registering a record it is important to make sure the record contains all of the information you want included and the information is correct. In addition to the initial information entered, you can also include Identifiers and Analytics data to a permanent record. For more information, see Adding Identifier Information to Records on page 170 andManaging Analytics Data on page 179 respectively. To add records to the permanent database:
record to be reviewed, or you would like to view a list of all compounds currently in the temporary table: click Review/Register. If you would like to search for specific records: click Search Temporary. For more information about searching the temporary table see Searching and Viewing Records in the Temporary Table on page 167. A list of records appears reflecting your choices. 2. Take the appropriate action:
If you want to register Then
all the compounds in the Registered

Compounds Results List
1. Click Register
All. A window appears asking you how duplicates should be handled.

2. Select how
duplicates should be handled.

3. Click OK.
compounds individually
1. Go to the
compound you want to register and then click

Register/ Review. 2. Click Register.
Registration Enterprise169 Registration
The Register Compounds Results Form changes to show that you successfully registered compounds. The Registration Numbers and Batch numbers appear for each record. For more information about editing a record before registering it, see Editing Records in the Temporary Table on page 168.
Administrator
Adding Identifier Information to Records

Chemical names and synonyms can be added to records to help identify compounds more easily. These additional types of information are all considered identifiers. Before adding identifier information to records it is necessary to obtain a Registry Number for the record. The registry number is assigned to a record when the record is registered and is included in the record when viewed in the permanent database. To add information to permanent records with identifiers:
1. From the Main Menu, choose Add Identifiers.
This form displays a summary about the compound selected, and on the bottom allows the addition of chemical names, synonyms, and CAS numbers. 3. Take the appropriate action:
If you want to add Then in the
The Add Records Input Form appears.
a chemical name to the record
Chemical Name
box, type a chemical name.

Synonym
2. Type a Registry Number of a registered compound and click OK.
a synonym for the compound

box, type a synonym.
The New Identifiers Submission Form appears.
A dialog box appears that confirms you added an identifier to the record. 5. Click OK. The Add Records Input Form reappears.
CambridgeSoft Registration
Adding Analytics Data to a Record

The Registration Enterprise software will allow you to record analytics data linked to the correct batch of compounds. This not only helps to identify the record later, but also keeps all of your data together. For more information, see Defining New Experiments on page 179. Before adding analytics data to records it is necessary to obtain a Registry Number for the record. The registry number is assigned to a record when the record is registered and is included in the record when viewed in the permanent database. To add analytics data to permanent records:
1. From the Main Menu, choose Add Analytic Data.
3. From the Experiment Type menu, choose an experiment type, and then click Add Data.
The Result View Form changes.
The Add Records Input Form appears.
4. Add parameters and results data to the record and click Commit Data.
The analytics data is added to the record.
Query and Reporting

Records in the Registration Enterprise database are searched using any of the fields that were entered in the initial record. A query contains information about fields to search under and what to search for. Creating a query is the first step in finding the correct record. For more information about the different kinds of queries you can create, see Searching ChemOffice Enterprise Applications on page 194.
2. Type a Registry Number with a batch number and click OK.
The Results Form View appears.
Searching for Registered Compounds

When a compound is registered, it is moved from the temporary table to a permanent table. To begin your search:
1. From the Main Menu, choose Search.
The Query Input Form appears.
Registration Enterprise171 Query and Reporting
Making your search as specific as possible is often helpful, especially when the number of records in the database is large. Most often, the more specific a search is, the lower the number of records returned will be. If you are having trouble finding the correct record, it may be that your search is too specific. Try broadening your search in order to return more records. For more information about the different kinds of queries you can create, see Searching ChemOffice Enterprise Applications on page 194.
Administrator
2. Enter the desired information in the appropriate boxes and click Search.
Analytics Spreadsheets
It is possible to see records grouped by experiment in a spreadsheet, or list, format. To view records by experiment:
1. From the Main Menu, choose Show Spreadsheet.
The Analytics Form opens.
CambridgeSoft Query and Reporting
Managing Tables
The following parts of the Registration Enterprise tables can be changed, or managed:
Projects Sequence Structure Comments People Salts Solvates
If you want to see
Then
structures in the spreadsheet
select the Show

Structures
checkbox. records from a particular type of experiment choose the

experiment name in
the Select Experiment Type menu.
To open a table to make changes:

From the Main Menu, choose Manage Tables.
The Manage Tables page opens.
3. Click Show S/Sheet.
A spreadsheet opens with the experiment data.
Defining Projects
A project name can be included as part of a compounds record. The Projects table defines the Projects that appear when a user of the system creates a compound record.
Administration
All of the contents of menus, identities of users and passwords, and definitions of types of data can be manipulated from within Registration Enterprise. The administration section allows for the maintenance of Registration Enterprise and its users. This section is often not available to regular users.
To open the Projects tables:

From the Manage Table page, click Projects.
A table that defines the Projects opens. To add a new project to the Projects table: 1. From the Projects table, click new. A page appears allowing the definition of a new project.
Registration Enterprise173 Administration
Defining Sequences
A prefix and a starting number for compound registration numbers can be specified when a record is created. The Sequences table defines the compound registration numbers for each record. This information appears in the Prefix menu when records for compounds are created. To open the Sequence tables:
From the Manage Table page, click Sequence.
Administrator
If you want to
Then
name the project
in the Project Name box, type a name for the project. if this project should be an option, from the Active menu, choose True. if this project should not be an option, from the Active menu, choose False.
A table that defines the Sequence appears. To add a new registration number prefix and starting number to the Sequence table:
1. From the Sequence table, click new.
decide if this new project name should appear in the project menu while a user creates a record
A window allowing the definition of a new sequence appears.
If you want to
Then
The Projects table appears with the new project. To edit a project in the Projects table:
1. From the Projects table, click the ID number
define a prefix for compound registration numbers
in the Prefix box, enter a prefix.
that corresponds to the project to be edited. A window allowing redefinition of the project appears.
2. Follow step 2 from the previous section. 3. Click Update Record.
The Projects table is updated.
CambridgeSoft Administration
If you want to
Then
This information appears in the Structure Comment menu when you create records for compounds. To open the Structure Comments tables:
From the Manage Table page, click Structure
Comments.
specify the number with which to start compound registration numbering decide if this prefix should appear in the prefix menu while a user creates a record
in the Next in Sequence box, type a number.
A table that defines the Structure Comments appears.
if this prefix should be an option, from the Active menu, choose True. if this prefix should not be an option, from the Active menu, choose False.
To add a new structure comment to the Structure Comments table:

1. From the Structure Comments table, click new.
A window allowing the definition of a new structure comment appears. 2. Take the appropriate action:
If you want to Then
The Sequence table appears with the new information. To edit a sequence in the Sequence table:
1. From the Sequence table, click the ID number
name the structure comment
in the Structure Comment box, type a name for the structure comment.
that corresponds to the sequence you want to edit. A window allowing redefinition of a sequence appears. 2. Follow step 2 from the previous section. 3. Click Update Record. The Sequence table is updated.
decide if this structure comment should appear in the structure comment menu while a user creates a record
if this structure comment should be an option, from the Active menu, choose True. if this structure comment should not be an option, from the Active menu, choose False.
Defining Structure Comments

A comment about the structure of a compound can be included when creating a record. The Structure Comments table defines the structure comments that appear when a record is created.
NOTE: The no comment structure comment overrides the need to populate the structure field if the structure field is a required field.
The Structure Comments table appears with the new structure comment. To edit a structure comment in the Structure Comments table:
1. From the Structure Comments table, click the ID number that corresponds to the structure
If you want to
Then
Administrator
include the code for the person
comment you want to edit. A window allowing the redefinition of a new structure comment appears. 2. Follow step 2 from the previous section. 3. Click Update Record. The Structure Comments table is updated.
in the Chemist box, type a code for the person.

Code
include an unbound user identification
from the Unbound User_ID menu, select an ID. from the

Supervisor/ Workgroup_ID
Defining Registration Enterprise People

The name of a person can be included with a record. The People table defines the properties of each person that appears in the People menu. To open the People tables:
From the Manage Table page, click People.
include a supervisor or workgroup identification
menu, select an ID.
include the first in the First Name name of the person box, type a name. include the middle in the Middle name of the person Name box, type a name. include the last in the Last Name name of the person box, type a name. include a work site for the person from the Site menu, select a work site location. in the Telephone box, type a phone number.
A table that defines the People appears. To add a new person to the People table:
1. From the People table, click new.
A window allowing the definition of a new people appears.
include the phone number of the person
If you want to
Then
To open the Salts tables:

From the Manage Table page, click Salts.
include the E-mail address of the person decide if this person should appear in the person menu while a user creates a record
in the E-mail box, type an E-mail address. if this person should be an option, from the Active menu, choose True. if this person should not be an option, from the Active menu, choose False.
A table that defines the Salts appears. To add a new salt to the Salts table:
1. From the Salts table, click new.
A window allowing the definition of a new salt appears.
If you want to
Then
The People table is updated. To edit a person in the People table:

1. From the People table, click ID number that
enter a name for the salt
in the Salt Name box, type a name for the salt. in the Salt MW box, type a weight for the salt.
corresponds to the person you want to edit. A window allowing the redefinition of a people appears. 2. Follow step 2 from the previous section. 3. Click Update Record. The People table is updated.
NOTE: The default in the People Table is to display the login name as the last name for the person. This can be changed by adding the person, and then editing the user information later.
include the molecular weight of the salt
Defining Salts
A salt can be included when a compound record is created. The Salts table defines the Salts that appear when a record is created.
If you want to
Then
To add a new solvate to the Solvate table:

1. From the Solvate table, click new.
include the molecular formula of the salt decide if this salt should appear in the salt menu while a user creates a record
in the Salt MF box, type a formula for the salt. if this salt should be an option, from the Active menu, choose True. if this salt should not be an option, from the Active menu, choose False.
A window allowing the definition of a new solvate appears.
Administrator
If you want to
Then
enter a name for the solvate
in the Solvate Name box, type name for the solvate.
The Salts table appears with the new salt. To edit a salt in the Salts table:
1. From the Salts table, click the ID number that
corresponds to the salt to be edited. A window allowing the redefinition of a new salt appears.
include the molecular weight of the solvate include the molecular formula of the solvate decide if this solvates should appear in the solvate menu while a user creates a record
in the Solvate MW box, type a weight for the solvate. in the Solvate MF box, type a formula for the solvate. if this solvate should be an option, from the Active menu, choose True. if this solvate should not be an option, from the Active menu, choose False.
The Salts table is updated.
Defining Solvates
A solvate can be included when a compound record is created. The Solvate table defines the Solvates that appear when a record is created. To open the Solvates tables:
From the Manage Table page, click Solvates.
A table that defines the Solvate appears.

The Solvate table appears with the new solvate. To edit a solvate in the Solvate table:
1. From the Solvate table, click the ID number that
If you want to
Then
corresponds to the solvate to be edited. A window allowing the redefinition of a new solvate appears. 2. Follow step 2 from the previous section. 3. Click Update Record. The Solvate table is updated.
name the experiment
in the Name box, type a name for the experiment. in the Description box, type a description for the experiment. in the Created box, type a date.

Please see Manage Users and Roles on page 192 for more information concerning managing users and roles.
include information describing the experiment include the date you create this experiment include the date you change this experiment include a version identifier for this experiment
Defining New Experiments

Different facilities perform different tests with compounds. For this reason, Registration Enterprise allows you to define your own experiment. The Experiments table is used to define the Experiments that appear when a record is created. To open the Experiments table:
From the Main Menu, click New Experiment.
in the Modified box, type a date.
in the Version box, type a way to identify the different version.
A table that defines the experiments appears. To add a new experiment to the Experiments table:
1. From the Experiments table, click new.
A window allowing the definition of a new experiment appears.
The Experiments table appears with the new experiment. To edit an experiment in the Experiments table see Defining Experiment Type on page 180.
Managing Analytics Data

The following types of analytics data can be created and edited from the Managing Analytics data, such as:
Result type Experiment Type Parameter type
To access the Managing Analytics Data table. From the Main Menu, click Manage Analytics.
The Result Types table is updated. To edit a result type in the Result Types table:
1. From the Result Types table, click the ID
Defining Result Type

A result type requested with an experiment when a compound record is created can be modified using the Result Types table. To open the Result Types tables:
From the Manage Analytics page, click Result
Types.
Administrator
number that corresponds to the result type you want to edit. A window allowing the redefinition of a result appears.
A table that defines the Result Types appears. To add a new result type to the Result Types table:
1. From the Result Types table, click new.
A window allowing the definition of a result appears.
The Result Types table is updated.
Defining Experiment Type

To open the Experiment Types tables:
From the Manage Analytics page, click
2. Take the appropriate action: Experiment Types.
If you want to
Then
A table that defines the Experiment Types appears. To add a new experiment to the Experiments table: on page 179: To edit a new result type to the Experiment Types table
1. From the Experiment Types table, click the ID
name the result type
in the Name box, type a name for the result type. in the Description box, type a description for the result type. in the Units box, type a description for the units of the result type.
include a description of the result type
number that corresponds to the experiment type you want to edit. A window allowing the redefinition of an experiment appears.
include a description of the units of the result type
If you want to
Then
name the parameter type
in the Name box, type a name for the parameter type. in the Description box, type a description for the parameter type. in the Units box, type a description for the units of the parameter type.
2. Edit the fields you wish to edit, and add and
delete result and parameter types. For more information about adding result and parameter types, see Defining Result Type on page 180 or Defining Parameter Type on page 181 respectively. 3. Click Update Record. The Experiments table is updated.
include a description of the parameter type
include a description of the units of the parameter type

Defining Parameter Type

A parameter type requested with an experiment when a compound record is created can be modified using the Parameter Types table. To open the Parameter Types tables:
From the Manage Analytics page, click
Parameter Types.
The Parameter Types table appears with the new parameter type. To edit a parameter type in the Parameter Types table:
1. From the Parameter Types table, click the ID
A table that defines the Parameter Types appears. To add a new parameter type to the Parameter Types table:
1. From the Parameter Types table, click new.
number that corresponds to the parameter type you want to edit. A window allowing the redefinition of a parameter appears.
A window allowing the definition of a parameter appears.

The Parameter Types table is updated.
Managing Workgroups
To open the Workgroups tables:
From the Main Menu, click Managing
Workgroups.
Steps to Import a SDFile

To start using ChemLoader and import an SDFile into Registration Enterprise:
1. Browse to: \\Inetpub\wwwrootChemOffice\chem_reg\Chem Loader_Client
Administrator
A table that defines the Workgroups appears. For more information about adding workgroups, see Defining Registration Enterprise People on page 176.
and open ChemLoader.exe.

NOTE: ChemLoader can be run from client machines. See your system administrator for a copy of the utility.
Importing SDFiles
SDFiles are Structure Data Files used by ChemOffice Enterprise to manage structure information and data information in one file. If data is already stored in SDFiles, and you would like that data imported into Registration Enterprise, without tediously entering it by hand, you can import the appropriate .sdf files by importing the data into ChemFinder and then into Registration Enterprise. These files become records in the temporary table or the permanent database in Registration Enterprise, depending on the options chosen inside ChemLoader. When an .sdf file is imported into Registration Enterprise, the following steps must be taken:
1. Import an .sdf file into a ChemFinder database.
The ChemLoader dialog box appears.
2. Choose Input and Output Databases 3. Match Fields in the input and output databases
For more information, see the ChemFinder Manual. 2. Open ChemLoader on a server machine. 3. Import the files. ChemOffice Enterprise must be installed somewhere on the server machine being used in order to access ChemFinder. For more information about ChemFinder, see the ChemFinder Manual. ChemOffice is installed by default with the ChemOffice Enterprise.
chosen. 4. View the matches. 5. Import the matches into Registration Enterprise.
Choosing Input and Output Databases

To choose input and output databases:
1. Click the Browse button to the right of the words Input Database.
The Open dialog box appears.
CambridgeSoft Importing SDFiles
5. Enter a username and password. 6. Indicate where the data should be imported to
2. Choose an input database and click Open.
by selecting the appropriate radiobutton: Add data to temporary table only OR Add data to permanent table. 7. Click OK. The server name appears in the Output Database box found at the top of the ChemLoader window. All of the information, such as tables and fields, associated with the server appear in the appropriate sections.
The database name appears in the Input Database box found at the top of the ChemLoader window. All of the information, such as tables and fields, associated with the input database appear in the appropriate sections. 3. Click the Browse button to the right of the words Output Database. The Select Server dialog box appears.
Matching Fields in the Input and Output Databases

To match fields in the input and output databases:
1. Highlight the tables containing the fields (one
under input database and one under output database) 2. Highlight the fields to be matched in the input and output tables (one under input database and one under output database). 3. Click Match Fields. The fields in the separate databases become linked, shown by a line between them.
4. Choose a SERVER by either:
selecting a SERVER from the list of servers
OR entering a server name manually into the Server textbox.
4. Repeat step 2 to match more fields manually.
Registration Enterprise183 Importing SDFiles
View Matches and Import

To view the matches made and import the data into Registration Enterprise:
1. Select the appropriate importing options:
If you want to
Then
NOTE: The following options are applied to all
include a compound name in the imported files
imported records.
select a compound from the Compound pulldown menu. select a notebook from the Notebook pulldown menu. select a salt from the Salt pull-down menu. select a batch from the Batch pulldown menu. select a batch from the scientist pulldown menu.
Administrator
If you want to
Then
include a notebook name in the imported files
include records from the input database that start at a specific place in the database include records from the input database that end at a specific place in the database record the importing process in a log file include a sequence in the imported files include a project name in the imported files
enter a starting record number in the Start Index textbox.
include a salt name in the imported files include a batch name in the imported files include a scientist name in the imported files
2. Click Matches > View.
enter an ending record number in the Stop Index textbox.
enter a logfile location in the Log File textbox. select a sequence from the Sequence pull-down menu. select a project from the Project pull-down menu.
The Matching field list appears.
3. Click OK. 4. To import the records into Registration Enterprise click Import.
A progress Dialog dialog box appears.
CambridgeSoft Importing SDFiles
When the import is complete the import dialog box closes and the records have been imported to the appropriate place in Registration Enterprise. No additional steps have to be taken to use the records normally inside the Registration Enterprise. To abort the import:
In the Dialog dialog box, click Cancel.
On the other hand, Roles do not distinguish which rows a user has access to within a given table. In a system without Row Level Security (RLS) activated, User A sees all compounds in the registry, as does User B. With the implementation of RLS, the rows (records) of data are linked to projects and projects are linked to people. Thus, User A is assigned to a particular project, and will only be able to see compounds that are linked to that project.
The User Interface

The number of registered compounds is displayed on the Registration Enterprise homepage to the left of the search buttons. With RLS implemented, this value reflects the records a user can see, not the number in the registry. That is, User A may see 10, while User B sees 20. If any screen that has a project drop-down is viewed, that drop-down will only show projects that the user in linked to, unlike before RLS, when all projects were listed. Thus users will only be able to add compounds or search compounds associated with projects for which they have rights.
The import stops. No additional records are added to Registration Enterprise, but records already imported remain.
Optional Features
There are a number of features available to Registration Enterprise users that are not, by default, in activated. Please see your system administrator for more information about activating any features described in this section.
How are Projects linked to People

When a project is created in the Administration Registry Tables, users of the system are given permissions to those projects. If a particular project is removed from a user, the user will no longer be able to view records in that project. The actual data doesnt change, only who can see it. Users only view records relevant to projects they are assigned to.
Row Level Security (RLS)

Overview
Row Level Security is a level of security implemented above the standard Oracle roles. The purpose of using Roles in Registration Enterprise is to restrict access to elements of the interface and data to certain users. For example, User A has access to one set of user-interface elements (such as buttons and menus) while User B is limited to a subset of those available to A. In addition, Roles limit what a user can do with the data; User A can register data and edit that data, User B can only register.
The Unspecified Project

Any record assigned to the unspecified project is inserted into the Temporary Table. The Unspecified project can be assigned to any user, but in general probably should be limited to an administrator. In this type of system, the unspecified project should only be used when the record is added from a registration attempt from another application that doesnt have a valid
Registration Enterprise185 Optional Features
project_id. In this case, the administrator assigned to the unspecified project can check the temporary table for these types of records, and assign a relevant project to each record.
Activating RLS
For details regarding the activation of the RLS feature, please see the Registration Enterprise Admin Guide or your system administrator.
Administrator
Duplicate Checking
If RLS is enabled, Registration Enterprise inspects both the compound and the project when deciding if a duplicate exists. If the compound being added is a duplicate in the entire system, but not a duplicate within a project, an end user would see no duplicate window appear and the compound is registered as usual. However since the same compound is a system duplicate the record is placed in the Duplicates Table. If a compound is a duplicate within a project, the Duplicate Window appears.
Viewing System Duplicates
Salt and Solvate Recognition

Both compound level records as well as batch level records contain salt and solvate information. There are a number of options which indicate how salt and solvate information is recorded. The default behavior is to automatically populate the batch level record with salt and solvate information from the compound record. The options include:
DEFAULT: Populate the batch level record
A new button is displayed on the homepage called View Duplicates if a user has the correct privileges. Clicking this button retrieves and displays all of the duplicate records using the standard ChemOffice Enterprise List/Display View. The Detail button yields - in red - the duplicate registration number. Currently when duplicates are added they are added twice. That is, if compound A is being registered and Compound B is found to be a duplicate in the system, then the entries in the Duplicates Table will be:
Compound A -> Compound B Compound B -> Compound A
with salt and solvate information in the compound level record, and allow the equivalents to be changed at the batch level. Populate the batch level record with salt and solvate information in the compound level record, and allow all fields to be changed at the batch level. The salt and solvate information is kept completely separate in compound and batch level records. To adjust this default, please see your system administrator.
Customizable Fields
The Registration Enterprise has a number of fields which are by default hidden, but are available to be configured if none of the default Registration fields contain necessary information. The following customizable fields exist:
4 text fields 4 integer fields 4 real number fields 4 date fields
Therefore, when duplicates are checked users see both sides of the picture: A is a duplicate of B and conversely B is a duplicate of A.
Deleting a Duplicate
If a duplicate record is deleted, it is removed from the Duplicates Table.
CambridgeSoft Optional Features
The name, datatype, and display type can be adjusted for any of the above mentioned fields. If you feel it is necessary to include an additional field to records, please see your system administrator. Complete details describing the field options available are available in the Registration Enterprise Admin Guide and the ChemOffice Enterprise Admin Guide.
To print records: 1. Click Print. The Print dialog box appears. 2. Check the settings and then click OK. A Registration Enterprise record is printed.
Logging Off
You can end your Registration Enterprise at anytime by logging off. To log off:
Click Log Off.
Choosing Preferences
For more information, see the ChemOffice Enterprise Users Guide.
Printing
You can print records from Registration Enterprise.
The Registration Enterprise Log In dialog page appears. You can log back in and continue using Registration Enterprise, or browse to a different site.
Registration Enterprise187 Choosing Preferences
Administrator
188Registration Enterprise CambridgeSoft Logging Off
Section IV: ChemOffice Enterprise

This section provides information about CambridgeSofts ChemOffice Enterprise and Oracle Cartridge, the core structure for all other enterprise solutions. Inventory Enterprise, Registration Enterprise, and BioAssay. Entering information in one of these 3
applications is reflected in the rest, simplifying the effort by users, and limiting the risk for error.
ChemOffice Enterprise
Sharing information within a company has become easier with the use of the internet, and companywide intranets. CambridgeSofts ChemOffice Enterprise makes it possible for pharmaceutical companies, and laboratories to use this technology to store, manipulate and share chemical structure data, inventory information, and assay data by delivering customized information directly to each users desktop.
ChemOffice Enterprise is installed on a server to be

accessed by any number of client machines on the network. All ChemOffice Enterprise applications are accessed through the a web browser. A familiar looking interface, the ChemOffice Enterprise applications use multiple web input forms to receive, retrieve, and display data.
CS Oracle Cartridge
The CambridgeSoft Oracle Cartridge introduces a new way of dealing with chemical structure and reaction data in an Oracle database, improving portability and consistency in applications. Since the CS Cartridge is accessed through Oracle, this opens the door for programmers interested in manipulating chemical structure data directly from their code without learning a new language. Using the CS Cartridge is as easy as using a few simple SQL commands. The CambridgeSoft Oracle Cartridge supports CDX, CDXML, MolFile, RXN, and SMILES formats making it flexible enough to be included with both new and legacy data, without the need for conversion.
ChemOffice Enterprise includes applications

addressing Knowledge Management, Research & Discovery, and Biological Informatics concerns of any cooperation struggling with ways to organize and distribute chemical and biological data. The real strength of the package is revealed when multiple applications are integrated together allowing an individual, for example, to track the amount of a particular registered compound, which is available in a storage plate, being used for assay testing in a different facility. Such a process utilizes
Chem & Bio Office Enterprise, Workgroup & Databases 2006 ChemOffice Enterprise
189
Administrator
190 CambridgeSoft CS Oracle Cartridge
Chapter 7: ChemOffice Enterprise

About ChemOffice Enterprise
ChemOffice Enterprise is a World Wide Web (web) chemical information server. Through a web browser, you can use the ChemOffice Enterprise web applications to search databases for chemical and biological information. ChemOffice Enterprise is the basis for CambridgeSofts enterprise applications. After logging in, a cookie is written to the client machine, holding login information. The cookie expires after 25 minutes of inactivity. Therefore, login information is recognized even after a browser is closed.
Logging In
To login to the ChemOffice Enterprise suite of products:
1. Access the following URL: http://servername
Installation and Administration

Installation instructions, configuration options, and other administration tips can be found in the Admin guide for the ChemOffice Enterprise and each of its applications. Please see the applications readme file and Administrators Guide (if applicable) for more information.
where server name is the name of the server where ChemOffice Enterprise 2005 is installed. Contact your server administrator for this name. 2. Access the ChemOffice Enterprise homepage and click on the Global Login link. A login box appears.
Global Login and Security

The ChemOffice Enterprise uses a global login interface to manage user information for most applications (Sample not included). After logging in once with your user name and password, users have access to all ChemOffice Enterprise applications that they have permissions to, without having to login to each application separately.
3. Login with a valid username and password and
click OK. The Global Login page appears.
ChemOffice Enterprise191 About ChemOffice Enterprise
The Manage Users interface appears.
Administrator
NOTE: The links visible on this page depend on the
permissions of the user who is logged in. This page includes links to all of the applications the logged in user has access to. 4. Click on a link to enter a particular application. To make changes to the users in the system:
1. Select the application in which the user exists

Users and Roles are managed universally for all ChemOffice Enterprise applications. Links to User Management are available from each application as well as from the main global login page, if the user has the correct privileges.
from the View Users From drop down menu.

users.
2. Click Refresh. 3. Click Add User (to add a new user) or
Users
To access the Manage Users interface:
From the Global Login homepage, click
highlight a user name and click Update User (to edit an existing user). A page allowing you to enter user details appears.
Manage Users.
192ChemOffice Enterprise
CambridgeSoft Global Login and Security
To make changes to the roles in the system:

1. Select the application in which the role exists
from the View Roles From drop down menu.

roles.
2. Click Refresh. 3. Click Add Role (to add a new role) or highlight
a role name and click Update Role (to edit an existing role). A page allowing you to enter role details appears.
4. Enter user details as desired. Fields highlighted
in red are required.

5. Select the roles for the user. To select more
than one role at once, hold down the CTRL key while highlighting. 6. Click OK.
Roles
To access the Manage Roles interface:
From the Global Login homepage, click
Manage Roles. The Manage Roles interface appears.
4. Enter role details as desired. Fields highlighted
in red are required. 5. Select the roles for the role. To select more than one role at once, hold down the CTRL key while highlighting. 6. Click OK.
ChemOffice Enterprise193 Global Login and Security
Searching ChemOffice Enterprise Applications

ChemOffice Enterprise applications are accessible from any remote computer that has access to the server machine with the ChemOffice Enterprise and its applications installed. ChemInfo is a collection of databases which can be used with the ChemOffice Enterprise. For more information about the ChemInfo Databases, please see Scientific Databases on page 247. All of the ChemOffice Enterprise applications incorporate a system of forms which allow the user to search a database of information. Searches are performed by entering information in fields on a search form. The information entered makes up a search query. Before beginning a search you must take the following steps: 1. Login to and open a ChemOffice Enterprise application. 2. Choose the appropriate search form. 3. Enter your search criteria and click Search. Due to the similarities between applications, in this chapter, the Sample application is used to illustrate the basic functionality of the available ChemOffice Enterprise applications. For more detailed information about a particular application, please see, its chapter in this section.
Accessing a ChemOffice Enterprise Application

To access a ChemOffice Enterprise application:
1. Access the following URL: http://servername
Administrator
where servername is the name of the server where ChemOffice Enterprise 2005 is installed. Contact your server administrator for this name. 2. Click the ChemOffice Enterprise application link you want to search. For this example, click Sample. The Query Input Form appears.
CambridgeSoft Searching ChemOffice Enterprise Applications
The Query Input Form User Interface

The Navigation Toolbar
The navigation toolbar appears at the top of most search forms in the ChemOffice Enterprise. It consists of a menubar and a series of buttons. The actions available in the Sample application are listed:
Feature Description
Feature
Description
History Menu Queries - Allows users to retrieve a query which was executed in the current session (does not require having saved the query). Hit lists - Allows users to retrieve a hit list which was created in the current session (does not require having saved the hit list). Queries Menu Restore - Displays the last query entered in the Query Input Form, or one of the saved queries. Save - Saves the current query. Manage - Allows users to manipulate (restore, edit, and delete) saved queries and queries in the current history.
Total Records The number next to this image indicates the total number of records in the database being searched. File Menu Preferences - Accesses the Preferences dialog box, where you can set search preferences for the session you are currently in. For more information, see Setting Your Display and Search Preferences on page 211. Print - Prints the current window (equivalent to using the browser's print button). Export Hits - Exports hits to a SD or RD File.
ChemOffice Enterprise195 Searching ChemOffice Enterprise Applications
Feature
Description
Feature
Description
Hit Lists Menu Restore - Displays the last hit list created, or one of the saved hit lists. Save - Saves the current hit list. Manage - Allows users to manipulate (restore, edit, and delete) saved hit lists and hit lists in the current history. Marked Hits Menu Show Marked - Displays all marked records. Clear Marked - Clears the marked hits. Help Menu Contents - Accesses the online Help. About - Provides information about the version of the ChemOffice Enterprise software and the database being searched. Log Off Menu Ends the current session and clears any resources used by the user.
Search Button Starts a search. Clear Form Deletes all information in the input form. Add Mode Switches to Add Mode which gives users the ability to add records to the database. Retrieve All Performs a search that retrieves all records in the database.
Administrator
Search Input Form

The following is a list of fields found in the Sample application. For more information about a field in another ChemOffice Enterprise application, please see the applications chapter in the ChemOffice Desktop to Enterprise Solutions Manual.
Search Field
Search Type
Search Field
Action
Synonym
Enter a synonym for a molecular name. Enter a molecular weight or a range of molecular weights. For more information, see Searching With Numerical Ranges on page 202. Enter a molecular formula. For more information, see Searching With Molecular Formulas on page 201.
Molecular Weight
Action
pull-
down menu.
Select the type of structure search for your query: Substructure, Full Structure, Exact Structure, and Tanimoto Similarity. For more information about structure types, see Searching With Structures on page 199. Draw a structure. For more information about drawing structures, see the ChemDraw Users Guide. Enter a molecular name or a portion of a molecular name.
Formula
Performing a Simple Search

Queries are used to search for information in databases. Queries can contain different types of information and can be simple or complex, depending on the database you want to search. This example shows how to create a simple text query for searching the Sample database. To create a simple text query:
1. Login to the Sample Database. 1. In the Molecule Name box, type benz. 2. Click Search.
Structure box and ChemDraw Tools toolbar
Molecule Name
The Results List View window appears.
Searching by Different Query Methods

The following is a list of the basic types of searches or query methods utilized in ChemOffice Enterprise applications:
Text Structure Molecular Formula Numeric (e.g. Molecular Weight) Combination (a combination of the above
Administrator
ChemOffice Enterprise finds 30 records that match your query. These results can also be called hits. For more information about:
This subject See
types) Each of the above methods include distinct features which, when used correctly, can help to manipulate a search. In addition, search preferences can be modified to allow valence modifications. For more information on setting preferences, see Setting Your Display and Search Preferences on page 211.
Searching With Text

One example of a text field, in the Sample Application, both Molecule Name and Synonym are text fields. When entering search criteria into a text field, use the following rules:
Use wildcard characters (*) to broaden search
changing the way results appear.
Setting Your Display and Search Preferences on page 211.
using results for other Search Results on searches. page 203. searching with other types of queries. Searching by Different Query Methods on page 198.
results. Use equals (=) to narrow search results. A regular text field is not a free text search so do not use AND, OR, or NOT for queries.
For example, the following searches actually mean:

Text entered
ben
Search Results include
of search is indicated by the choice made in the structure pull-down menu found above the structure box. Drawing a structure in the box provided is facilitated by the ChemDraw toolbar. The ChemDraw toolbar makes particular pieces of a structure available with one mouse click. For more information about using the ChemDraw toolbar, please see Drawing Chemical Structures in the ChemDraw Manual. If the ChemDraw toolbar is not visible when you are ready to start drawing: 1. Right click anywhere inside the structure box. 2. Go to View>Main Tools. The ChemDraw Toolbar appears
Records that start with ben, with any combination of characters following. Matches include benzene and benzofuran, but not bromobenzene. Records that include ben anywhere within the field. Other characters can be found before or after ben. Matches include benzene, benzofuran, and bromobenzene. Records that include Benzene with no other characters in the fields entry. Records that have ben as the first three letters of the entry, followed by any number of characters, followed by chl and any number of characters to end the entry. A match would include Benzyl chloride but not Benzene.
*ben
=Benzene
Ben*chl
Searching With Structures

Searching by chemical structure is greatly simplified by using a ChemOffice Enterprise structure search. There are four types of structure searches. The type
The following is a list of types of structure searching found in the Structure pull-down menu:
Substructure - A substructure search is a default structure search type. Substructure searching finds structures that contain the query and any additional attachments at the open
position. You can attach different features, such as atom lists and variable bond types, to a structure using ChemDraw plug-in, to perform a narrower or border search.
Administrator
To perform a substructure search

1. Click New Query. 2. Draw pyrrole 3. From the Search Type menu, choose
Substructure. Search Type list.
4. Click Search.
Seven records are found because the pyrrole moiety is found in seven structure in the database.
Full Structure - Full structure searching retrieves structure as drawn, with no additional attachments. Isotopes are recognized as hits.
4. Click Search.
Three records including isotopes are retrieved.
To perform an full structure search.

1. On the result form, click New Query. 2. Draw a structure. 3. From the Search Type list, select Full Structure.
Exact Structure - Exact structure searching retrieves only structures as drawn (taking stereochemistry into account). Isotopes are not recognized as hits.
To perform an exact structure search.

1. On the result form, click New Query. 2. Draw a structure. 3. From the Search Type list, select Exact
Structure.
4. From the Search Type list, select Exact
Structure.
idea of the types of compounds you are looking for, but do not know the precise target compound. Similarity searching matches general structural features and not specific atoms and bonds, so highlighting specific areas would be inappropriate To perform a similarity search. 1. On the result form, click New Query. 2. Draw s structure. 3. From the Search Type list, select Tanimoto Similarity. 4. Click Search. The application uses a Tanimoto calculation to determine if compounds are similar. How similar the results should be can be specified in the Preferences dialog box. For more information on setting preferences, see Setting Your Display and Search Preferences on page 211.
5. Click Search.
Searching With Molecular Formulas

Searching for molecular stoichiometry is accomplished with the inclusion of a formula query method. Formula queries consist of element symbols and element counts or ranges. When searching by formula, use the following rules:
Capitalize the symbols properly. Use symbols that are one or two letters, and
One record is retrieved, as shown below.
Tanimoto Searching - The Tanimoto Similarity option finds structures that have structural features that generally correspond to those in the query. Similarity searches are usually indistinct. In a full structure similarity search, the results are guaranteed to include all those you would obtain from a substructure search with the same query and usually some additional hits. Similarity searches are useful if you have a general
upper or lower case. Use element counts that are single integers or ranges (two integers separated by a hyphen). If a count is omitted, it is assumed to be 1. Note that formula searches are completely non-structural. The formula CH3CH2OH matches dimethyl ether and ethyl alcohol because both compounds have the same molecular formula: C2H6O.
For example, the following searches really mean:

Formula Results
Note that the number of significant digits
determines the precision of the search. A hit is any value that rounds off to the query. For example, the following searches really mean:
Molecular Weight Results
Administrator
C6H6*
Entries with 6 carbons and 6 hydrogens, plus any number of other elements in the formula field. Matches include C6H6, C6H6N2O. 2 carbons and 6 hydrogens. 3 carbons and 6 hydrogens. 6 carbons plus any number of other elements. 6 carbons and between one and three nitrogens, plus any number of other elements. Matches include C6H7N and C6H5NO2.
78.15 78 89.590.5 90.0591.05 90100 >=90 and <=100 >90 and <100
78.145 to 78.155. 77.5 to 78.5. 89.5 to 90.5. 90.05 to 91.05. 90 to 100. 90 to 100. 90 through 100, exclusive.
CH3CH3 (CH2)3 C6*
C6 N1-3*
Searching With Numerical Ranges

All numeric fields allow the inclusion of one particular number or a range of numbers. The Molecular Weight field is an example of a numeric range field found in the Sample Application. If a numeric search is performed with one number, the application will interpret the number as a range. For example, if 78 is entered, the range used spans .5 above and .5 below the number (77.5-78.5). When searching by molecular weight, use the following rules:
To search over a range of weights, use a hyphen
Combination Searching
Combining the types of searches described above allows the user to really take advantage of the searching power of the ChemOffice Enterprise. The ChemOffice Enterprise searching applications implicitly support combination searching as a Boolean AND search, but does not support OR and NOT searches. To perform a simple combination query: 1. From the Sample Application Query Input Form, enter *ene in the Molecule Name box. 2. Enter 100-200 in the Molecular Weight box. 3. In the Structure box, draw a chlorobenzene. 4. From the Search Type list, choose Substructure. 5. Click Search.
between the values at either end of the range. Ranges may also be indicated using inequality operators (<, >) together with the AND operator.
The Results List View window appears. The ChemOffice Enterprise finds 1 record that matches your query.
Viewing Results in List View

The List View allows the user to view information about multiple records at once. In general, List View does not display all the fields available for a record. Use the browse buttons to view additional hits. To change from Form View to List View:
In a Results Form View window, click Return to
List.
Notice that if the molecular weight range (for example) was not included, more results would have been returned.
The record you want to see appears in the Results List View window, along with the other search results.
Search Results
Performing a search within an application results in a list of items matching your query. All result forms in the ChemOffice Enterprise applications have similar formats, but vary according to what you are searching for, and what is returned. This section describes the results obtained when searching the Sample Database. In order to follow along, login to the Sample Database and perform the search described in Performing a Simple Search.

There are two result formats available:
List View Form View
The appearance of search results can be changed in the Display Preferences. For more information about Preferences, see Setting Your Display and Search Preferences on page 211.
Viewing Results in Form View

Form View allows the user to view all of the information available in one record. To change from List View to Form View: 1. In a Results List View window, go to the record you want to see in Form View. 2. Click Show Details.
ChemOffice Enterprise203 Search Results
The record you want to see appears in the Results Form View window.
The following buttons are available at the top of the results form to allow the user to view additional records:
If you want to see Then click
Administrator
the next group of records.
Next Record
the last record of all Last Record the records returned from the search.
Browsing Other Records

After the ChemOffice Enterprise completes a search, the results appear in a Results window. Sometimes, not all the records returned from the search appear in the Results window. For example, if a search was performed in the Sample application to find the molecule named benz, although the application returns 13 records, only one through five of the 13 appear in the current Results List View window.
NOTE: The maximum number of records displayed on one page in Results List View is set in the Preferences box. The default is five records. For more information, see Setting Your Display and Search Preferences on page 211.
the group of records Previous Record you saw most recently. the first record of all First Record the records returned from the search. a specific record.
Record Number
Type a number in the box, within the given range. Click OK.
Viewing All Records

ChemOffice Enterprise retrieves a set number of records at a time, and these records are displayed several at a time in the Results View window (the number of records displayed depends on user preferences). The number of records retrieved depends on a setting in the applications INI file. For information about the maximum number of
CambridgeSoft Search Results
hits retrieved for your application, please see your system administrator. The default number of maximum hits for Sample is 100. To retrieve the first 100 records of a database: 1. From the Query Input Form, click Retrieve All. The Results List View appears, showing records 15 of 100 hits. To see the next 100 records:
In a Results Form View window, click Get More
Hits.
The Show Last List button appears on the left side of the window, below the Clear Marked button. To see the most recent Results List View:
From the Results List View, click Show Last List.
The most recent Results List View appears. To remove a record from the marked records list:
From the Results Form View or the Results List
View, click Unmark Record.
The Results List View changes, showing records 101105 of 200 hits.
Marking and Unmarking Records

Records retrieved from a search can be marked to allow viewing later without repeating the search. To mark a record to view again later: 1. From the Query Input Form, in the Molecule Name box, type benz. 2. From the Search Type menu, choose Substructure. 3. Click Search. The Results List View window appears. The Sample Application finds 13 records that match your query. 4. Click Mark Record for records #1 and #3. The Mark Record button changes to the Unmark Record button for records #1 and #3 only. The Show Marked and Clear Marked buttons appear on the left side of the window. To see the records marked in a List View:
View, click Show Marked.
The Unmark Record button changes to the Mark Record button for the records you unmarked. To remove all of the marked records from the marked records list:
View, click Clear Records.
The Unmark Record button changes to the Mark Record button. No records remain marked.
Manipulating Queries
The Queries menu gives users access to tools, which allow you to restore, save, and manage queries which have been performed. This is especially useful to users interested in using a particular query more than once without going through the process of entering the parameters each time.
Restoring Queries
Restore Query allows the user to restore previously entered search criteria to an input form. There are two options when restoring a query:
Restore the last query entered Restore a saved query
Records 12 of 2 hits appear in the Results List View window.
To Restore the Last Query:

1. Select Restore > Last from the Queries
3. Click Restore.
The query input form appears:
Menu. The query input form appears:
Administrator
4. Edit your criteria and click Search. 2. Edit your criteria and click Search.
Saving Queries
Users can save a query to be recalled at a later time. This is often useful when you expect to run the same search more than once.
To Restore a Saved Query:

1. Select Restore > Saved from the Queries
Menu.
2. Select the appropriate query from the listbox.
To Save a Query:
1. After performing a search, select Save from
The Manage Queries dialog appears.
the Queries Menu
2. Enter a name and description for the query. 3. Select the Make Public checkbox if you would
Restoring Queries For information about restoring queries, please see Restoring Queries on page 205.
like other users to be able to access the query. 4. Click OK. Your query is saved. For information about retrieving this query, please see Restoring Queries on page 205.
To Restore a Query from the Manage Queries dialog:

1. Select the appropriate query from the listbox. 2. Click Restore.
Managing Queries
The Manage Queries dialog box allows users to restore, edit, and delete queries in the current history and saved queries. Saved queries are user specific. To start managing your queries, select Manage from the Queries menu.
The query input form appears.

Editing Queries
Edit Query allows the user to enter new identifier information for the query, such as a new name and description, or make the query public. Making a query public makes your query accessible by any other user of the system. To edit a query:
1. Select the appropriate query from the listbox. 2. Click Edit.
The edit query window appears:
Restore one of the saved hit lists
To Restore the Last Hit List generated:

Select Restore > Last from the Hit Lists
Administrator
3. Enter the appropriate information and click
Menu. The hit list is displayed in list form. To Restore a Saved Hit List:
1. Select Restore > Saved from the Hit Lists
Menu.
OK. The query information has been edited and you are returned to the Manage Query window.
Delete Queries
Only saved queries can be deleted. History queries remain in the query list until the history is cleared. To change when the history is cleared, please see your system administrator. To delete a query:
1. Select the appropriate saved query from the 2. Select the appropriate hit list from the listbox. 3. Click Restore.
listbox. 2. Click Delete. The query is deleted from the list.
The hit list is displayed in list form.
Saving Hit Lists

Save Hit List allows a user to save a hit list and recall it at a later time. To Save a Hit List:
1. After performing a search, select Save from
Manipulating Hit Lists

The Hit Lists menu gives users access to tools, which allow you to restore, save, and manage hit lists which have been generated by the current user.
Restoring Hit Lists

Restore Hit List allows the user to restore a hit list which was previously generated. There are two options when restoring a hit list:
Restore the last hit list generated
the Hit Lists Menu. 2. Enter a name and description for the hit list. 3. Click OK. Your hit list is saved. For information about retrieving this hit lists, please see Restoring Hit Lists on page 208.
Managing Hit Lists

The Manage Hit Lists dialog box allows users to restore, edit, and delete hit lists in the current history and saved hit lists. Saved hit lists are user specific. To start managing your hit lists, select Manage from the Hit Lists Menu. The Manage Hit Lists dialog appears.
Restore Option
Result
Subtract from Current List
A hit list is displayed which contains all of the hits in the current list, not including any hits also found in the saved list.
Union with A hit list is displayed which Current contains all of the hits in the List saved list as well as those in the current list.
To restore a hit list:
1. Select the appropriate hit list from the listbox. 2. Select the appropriate radio button (to indicate
Restoring a Hit List
When restoring a hit list from the Manage Hit Lists dialog box, saved hit lists can be merged in specified ways to generate a new hit list. The options when restoring a hit list are:
Restore Option Result
how you would like the list restored). 3. Click Restore. The hit list is displayed in list view.
Editing a Hit List
Edit Hit List allows the user to enter new identifier information for the hit list, such as a new name and description, or make the hit list public. Making a hit list public makes your hit list accessible by any other user of the system. To edit a hit list: Edit Hit List allows the user to enter new identifier information for the hit list, such as a new name and description. To edit a hit list:
1. Select the appropriate hit list from the listbox. 2. Click Edit.
Replace Current List Intersect with Current List
The saved list is displayed in list view as it was saved.
A hit list is displayed which contains only the hits found in both the saved list and the current list.
The edit hit list window appears: 3. Enter the appropriate information and click OK.
The hit list information has been edited.

Delete a Hit List
6. Change the query. 7. Click Apply.
Only saved hit lists can be deleted. Hit lists in the history remain in the hit list until the history is cleared. To change when the history is cleared, please see your system administrator. To delete a hit list:
1. Select the appropriate saved hit list from the
The Results View window appears.
Administrator
Refining Over Current Records Found

In a large dataset, you may want to modify your search criteria to search over the current result set rather than the entire database. To refine over the current records:
1. In the Refine Query Input Form, enter your
listbox. 2. Click Delete. The hit list is deleted from the list.
Refining Search Results

A query can be changed to narrow search results. This can be accomplished by either editing the current query and searching over the records that have already been retrieved, or by editing the current query and searching over the whole database again. To refine a search over the current records: 1. Create a query. 2. Click Search. The Results View window appears. 3. Click Refine. The Refine Query box appears.
query. For example, if you want to refine the search to only compounds that have a hydroxyl attached: a. Draw methanol. b. From the Search Type list, choose Substructure. 2. Click Apply. Results from the example refined search (above), contain all of the compounds in the dataset which include the hydroxyl group. Records in the database which were not hit in the original search will likewise, not be part of the refined search.
Undoing a Refined Search

To return to results obtained previous to a refined search:
Click Undo Refine.
The results from the previous search appear.
Exporting Search Results

The results of a search can be saved as a .sdf file. A .sdf file can be exported to ChemFinder and other ChemOffice Enterprise applications. Information such as structure, molecular weight, and formula are automatically exported in the file. Additional information can be selected to be included in the file.
4. Click Refine over current records found. 5. Click OK.
The Refine Query Input Form appears.
To export search results: 1. After marking his, from a Results View, click Export Hits. The Export Hits dialog box appears.
application is configured. Please see your system administrator for more information about when the history is cleared. Use the History menu to restore a query or hit list in your history:
1. Select Queries or Hit Lists from the History
Menu. The History menu dialog box appears.
2. Select the information you want to include in 3.
4. 5.
6.
the file. Select a type of SD file: flat - in the event of multiple results for one field: a record is created for each result. nested - multiple results for one field all appears in one cell. Click OK. Click to Download. The Save As dialog box appears, containing a numerical name for the sdf file, based on the date and time. Select a download location and click Save.
2. Select the appropriate query or hit list from the
list box. 3. Click Restore.
Setting Your Display and Search Preferences

Display and search preferences are set in the ChemOffice Enterprise Preferences dialog box. To set display preferences: 1. From a page in a ChemOffice Enterprise application, click Preferences. The Preferences dialog box appears.
Histories
The application history can be used to retrieve queries and hit lists which had been executed earlier, but were not necessarily saved. The history is cleared periodically, according to how the
ChemOffice Enterprise211 Setting Your Display and Search Preferences
The new preferences are applied to your next search. To set search preferences: 1. Click Preferences. The Preferences dialog box appears.
Administrator
If you want your Then, in the search to Search Preferences section
match the charges or Click Hit any radicals to the charge on heteroatom in your heteroatom. query structure. match the charges or Click Hit any radicals to the carbon charge on carbon. in your query structure. require that the Click Reaction Query reaction centers in Hit Reaction Center. the query overlap the reaction centers in the target
If you want to
Action
see search results one From Results record at a time. Display, click Form. see search results several records at a time. From Results Display, click List.
specify the number From the Number of records you see in Displayed in List List View. View, type a number in the Number box.
3. Click Apply.
CambridgeSoft Setting Your Display and Search Preferences
specify exact structure searching options
Select the appropriate checkbox next to Permit Extraneous Fragments in Full Structure or Reaction searches. If Permit Extraneous Fragments (for structure or reaction searching) is selected, the search wil allow hits to contain molecular fragments in addition to that which was hit by the query.
match the cis/trans double bond geometry to your query structure. make thick bonds represent relative stereochemistry require absolute relative stereochemistry
3. Click Apply.
Click Match double bond stereo.
Click Thick Bonds Represent Relative Stereochemistry Click Absolute Relative Chemistry
ChemOffice Enterprise applies your preferences to your next search.
Server Information
You can retrieve information about the server software currently in use and the database being searched from the application window. To get Server information:
Click the About button in the ChemOffice
match the similarity of your query structure by a specific percentage.
From the Similarity search box, type a number between 0 and 100. A lower value requires the target to be less similar than your query structure.
Enterprise navigation bar. To return to the previous page:

Click OK.
match the tetrahedral Click Match chirality to your tetrahedral stereo. query structure.
Logging Off
When you first access a ChemOffice Enterprise application, you start a user session with the server. Although the server times out after a period specified by your administrator, you can log off when you are finished with the session.
ChemOffice Enterprise213 Server Information
To log off:
Click Log Off.
You are logged off and the server resources that you use are released.
Administrator
214ChemOffice Enterprise CambridgeSoft Logging Off
Chapter 8: CS Oracle Cartridge

Overview
The CambridgeSoft Oracle Cartridge allows the storage of chemical structures, and performing fast substructure searches in an Oracle database. There is minimal overhead for the programmer, and all relevant pieces of data are stored inside the database. Therefore, every service, like transaction processing and backup procedures, apply transparently to the cartridge with no special action required from the database administrator.
Installation
Please take the following steps to install the Oracle Cartridge (for the first time):
1. Double-click the SetupCartridge.exe
Windows program. The following dialog appears:
Installation
Minimum Requirements
Oracle 8i or 9i ChemOffice 7.0 or later
Before Installation
Before attempting to install the Oracle Cartridge, please take the following steps:
The file init.ora must contain the following
line: COMPATIBLE=8.1.0 or higher. Users planning to index their tables with the cartridge must have the following privileges granted: CREATE TABLE CREATE ANY INDEXTYPE
2. Fill in the required fields for the required
platform, then hit OK. The installation program checks if Oracle is configured correctly to be able to run the extproc agent. Without the correct configuration, the cartridge can not be used. See See Setup Problems on page 234. During the installation the installer executes a sql script, and copies files to the server.
In Windows installations the installer must run
on the server.
CS Oracle Cartridge215 Overview
In Unix installations, the server must run an
ftp service. If the server does not run an ftp service, or using it is not allowed for security reasons, the Unix system access must be left empty. In this case the files to be copied to the ${ORACLE_HOME}/lib/CsCartridge are copied to the users temporary directory. By default, that directory is: Documents and settings\user_name\Local Settings\Temp and it is the DBAs responsibility to copy them to the target directory. The install program can work in four distinct modes: Full install. If a previous installation exists, it is completely replaced with the new installation. All stored procedures and support files are replaced. Any existing index created by a previous installation of the cartridge becomes orphaned. The indexes still exist, but they are unusable. All of those indexes have to be dropped and re-created with all the overhead involved. Partial install. In this case no stored procedure or no object in the Oracle database is affected, only the shared library containing the external functions and procedures are replaced. All previously created indexes are still valid, they can be used without any further action. Partial install is useful if a new minor build of the cartridge is available, and there was no change in the data model. Partial install should be chosen only after consulting with CambridgeSoft to ensure that the data model in the old version and the new version are the same. Minimal install. This is not a real installation, the install program only creates an SQL script, which if executed using an appropriate tool, like SQL plus, results in the same database objects as a normal install. This option should
not be used generally. Sites with higher than usual security requirements may opt for first creating the SQL script, review it end execute it manually. No install. This is after installation test if the installation was manual.
Administrator
Un-installation
To uninstall the Oracle Cartridge, please do the following:
1. Remove the directory as follows:
On Windows:
${ORACLE_HOME}/bin/CsCartridge On UNIX: ${ORACLE_HOME}/lib/CsCartridge 2. Execute the DROP USER CsCartridge command while connected to Oracle as a system administrator. If the name of the instance is not CsCartridge, then the appropriate instance name must be used.
Re-installation
Re-installing the Oracle Cartridge can be accomplished by following the same steps as See Installation on page 215. The "Partial install" option also can be chosen with re-installation. This option should be chosen only if it is known, that the data model used by the cartridge did not change from the installed version. Partial install is fast, existing indexes do not have to be re-built, but it is recommended to consult with CambridgeSoft's support if partial install is planned. If a full installation was performed over an existing installation, then all the existing cartridge indexes have to be recreated. Those indexes still exist, but orphaned, without any data supporting them. They have to be first dropped, then re-created with the appropriate CREATE INDEX command. The installer program helps with this project. In the case of a re-installation the installer program pops up
216CS Oracle Cartridge
CambridgeSoft Installation
dialogs with every existing cartridge index, and prompts the user if re-creating the index is desired. The user has to enter the password for the schema of the table, and may change the CREATE INDEX sql statement. To enable this feature the "Recreate existing indexes" check box must be checked.
CREATE TABLE CREATE LIBRARY CREATE PROCEDURE CREATE OPERATOR CREATE INDEXTYPE CREATE TYPE SELECT ANY TABLE UNLIMITED QUOTA ON the
Multiple Installations
The CambridgeSoft Oracle cartridge is installed under normal circumstances into the CsCartridge schema, and the data files are stored into the $ORACLE_HOME/binCsCartridge (windows) or $ORACLE_HOME/lib/CsCartridge (unix) directory. It is possible to change this default setting by changing the name of the instance field in the install program. This can ensure, that two separate instances exist at the same time. Most likely this can be desired, when different versions of the cartridge are planned to be compared against each other. Normally this feature should not be invoked, and it takes highly skilled supervision to maintain two cartridge instances. Most likely client programs do not ask the end user to choose a cartridge instance, but resort to the default CsCartridge name. This is the name we use throughout this documentation. But ad-hoc sql easily can be used against two installs, and client programs can consider various cartridge installations. So if the "cartridge instance name" is CsCartridge2, then everywhere CsCartridge2 must be used instead of CsCartridge, when the cartridge is used.
T_CsCartridge tablespace The CsCartridge user in turn grants EXECUTE privileges to PUBLIC on all the functions, operators, and types designed to be accessible from external accounts. It also grants all privileges on tables it creates in its schema to the response of a user request to index a table.
DDL Considerations
DDL (Data Definition Language) statements include statements used to create and manipulate data. Examples include (but are not limited to) CREATE, and DROP. Chemical structures must be stored in either BLOB (binary large object) or CLOB (character large object) data type fields. BLOB fields must contain CDX documents. CDX documents are created by the ChemDraw application, and by the ChemDraw ActiveX control. CLOB fields can contain encoded CDX documents, CDXML documents, SMILES strings or MolFiles. A SMILES string is a way to describe a chemical structure in a line of text. MolFiles are ASCII files containing atom and bond property
Security
The CsCartridge.sql script creates a new user with the name of CsCartridge and password also set to CsCartridge. The following system privileges are granted to CsCartridge:
GRANT CREATE SESSION TO
CsCartridge
CS Oracle Cartridge217 DDL Considerations
information. When MolFiles are used as input, carriage return/linefeed characters must be replaced by a single back-slash (\) character.
NOTE: For more information about CDX and MolFile formats, please see "Exporting and Importing Using File Formats" in the ChemDraw Users Guide. For additional help in creating SMILES strings, please see "SMILES and SMIRKS Strings" in the ChemDraw Users Guide.
The ChemDraw ActiveX control as well as a number of other applications, can save documents in any of the above formats.
Creating The Index

To enable the fast substructure search feature of the cartridge, the field containing structure information must be indexed as follows:
CREATE INDEX ix ON tab(fld) INDEXTYPE IS CsCartridge.MoleculeIndexType [PARAMETERS('keyword=value[,keyword=valu e]...')];
where:
ix - is an arbitrary name. This name should be
short, because the cartridge concatenates it with the user name to create different tables, and the length of table names is restricted to 20 characters. tab - is the name of the table containing a field designated to store chemical structure information. fld - is the name of the field designed to store chemical structure information. param - is a string containing keyword=value pairs delimited by commas The PARAMETERS clause is optional. The individual parameter settings must be separated by commas. The supported keywords are as follows:
TABLESPACE=tablespace_name
If present, then the tables created by the cartridge will not be created in the default T_CsCartridge tablespace, but rather in the tablespace_name tablespace provided by the user. The creator of the tablespace must have already allocated a reasonable quota to the CsCartridge user on that tablespace. SKIP_POPULATING=[YES|NO] If present, the indexes will be created normally, but data stored in the table will not be used to populate the tables created by the cartridge. The user has to do it manually. This option should be used only for troubleshooting. That is, use this option only if an earlier attempt to create an index failed for some reason. The cartridge tables can then be populated by one or more UPDATE statements following the pattern below: UPDATE tab SET fld = fld; One table can contain any number of fields designed to store chemical structure information, and some or all of them can be indexed by the cartridge. If indexing of the structure field is not desired, use the following: DROP INDEX ix This will disable the cartridge, and remove all data, created in conjunction with the working of the cartridge, from the database. REACTION_SEARCH=[YES|NO] Substructure search screens are generated differently if this option is set to YES. Reaction searches are expected to be somewhat faster. RAISE_ERROR=[YES|NO] This option specifies if the cartridge should raise an error if a document is passed to it, which can not be interpreted as any of the supported data formats. If it is set to NO, no
Administrator
CambridgeSoft DDL Considerations
exception will be raised, and an entry will be stored into the CsCartridge.schema_index_E table. NORMAL=[YES|NO|INDEX] If present, this option instructs the cartridge whether to create and maintain screen tables for regular substructure search. The default is INDEX. SIMILAR=[YES|NO|INDEX] If present, this option instructs the cartridge whether to create and maintain screen tables for similarity search. The default is NO. FULLEXACT=[YES|NO|INDEX] If present this option instructs the cartridge whether to create and maintain screen tables for full structure search allowing tautomer matches as well. The default is NO. SKELETAL=[YES|NO|INDEX] If present, this option instructs the cartridge whether to create and maintain screen tables for substructure search, which honors tautomer matches as well. The default is NO. THREE_D=[YES|NO|DISTANCE|ANGLE ] If present, this option instruct the cartridge to maintain tables for 3d searching. The default is NO. REACTION_SCREENING=[YES|NO] If present, this option instructs the cartridge whether to create and maintain screen tables which can be used for performing better similarity searches, and increase the speed of the substructure search for reaction searches. The default is NO. THREE_D_RESOLUTION=[HIGH|LOW] If present, this option instructs the cartridge what level the screening should be carried out. Default is HIGH. DEFAULT_CUSTOM_SCREENS=[YES|NO]
If present, this option instructs the cartridge whether to use the structures from the default custom screens table. The default is NO. UNIQUE=[YES|NO|STEREO|RELATIVE TETSTEREO] If present, this option instructs the cartridge if duplicate structures are banned. If UNIQUE is YES, then structures must differ from each other except for stereochemistry. If UNIQUE is STEREO then a strict canonical code is used to check the identity of chemical structures. If the UNIQUE option is set to RELATIVETETSTEREO, then stereochemistry is considered, and bold bonds are treated as wedges. The default is NO. Version 9 of the CambridgeSoft Oracle cartridge distinguishes four different kinds of screens. NORMAL, SIMILAR, FULLEXACT and SKELETAL. NORMAL is used for regular substructure search screening. SIMILAR may be used for similarity search. The FULLEXACT screens are used for tautomer full structure search, and the SKELETAL screens are used for tautomer aware substructure search. If one of those screens should be present for a search, but are not, then the cartridge does not make any screening. Results will be generated as expected, but the program will be slower in lack of screening. Three different values can be assigned to these parameters: NO, YES or INDEX. If 'NO' is chosen, then a particular kind of screening will not be available. If 'YES' is chosen, then screening bitvectors will be stored and used for that particular screen. In this case the database will be screened when substructure search is requested resulting in faster turnaround. If 'INDEX' is chosen, then an inverted screen table will be maintained by the cartridge making the screening phase even faster. Choosing this option results in fastest turnaround for substructure searches, the trade-off is slower maintenance, and the occasional need for synchronization and analyzing the index. 'INDEX' is the default for
normal screens, and 'NO' is the default for the remaining screens. 'INDEX' is recommended for large tables which do not change frequently and high substructure search speed is expected. The settings chosen at the time the index was created can not be modified later by using the ALTER INDEX command. Three dimensional data is stored only if the THREE_D option is set to YES when the index is created. This setting can not be changed later by the ALTER INDEX command. If the THREE_D option is set to DISTANCE, then the cartridge stores and maintains only atomatom distances information, if it is set to ANGLE, then only angles defined by three atoms or a centroid are stored. Setting the THREE_D_RESOLUTION to LOW is also one way of making the three dimensional screening process faster, and to reduce the size of a three D enabled database. It will decrease the quality of the screening. Only the first significant digits of the distances and angles will be stored. The REACTION_SCREENING options directs the cartridge to maintain screens for both the reactants and the products of a reaction in addition the regular screens. This information is used, when similarity search is to be restricted to either the reactants or to the products. Similarity search when both reactants and products are specified are not considered valid, and result in "invalid query structure" error raised. A structure on the left side of a reaction arrow is considered reactant, and on the right side of a reaction arrow is considered a product. No other action is required to do reactant/product similarity searches. The screens maintained by the cartridge when REACTION_SCREENING is enabled are also used for substructure searching. This usage is mostly transparent to the user, because the only difference is, that substructure searches for reactions are faster. Though it must be noted, that
substructure search will be faster only when synchronization is recent, and not many records are in the temporary tables.
Example
CREATE TABLE moltable(mol CLOB); CREATE INDEX mx ON moltable(mol) INDEXTYPE IS CsCartridge.MoleculeIndexType;
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It is important to remember, when creating an index in a different schema than the logged-on user, both the index name and the table name must be qualified by the schema name. Otherwise, the cartridge will not connect its tables to the original table. For example:
CREATE INDEX mx ON USER1.moltable(mol)...
is incorrect. The correct format is:

CREATE INDEX USER1.mx ON USER1.moltable(mol)...
NOTE: Creating an index may be time consuming if the table already contains lots of records when the index is created.
Maintenance of the Index

When a MoleculeIndexType kind of index is created the CambridgeSoft data cartridge software creates a few tables (described later in details), and populates those tables from the data records found in the table the index is created on. If this table contains hundreds of thousands of records this process may take a few hours, and has high demands on system resources. That process can fail if any tablespace the cartridge stores data into overflows. The cartridge maintains "inverted" tables in order to implement fast substructure and 3d search. The maintenance of those tables is time consuming, and may result in users waiting for each other when simultaneously updating the same table. To ensure,
CambridgeSoft DDL Considerations
that updating the database is also reasonably fast, the cartridge does not update its inverted tables, when a client program updates an indexed table. Instead, it just simply stores a remainder into a temporary table about the update. The changes accumulated in the inverted tables are not merged into the main inverted tables until the DBA explicitly requests by executing an
ALTER INDEX ix PARAMETERS('SYNCHRONIZE');
AnalyzeIndexTables. That procedure has two parameters, the name of the user's schema, and the name of the index. An example of the usage of the AnalyzeIndexTables command follows: CALL CsCartridge.AnalyzeIndexTables('myschema ', 'myindex');
command. Whether or not this synchronization was executed is transparent to the user. The only visible effect of not executing the synchronization is a lower speed for substructure search. Most likely there will be no effect on search speed until a few tens of thousands record accumulation in the temporary tables. Even when the synchronization is executed, the inverted tables are not updated fully. Some statistics, which influence the execution of a substructure search are still not updated. Those statistics are recalculated to match the contents of the inverted tables, when an
ANALYZE INDEX ix COMPUTE STATISTICS;
The ANALYZE command can also be used to verify the integrity of the cartridge index. Normally, this command should just return without any message. If it throws an exception, then the domain index is in an unusable condition, and the index may need complete rebuild. The command to execute is
ANALYZE INDEX ix VALIDATE STRUCTURE;
Oracle Corporation does not recommend using the ANALYZE command most of the cases directly from version 9i. Below is a a quote from the SQL reference of Oracle 9i: Oracle Corporation strongly recommends that you use the DBMS_STATS package rather than ANALYZE to collect optimizer statistics. That package lets you collect statistics in parallel, collect global statistics for partitioned objects, and fine tune your statistics collection in other ways. Further, the cost-based optimizer, which depends upon statistics, will eventually use only statistics that have been collected by DBMS_STATS. See Oracle9i Supplied PL/SQL Packages and Types Reference for more information on this package. However, you must use the ANALYZE statement (rather than DBMS_STATS) for statistics collection not related to the cost-based optimizer, such as:
To use the VALIDATE or LIST CHAINED ROWS clauses To collect information on freelist blocks
command is executed. The execution of this command is also time consuming. This command has to be executed just rarely, only when a large portion of a database is replaced. It should be executed, when the database is close to its expected full size. Or every time if the size of the indexed table doubles. The execution of those two commands is the responsibility of the DBA. Right now, there is no mechanism implemented to execute the commands automatically. The lack of the execution of those commands in a timely fashion may result in diminished performance. Executing the ANALYZE INDEX command does not analyze the tables maintained by the cartridge. This is usually is not necessary, only if the tables and/or columns maintained by the cartridge are directly referenced. This must be done explicitly by the DBA by calling the provided procedure
Unique index
When the index is created it is possible to control if duplicate structures are allowed. Due to the ambiguities of defining the identity of a chemical
structure many options are available. Those options can later be changed according to the needs of an application for the duration of a transaction. For that purpose, the ChangeOption stored SQL procedure can be used. Of course it can be used for other purposes as well, but that was the main reason for the implementation. The syntax of the ChangeOption procedure is ChangeOption(schema_name, index_name, identifier_name, value); All parameters are strings enclosed in single quotes. To allow duplicates on a given index call the ChangeOption procedure like
CALL CsCartridge.ChangeOption('my_schema', 'my_index', 'UNIQUE', 'NO');
Fast Substructure Search

Fast substructure search can be invoked by the MoleculeContains operator in a SELECT statement as follows:
SELECT ... FROM tab WHERE CsCartridge.MoleculeContains(fld, query4000, query8000, options)=1
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where:
tab - is the name of the table to be retrieved fld - is the name of the field indexed by the
To restrict duplicates to identity defined by same stereochemistry make a call like

CALL CsCartridge.ChangeOption('my_schema', 'my_index', 'UNIQUE', 'STEREO');
If you want to make these settings permanent, execute a commit command. Otherwise, the settings will effect only the current transaction.
DML Considerations
DML (Data Manipulation Language) statements include statements used to manipulate data. Examples include (but are not limited to) SELECT, INSERT, DELETE, and UPDATE. Data maintenance related to the cartridge is for the most part automatic, and no extra work is required. Every time a record is inserted into a table containing an indexed field, the cartridge is automatically invoked by the Oracle server. The cartridge is also invoked if a record is deleted, or if an indexed field storing a chemical structure is updated.
cartridge query4000 - is the first 4000 characters of the query string. The query string can be an encoded CDX document, a SMILES string, or a MolFile. For more information about these formats, please see See DDL Considerations on page 217.. The Oracle server limits the size of string literals to 4000 characters. query8000 - is the second 4000 characters of the query string. Queries exceeding the 8000 character limits will fail. Since CDX documents can be very large, this limitation may become important. However even in this case, an 8000 byte limit should not impose too much of a restriction. options - is a string containing keyword=value pairs separated by commas. The interpreted keywords are: ABSOLUTEHITSREL=[YES | NO] Default is NO COMPLETE=<number> - to limit the number of hits tested against atom by atom matching DOUBLEBONDSTEREO=[YES|NO] double bond stereo matching. Default is YES. FRAGMENTSOVERLAP=[YES|NO] fragments can overlap. Default is NO. FULL=[YES|NO] - to specify full structure search. Default is substructure search
CambridgeSoft DML Considerations
HITANYCHARGECARBON=[YES|NO]
COST=<number>-to communicate with
hit any charged carbon. Default is YES. HITANYCHARGEHETERO=[YES|NO] hit any charged hetero atom option. Default is YES. IDENTITY=[YES | NO] - Default is NO MASSMAX=<number>- to prescribe maximum molecular mass to matching records MASSMIN=<number> - to prescribe minimum molecular mass to matching records PERMITEXTRANEOUSFRAGMENTS=[ YES |NO] - permit extraneous fragments. Default is NO. PERMITEXTRANEOUSFRAGMENTSIFR XN=[YES |NO] - permit extraneous fragments. Default is NO. REACTIONCENTER=[YES|NO] - to specify if reaction search can match only reaction centers. Default is YES. RELATIVETETSTEREO=[YES | NO] Default is NO SIMILAR=[YES|NO] - similarity search. Default is NO. SIMTHRESHOLD=<number> - to set the similarity percentage when SIMILAR=YES is set as well. Otherwise disregarded. Default value (used if it is omitted) is 90 percent. TAUTOMER=[YES|NO] - Default is NO TETRAHEDRALSTEREO=[YES|NO|SA ME|EITHER|ANY] - tetrahedral stereo matching. Default is YES. USE_THREADS=[YES|NO] - Default value is read from the Globals table SELECTIVITY=<number>-to communicate with the Oracle query optimizer. See Query Optimization on page 225.
the Oracle query optimizer. See Query Optimization on page 225. FUNCTIONCOST=<number>-to communicate with the Oracle query optimizer. See Query Optimization on page 225. There is no restriction for SELECT statements when used with the cartridge. Tables can be joined by other tables, and the WHERE clause can be formed by using all the options of Oracle. The COMPLETE option can be used by client programs, which expect huge databases and substructure searches resulting in large hit lists. The cartridge will apply the atom by atom matching only until the value specified in the COMPLETE option is satisfied. After this value is satisfied, everything which passes the screening process will be returned to the client program as a hit. It is the responsibility of the client program to call the CsCartridge.ContainsCDX.MolContains function to apply the atom-by-atom matching test. This function has the same syntax as the MoleculeContains operator. A major advantage of approaching this issue in this way is that the hit list will be returned at least ten times faster. The disadvantage is that atom-byatom matching must be invoked for every item in the hit list before the first number of records indicated by the COMPLETE option. Therefore, the number of hits will not be accurate. The use of this option is recommended, when the result is presented to the user in segments and the user is not expected to browse through a huge list. The USE_THREADS option directs the cartridge whether to apply multithreading when performing a search. The value is used in conjunction with the value stored into the Globals table. If the value in the Globals table is NO, then the option is
CS Oracle Cartridge223 DML Considerations
disregarded. It has effect only if the value in the Globals table is YES. Multi threading may make the program faster, and can improve user perception.
Safe Querying of Large Structures
Simple Example
SELECT mol FROM moltable WHERE CsCartridge.MoleculeContains(mol, 'c1ccccc1', '', 'MASSMIN=200, MASSMAX=500')=1; selects all records from the table moltable where the mol field contains benzene as a substructure (c1ccccc1), and the molecular mass is between 200 and 500.
Querying Large Structures

If a query exceeds 8000 bytes, another format of the MoleculeContains operator can be used to pass queries up to a length of 4 million bytes. In this form a maximum of 1000 segments each with a maximum size of 4000 characters can be passed to the cartridge in the place of the second parameter. However, even this form fails when using ADO if the query structure is passed as a list of literals. This strategy can be used only if the query is specified as a list of parameters and the parameters are passed separately. The Select statement would look like this: SELECT ... FROM tab WHERE CsCartridge.MoleculeContains(fld, CsCartridge.XArray(:xpar0, :xpar1, :xpar2,...), options)=1 where each parameter (xpar) represents a string up to 4000 characters in size. That 4000 characters is a theoretical value. Due to an Oracle bug the safe value is 666 (See Querying Large Structures on page 224.). For more information about the other variables in the above statement, please see See Fast Substructure Search on page 222. The programming required to pass the parameters to the Oracle Server depends on the environment used to develop the client application.
Unfortunately the above approach does not work on all platforms. According to test results, on some systems, where the server computer and client computer's character set is different, the ORA01460 unimplemented or unreasonable conversion requested exception is raised by the server. The cause of this error is an Oracle bug: #2233987. This bug is manifest on platforms where the server character set is not known by the client. Oracle 9i server may have a DB character set, which is not know to an Oracle 8i client. According to our research and consulting with Oracle Technical Support the workaround of this problem is to limit the size of strings passed in the XArray to 666 characters. That is very likely a good solution, however there may be configurations which are saddled with other similar problems. When both the client and the server run Oracle 9i, this problem has not been observed yet. To bypass the possibility of this problem:
The client program may pass the text of a
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SELECT statement to the MoleculeContains operator as its second parameter in the first form of MoleculeContains. The third parameter should be left blank. The first element of the SELECT statement's select list must be a CLOB field, and the execution of the SELECT statement should result in one output record. This data will be used by the cartridge as the query structure. The application program has to store the query structure before using the MoleculeContains operator. The CsCartridge user must have access to the table or tables referenced in its parameter. The programmer can use the Queries table in the CsCartridge schema to store query structures. The Queries table has three fields: ID - a numerical identifier
CambridgeSoft DML Considerations
primary key NOTE - text field to add some meaningful
explanation to the query, and the QUERY field itself. Also available is the QuerySequence SEQUENCE to ensure unique identification. A simple example to illustrate the programming required for the usage of this feature: INSERT INTO CsCartridge.Queries(id, note, query) VALUES(1234, 'benzene query', 'c1ccccc1'); SELECT mol FROM moltable WHERE CsCartridge.MoleculeContains(mol, 'SELECT query FROM CsCartridge.Queries WHERE id = 1234', '', '')=1; The SELECT statement passed as a string is executed as if the connected user was CsCartridge. References to tables outside the CsCartridge schema must contain table names qualified by their schema.
The INDEX hint can be used to instruct the optimizer to prefer using a particular index. The syntax of the INDEX hint is SELECT /*+ INDEX(table_name index_name) */ ..... Table_name and index_name are names of the preferred table and index, respectively. Using the INDEX hint is recommended when it is in doubt which implementation will be used by the optimizer, and IDENTITY=YES option is used, because identity search can be performed only by using the index.
Query Optimization
The cartridge implements user defined statistics, which are used by the Oracle query optimizer. These statistics are used by Oracle to decide whether to use the index scan implementation of the MoleculeContains operator or the functional implementation. Table scan means, that the cartridge is the first piece of software selecting a subset of rows from a table. The remaining conditions of a WHERE clause are evaluated later. If the WHERE clause contains a condition, which is more selective than the cartridge; which results in a smaller subset, then the execution of the query is probably slower than it should be. Such bad decisions can result in queries executed thousand times slower than they should be. There are two statistics implemented in the cartridge at this moment. Selectivity and Cost. Selectivity is set to 0, which communicates to Oracle, that the functional implementation is not selective at all. Cost is the CPU cost associated with an index scan. If the query options contain an IDENTITY=YES setting, then the cost returned to Oracle is set to 0, otherwise it is set to 1. According to experience, this results in Oracle preferring index scan when IDENTITY=YES, and use an other highly selective primary key if IDENTITY=NO. This approach is rudimentary, and will be refined later.
Using Optimizer Hints

The MoleculeContains operator has a dual implementation. One of the implementations employ the cartridge index and is used when the query optimizer decides to use index scan, and the the other implementation is a simple function called when the optimizer decides against using the cartridge index. This usually happens when there is a chance that including other conditions in a WHERE clause result in higher selectivity. In addition, ignoring the index can also be caused by join conditions in the WHERE clause. Picking the right algorithm for executing a SELECT statement can cause dramatic differences in speed. If the performance is poor when a complicated SELECT statement is executed, optimizer hints can be used to nudge the optimizer toward preferred execution methods.
CS Oracle Cartridge225 DML Considerations
However, if the calculation performed by the cartridge does not result most of the time in the desired results, then it is possible to override the values calculated by the cartridge. The SELECTIVITY=number, and the COST=number, options can be used to control Oracle's optimizer. This approach is more flexible, than using optimizer hints, because it just communicates information to Oracle used to make decisions, which are compared to similar information provided by other indexes and access methods. It's very important to know, that Oracle calls the user defined statistical functions once for a certain argument list. In other words, if the same values are passed to the MoleculeContains operator in the structure and option fields, the cartridge statistical functions will be called only once. So, if the second parameter a for the MoleculeContains operator contains a SQL statement, which in turn contains the real query, the optimizer will not invoke the statistical functions, and will act on false presumptions. So, that method of passing a query should not be used if the outcome of the optimizer is important.
options - can be an empty string or the string
'FULL=YES' or 'FULL=NO' The FormulaContains operator will select records from the database, where the counts of the specified atoms are in the prescribed limits. If the options field specified full match, then no other kinds of atoms are allowed in the formula. For example:
SELECT mol FROM moltable WHERE CsCartridge.FormulaContains(mol, 'C510Br2-4', '')=1;
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MolWeight Query
The cartridge allows quick search by molecular weight by the MolWeightContains operator. This operator can be used in the WHERE clause of a SELECT statement as follows:
SELECT ... FROM tab WHERE CsCartridge.MolWeightContains(fld, massMin, massMax, options)=1
where
Formula Query
A subset of a table can be selected by setting constraints on the formula of a structure by using the FormulaContains operator. This operator can be used in a SELECT statement as follows: SELECT ... FROM tab WHERE CsCartridge.FormulaContains(fld, formula, options)=1 where:
cartridge massMin - is a numeric value setting the minimal molecular mass retrieved massMax - is a numeric value setting the maximal molecular mass retrieved options - in this version the options field is not used For Example:
SELECT mol FROM moltable WHERE CsCartridge.MolWeightContains(mol, 70.0, 70.1, '')=1;
cartridge formula - is a list of atom symbols followed by a number and optionally another number introduced by a minus sign.
Support Functions
The cartridge supports the retrieval of chemical structure information in different formats beyond the default CDX format. At the present SMILES, RXN and Molfile formats are allowed.
CambridgeSoft Support Functions
Conversion functions are available, grouped together into the ConvertCDX package. The functions are:
CDXTo3dInfo(fld) CDXToB64(fld, i) CDXToCanonical(fld) CDXToCanonical(fld, option) CDXToCDXML(fld) CDXToCDXML(fld, i) CDXToFormula(fld, option) CDXToMolFile(fld) CDXToMolFile(fld, i) CDXToMolWeight(fld) CDXToMolWeight(fld, option) CDXToName(fld, option) CDXToRxnFile(fld) CDXToRxnFile(fld, i) CDXToScreen(fld, srcSelection,
formSelection) CDXToSmiles(fld) CDXToSmiles(fld, i)) CDXToCML(fld, option) CDXToMST(fld, option) where:

fld - is the name of a BLOB or CLOB field
storing chemical structure information in any form supported by the cartridge, but not necessarily maintained by the cartridge. i - is an index (starting at 1) referring to which 4000 character long chunk of the resulting text is being pointed to. This is necessary, because Oracle limits the size of string results in 4000 characters. option - is a field that is either empty or: SORTABLE
for the CDXToFormula function to generate formula strings where the elements are two characters wide, and the numbers are three characters wide with leading zeros. The field does not have to be indexed; only the content must match the supported content kinds of the cartridge. They can appear in a SELECT list, but there is no restriction on their usage or HTML for the CDXToName function to generate HTML tags for names, where the name needs subscripts, superscripts and styling. NORMAL or STEREO for the CDXToCanonical function. With the STEREO option the canonical code will consider stereochemistry when generating the canonical code, with NORMAL option or an empty option string stereochemistry is disregarded. MASSNATIVE or MASSMONOISOTOPIC or empty for the CDXToMolWeight(fld, option) function. With the MASSMONOISOTOPIC passed as option string, the exact mass is returned. The most abundant isotope's mass is used instead of the weighted average of the isotopes of the atoms of the molecules. The CDXToScreen function needs a parameter selecting the source, allowable values are 'NORMAL', 'SIMILAR', 'FULLEXACT', 'SKELETAL', and a parameter selecting the form of the output. Values are 'LIST', 'BITSRING'. If the requested screen does not exist, or input is incorrect empty string will be returned. Those conversion functions, which take i as the second parameters must be called with the actual value increased by one as long as the result is not an empty string. The index value 1 asks for the first 4000 bytes of the result, the index value 2 points to
CS Oracle Cartridge227 Support Functions
the second 4000 bytes of the result, and so on. The 4000 byte chunks of the results must be concatenated to really get the desired output. This by no way an effective way of retrieving those converted formats, that hopefully will be improved in later versions of the cartridge. In version 9 of the cartridge there are two forms of the CDXToMolFile, CDXToRxnFile, CDXToSmiles and CDXToCDXML functions. The new function implementations have only one parameter, the name of the field, and can return longer than 4000 byte long strings. The only drawback, that they can be used only if the server is an Oracle 9 server. Using the new implementations result in an error message when using against an Oracle 8 server. Also should be noted, that this functions return CLOBs instead of VARCHAR2 data, and the temporary CLOBs created by the cartridge linger in the server memory until the session is over. It advised, that the client session terminates as soon as possible after using these functions. Examples:
SELECT CsCartridge.ConvertCDX.CDXToMolFil e(mol) from .....
MoleculeContainsBLOBFunction operates on
BLOB fields. The remaining three parameters are the same as for the MoleculeContains operator. Example:
SELECT mol FROM tab WHERE CsCartridge.MoleculeContainsFunction(mol , 'c1ccccc1','','')=1;
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The cartridge also provides an opportunity to check data integrity by retrieving a md5 checksum for any CLOB or BLOB field. That feature can be invoked in a select statement with the following format:
SELECT CsCartridge.CheckSum.Calculate(fld ) FROM ...
The functional implementations of the MoleculeContains operator can also be used to perform atom-by-atom matching on fields. It can be used if the field is not indexed, and the result set will be the same, but the execution will be slow. This is because Oracle will sequentially read in the whole table, and select those records which pass the atomby-atom matching. There are two functions:
MoleculeContainsFunction operates on CLOB
A more advanced way of retrieving the molecular weight or the formula is using the MolWeight, Formula and Canonical operators. They can be used as normal functions, but they are implemented in a way to take advantage of the data calculated by the cartridge when records are stored. If the field name parameter passed to these operators refers to a field indexed by the cartridge, instead of processing the input data, the operators use data stored by the cartridge, thus improving the processing speed. However, these operators can not be used for search effectively, because they could never trigger index scan. If these operators are used in a WHERE clause, an ORA-29902: error in executing ODCIIndexStart() routine exception is thrown. The Canonical operator can not have a second parameter. In version 9 of the cartridge only the stereochemically unaware canonical code can be returned by using this operator. Usage example:
SELECT CsCartridge.MolWeight(mol), CsCartridge.Formula(mol, ''), CsCartridge.Canonical(mol) FROM moltable;
fields
Distributing databases
The CDXToMST function can be used to speed up index creation on tables already populated by a large number of records. The CDXToMST function returns a BLOB, which is an augmented CDX document. The new CDX document contains the original one and transparently to ChemDraw and other programs processing CDX documents, and it contains data calculated by the cartridge, yet not stored in the index structures. If a database is to be distributed as an Oracle dump file, then the following preparation is recommended: 1. UPDATE structures SET cdx = CsCartridge.ConvertCDX.CDXToMST(cdx, ''); COMMIT; 2. create a dump file of the structures table. Be sure, that it does not have a cartridge index. 3. In the installer program import the dump file using the imp program, and then create the domain index on the cdx column. The cartridge will use the data created in step 1 instead of processing the cdx document again. This cuts the time used to create an index by about 20 percent.
act accordingly. For a full list of the tables and fields maintained by the cartridge See Data Structures on page 240. The AUX package of the cartridge can be used to avoid compatibility problems with later versions. The AUX package contains trivial functions, which return the names of the tables and fields to be used to access the tables in the cartridge schema. With this extra care, future incompatibility can be avoided. The functions in that package will be explained later in the chapter. Generally, using these functions is more complicated than using operators returning the same value. The only reason stored data should be used directly, when the data is used to join two tables together. In this case execution of the SELECT statement may be much faster. The best way to use data stored by the cartridge is to create synonyms for the tables stored in the CsCartridge schema.
CREATE SYNONYM MyWeight FOR CsCartridge.sch_ix_W; for accessing molecular weight CREATE SYNONYM MyCode FOR CsCartridge.sch_ix_A; for accessing formula and canonical code
Using data maintained by the cartridge

Instead of using the support functions it is also possible to use the tables maintained by the cartridge to retrieve calculated data. Using these tables are much more effective, than using the support functions because no calculation has to be performed, but calculated and indexed data can be used. The disadvantage of using these tables is that, using them is not transparent, the names of the tables and fields can be changed in later versions, so client programs may become incompatible with different cartridge versions. To provide full compatibility with cartridge versions client programs have to check the cartridge version, and
This way, the fields of MyMol and MyCode tables can be used simply as if they were defined in the user's schema. Both of these tables have a field called RID. It contains the ROWID of the original table. The original table and the table maintained by the cartridge can be joined by an inner join by an original_table.ROWID = MyCode.rid condition in the WHERE clause. When the tables are joined, the data fields maintained can be used. Among them are:
MyMol.MolWeight which stores the molecular
weight of the structure.

MyCode.Formula contains the formula of the
structure
MyCode.CText contains the canonical code of
the structure
These fields are indexed, so using them in the WHERE clause of a SELECT statement may yield enormous speed improvement compared to nonindexed fields. Example:
CREATE TABLE mx(id, NUMBER, m CLOB); CREATE INDEX mxix ON mx(m) INDEXTYPE IS CsCartridge.MoleculeIndexType; CREATE SYNONYM MxWeight FOR CsCartridge.schemaname_mxix_W; -- replace schemaname with the name of your schema CREATE SYNONYM MxCode FOR CsCartridge.schemaname_mxix_A; -- replace schemaname with the name of your schema SELECT mx.id, MxWeight.MolWeight FROM mx, MxWeight WHERE mx.rowid = MxWeight.rid; - to list the identifiers and molweights for the table SELECT mx.id, MxCode.CText FROM mx, MxCode WHERE mx.rowid = MxCode.rid; -- to list the identifiers and canonical codes for the table SELECT mx.id, MxCode.Formula FROM mx, MxCode WHERE mx.rowid = MxCode.rod; -- to list the identifiers and formula for the table
CNFldName XXTabName(SchemaName VARCHAR2, IndexName VARCHAR2) returns the name of the table the data is stored in XXRidName returns the name of the field which stores the rowid of the original record XXFldName returns the name of the field which stores the data desired
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The MW functions must be used for MolWeight, the FM functions for formula, and the CN functions for canonical code. The following VB example code follows to illustrate how to retrieve the rowids of two different tables joined by their canonical codes. This SELECT statement will retrieve only those records that are chemically identical in both tables. Here the table names do not appear, the index names are used instead, to specify the tables.
Dim CNTab1, CNTab2, CNRidName, CNFldName As String Set c = New ADODB.Connection Dim r As ADODB.Recordset c.Open ConnectionString:="Provider=OraOLEDB.Ora cle.1;Persist Security Info=False;Data Source=" + "myserver", UserId:="myschema", Password:="mypassword" sql = "SELECT CsCartridge.Aux.CNTabName('myschema', 'my1index') FROM DUAL" Set r = c.Execute(sql) If Not r.EOF Then CNTab1 = r.Fields(0) sql = "SELECT CsCartridge.Aux.CNTabName('myschema', 'my2index') FROM DUAL" Set r = c.Execute(sql) If Not r.EOF Then CNTab2 = r.Fields(0) sql = "SELECT CsCartridge.Aux.CNRidName FROM DUAL" Set r = c.Execute(sql) If Not r.EOF Then CNRidName = r.Fields(0) sql = "SELECT CsCartridge.Aux.CNFldName FROM DUAL" Set r = c.Execute(sql) If Not r.EOF Then CNFldName = r.Fields(0)
If two tables are to be joined by chemical identity, then there is no better way to join them than the CText field maintained by the cartridge. The CText field is an index field, join by that this field saves one table scan. The functions of the AUX package:
MWTabName(SchemaName VARCHAR2, IndexName VARCHAR2) MWRidName MWFldName FMTabName(SchemaName VARCHAR2, IndexName VARCHAR2) FMRidName FMFldName CNTabName(SchemaName VARCHAR2, IndexName VARCHAR2) CNRidName
sql = "SELECT " + CNTab1 + "." + CNRidName + ", " + CNTab2 + "." + CNRidName + " FROM " + _ CNTab1 + ", " + CNTab2 + " WHERE " + CNTab1 + "." + CNFldName + " = " + CNTab2 + "." + CNFldName Set r = c.Execute(sql)
then:
SELECT eln_structures.key from eln_structures, CsCartridge.CS_NOTEBOOK_SX_E where eln_structures.rowid = CsCartridge.CS_NOTEBOOK_SX_E .rid
Error Handling
The cartridge can not communicate with the user. It can communicate erroneous situations only through either raising an exception or storing information related to the erroneous situation in a table. If the cartridge raises an exception, then the client program is terminated. The default action of the cartridge is to continue the program and store information about the failed chemical data in the database. This behavior can be changed by executing the following SQL statement:
UPDATE CsCartridge.<user-schemaname>_<user-index-name>_O SET Raise_on_error = 'YES'
will retrieve the identifying fields of those records, which are not indexed because of an error.
Performance
The MoleculeContains operator is implemented both as an index scan, and as a function. The query optimizer decides which implementation to use. If the WHERE condition contains more selective elements then the MoleculeContains operator, like a reference to a unique key, then Oracle will retrieve the only matching record, and then apply the function implementation, which will perform an atom-by-atom matching. When the index scan is executed, the cartridge creates a complicated query accessing different tables. The performance of that query can be dramatically improved by occasionally executing an ANALYZE INDEX statement on the INDEX created by the cartridge:
ANALYZE INDEX mx COMPUTE STATISTICS;
If the Cartridge does not raise an exception, then the CsCartridge.<user-schemaname>_<user_index_name>_E table will contain the rowid-s of those records containing invalid chemical data in their indexed fields. The rid field of this table contains the rowid of the indexed record, and the text field may contain additional information. A SQL statement, which joins this table with the indexed table lists the erroneous records. For example, if the following is true:
cs_notebook is the user's schema eln_structures is the indexed table name sx is the name of the index used by the
Executing this statement will calculate statistics on the tables created and maintained by the cartridge, and these statistics are used by the Oracle query optimizer. This command should be executed periodically depending on the frequency of the update of the table. Remark: In Oracle9 and higher the DBMS_STATS.GATHER_INDEX_STATS procedure is recommended instead of the ANALYZE command. It's syntax is
CALL DBMS_STATS.GATHER_INDEX_STATS('owner_nam e', 'index_name');
cartridge the key field is a good way of identify a record,
In order to ensure, that the optimizer is using the right algorithm to access the table the
CALL DBMS_STATS.GATHER_TABLE_STATS('own er_name', 'table_name'); command is recommended.
Troubleshooting
If there is a serious problem with the cartridge, it is sometimes appropriate to rerun the CsCartridge.sql script, which will re-install the cartridge software. After running the script every indexed table the cartridge indexed should be dropped, and recreated again. In addition, update every record in the table by executing the following SQL statement:
UPDATE tab SET fld=fld; COMMIT;
OR select CsCartridge.VERSION FROM dual; The version number stored in the CsCartridge.Globals table refers to the version of the install script, which installed objects into the CsCartridge schema. The version number returned by the VERSION function is the version of the CsCartridge.(dll/so/sl) shared library. The two can be different. The shared library should always be as old or newer than the install script. The version number returned by this function is stored in the initialized data segment of the shared library. It can be displayed on a UNIX system by the string CsCartridge.so | grep CsCartridge command.
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This is necessary for only those tables where the index was created without the PARAMETERS('CsCartridge') clause. If the problem persists, then the problem should be reported to CambridgeSoft.
Checking for fields indexed by the cartridge

The cartridge maintains the all_csc_indexes table in its own schema. The columns of this table are:
OWNER INDEX_NAME TABLE_NAME COLUMN_NAME COLUMN_TYPE
Checking for the Presence of the Cartridge

If the following query returns no result, then the cartridge is not present in the Oracle database.
SELECT username from all_users where username = 'CSCARTRIDGE'
Checking the Version of the Cartridge

This following statement yields a string containing the actual version of the CambridgeSoft Oracle Cartridge software.
select * from cscartridge.globals;
All of the fields are defined as VARCHAR2(30) columns. Every index created by the cartridge has an entry in this table. The content of this table can be retrieved by the public. By retrieving the content, the client program knows if a column is supposed to contain chemical structures. For Example: SELECT * FROM cscartridge.all_csc_indexes WHERE owner = 'me' and table_name = 'my_table' and column_name = 'my_column'
OR select value from CsCartridge.Globals where id = 'VERSION'
CambridgeSoft Troubleshooting
What to do if Creating an Index Fails

When the user executes a CREATE INDEX command, the cartridge reads all the rows from the table, and creates its own tables for fast substructure search. There are three different outcomes of the execution of the CREATE INDEX command 1. Success indicated by an "index created" message usually displayed by the client program 2. Invalid data in one or more records indicated by an "ORA-29863: warning in the execution of ODCIINDEXCREATE routine" message. In this case the user should check the content of the CsCartridge.Index_name_E table for the unhandled records, which are logged by the cartridge. The index is usable as it is, the noninterpreted records should be manually reviewed and corrected. The CsCartridge.Index_name_E table contains the rowid-s of the failed rows, and an error message, The user has to locate the failed rows by the rowid, and correct the errors. 3. If an exception is thrown by ORACLE, which is not handled by the cartridge, then the index creation results in an ORA-xxxxx message, and a call stack. If this happens, then the index is marked by Oracle as LOADING/FAILED/UNUSABLE, and the only command a user can execute regarding the index is the ALTER INDEX REBUILD command. The following: ALTER INDEX ixname REBUILD PARAMETERS('CONTINUE_POPULATI NG');
will attempt to continue processing the input data. If this process fails repeatedly, it is recommended to call support at CambridgeSoft. It may also be worth trying the following alternative:
DROP INDEX ixname FORCE; -- to remove the index even if it is in LOADING/FAILED/UNUSABLE state CREATE INDEX ixname ON tab(fld) INDEXTYPE IS CsCartridge.MoleculeIndexType PARAMETERS('SKIP_POPULATING=YES'); UPDATE tab SET fld=fld; COMMIT;
If the UPDATE fails, then the CsCartridge.schema_name_ixname_O.current_rowid points to the record which failed. The failed record should be deleted or corrected. After accomplishing this, the UPDATE and COMMIT commands must be executed again.
What to do if a Client Program Fails

Many different client program can use the features offered by the CambridgeSoft data cartridge. They may terminate unexpectedly due to a failure in the cartridge. In this case most likely CambridgeSoft has to be contacted to investigate the problem, and find a resolution. To help us to this we ask, that the user try to reproduce the problem, but before attempting to reproduce execute the
ALTER INDEX index_name PARAMETERS('TRACING=YES');
and/or the
ALTER INDEX index_name PARAMETERS('MONITORING=YES');
command(s). If tracing is on, then the cartridge keeps a log of all the executed SQL statements in a trace file. The name of the trace file is trace.txt, and it is located in a directory which name is a concatenation of the schema name and the index name connected with
CS Oracle Cartridge233 Troubleshooting
an underscore. This directory in turn is in the system temporary directory. The system temporary directory is usually C:\WINNT\TEMP on windows systems, and the /tmp directory on UNIX systems. The contents of this file can greatly simplify the bug fixing process. If monitoring is on, then the cartridge maintains a call stack. More precisely a part of the real call stack with selected items from the parameter lists a function or method is called with. This file is stored in a directory called 'CsCartridge_PIDS', and this directory is in the system temporary directory. The file name is a number, which reflects the actual PID of the process, and the extension of the file is .txt. That monitor file is not really updated, when control is passed to a function, but when an SQL statement is executed. But nonetheless it might help to resolve the problem with or without CambridgeSoft's support personnel. Both the trace file and the monitor file are readable ASCII text files. The contents of the monitor file can be displayed by the SELECT CsCartridge.MONITOR from DUAL; statement. The most detailed output of a DML process can be acquired by setting the global LOGGING on by the UPDATE CsCartridge.Globals SET value = 'YES' WHERE id = 'LOGGING'; This setting affects every domain index maintained by the CambridgeSoft Oracle Cartridge. If set, then the CsCartridgeTrace.txt file in the C:\WINNT\TEMP directory will contain a very detailed log of functions called by the cartridge. This ascii text file also may be valuable when an error is to be tracked. If the execution of a SQL statement fails, or other serious problem arises the cartridge records information into the trace file even if TRACING was set to NO.
Setup Problems
ORA-28575 unable to open RPC connection to external procedure agent
When using the cartridge for the first time some users may experience the above error message. This message is the consequence of some mistake in the ORACLE server's setup. It is issued by the Oracle server, when it tries to load the extproc program, an agent which in turn loads the CsCartridge.dll (Windows) or the CsCartridge.so (Unix) program into memory. Oracle uses the extproc program (called external procedure agent) to load external binaries into memory because, the binary executables written by independent developers are not trustworthy enough to be loaded into Oracle's main address space. The executables can crash, thus shutting down the whole service. Loading into the address space of the extproc agent, is optimal because even if it crashes, it just crashes the client program which triggered its use, leaving the server intact. To find the extproc program in the Oracle installation, Oracle uses two configuration files:
listener.ora tnsnames.ora
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If those files are missing, or are not set up correctly, or if the extproc program is missing, then Oracle can not load the extproc program, and issues the ORA-28575 error message. The listener.ora and the tnsnames.ora files are located in the $ORACLE_HOME/network/admin directory. The listener.ora file is used, whenever the listener service is restarted. On Windows computers it is started usually when the computer starts up, and can be stopped/started using the "services" list from the Control Panel. On Unix computers they are controlled by the $ORACLE_HOME/bin/lsnrctl command.
CambridgeSoft Troubleshooting
listener.ora
The listener.ora file must have the following lines LISTENER = (DESCRIPTION_LIST = (DESCRIPTION = (ADDRESS_LIST = (ADDRESS = (PROTOCOL = IPC)(KEY = EXTPROC)) ) ) ) SID_LIST_LISTENER =(SID_LIST = (SID_DESC = (SID_NAME = PLSExtProc) (ORACLE_HOME = C:\oracle\ora81) (PROGRAM = extproc) ) ) where the value of the KEY symbol may be different than EXTPROC, but must be the same as the value of the KEY symbol in the tnsnames.ora file. The same is true for the value of the SID_NAME symbol, but that it is always PLSExtProc. If this text file is changed, then the listener service must be restarted. Oracle 8 and 9 do not seem to use the ORACLE_HOME entry. Instead, Oracle uses the ORACLE_HOME entry in the Windows registry, and the ORACLE_HOME environment variable on UNIX systems. So, when the listener is started, then the ORACLE_HOME must point to the directory, where the Oracle server is installed. That usually reads, like /mount-directory/app/oracle/product/version If in doubt: Execute the statements in the same environment, where the listener is started:
ORACLE_HOME = /mountdirectory/app/oracle/product/versi on export ORACLE_HOME Start the listener with the command $ORACLE_HOME/bin/lsnrctl Check status, and stop/start it according to its status.
tsnames.ora
The tnsnames.ora file must have lines as follows: EXTPROC_CONNECTION_DATA.CAMS OFT.CO M = (DESCRIPTION = (ADDRESS_LIST = (ADDRESS = (PROTOCOL = IPC)(KEY = EXTPROC)) ) (CONNECT_DATA = (SID = PLSExtProc) (PRESENTATION = RO) ) ) The value of KEY must be the same as the value of KEY in the listener.ora file, and the value of SID must be the same as the value of SID_NAME in the listener.ora file.
ORA-06520 PL/SQL: Error loading external library

If the communication with the extproc agent is operable the user still can be faced with the above error message. This happens if the extproc agent cannot load the CsCartridge.dll or the CsCartridge.so into memory. The reason is either:
the CsCartridge library does not exist OR some libraries it depends on do not exist.
CS Oracle Cartridge235 Troubleshooting
Dependencies
The CsCartridge library depends on every platform on the existence of OCI library. (extension may be .dll, .so, .sl) In addition to the OCI library. (extension may be .dll, .so, .sl), please see See Oracle Cartridge Dependencies by Operating System on page 325. for a list of required files on the specified Operating Systems. In addition to the file requirements, the environment must be set up so that the system can find them. These issues are explained in detail in the system manuals of the actual platform. The AIX version of the cartridge is dependent on libraries from IBM's Visual Age C++ development system. The libC.a library is part of the Visual Age C++ development system. libclntsh.a must be
converted into a simple shared library as explained in the pre-installation activities for AIX. The remaining libraries are regular system libraries.
Using ADO
Microsoft's ADO is a convenient way to write client programs utilizing the cartridge. To create an Oracle service on any client computer, the Oracle client tools must be installed, and the Net8 assistant program must be used to create a service by entering the following information:
Net Service Name: any valid string would do
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(this string must be used in ADO) Protocol: TCP/IP Host Name: a computer running the Oracle server Port Number: 1521 (Oracle 8i) Service Name: the service name on the server.
DIM c as ADODB.Connection set c = new ADODB.Connection ServiceName = "" Rem the name of Oracle service UserName = "" Rem user name Password = "" Rem password s = "Provider=OraOLEDB.Oracle.1;Persist Security_ Info=False;Data Source=" + ServiceName + ";" s = s + "User ID=" + UserName + ";" s = s + "Password=" + Password c.Open s Dim r as ADODB.Recordset Set r = c.Execute("SELECT * FROM moltable WHERE_ CsCartridge.MoleculeContains(mol, 'c1ccccc1','', '')=1"); Rem process the recordset c.Close
NOTE: When using Microsoft ADO data controls to access the cartridge, the CursorLocation property must be set to adUseServer. Otherwise data updates will fail, if the structure field is larger, then 4000 bytes.
CambridgeSoft Dependencies
Example of passing large queries

Dim r As ADODB.Recordset ChemDrawCtl1.DataEncoded = True ' b64 encoded cdx is required Dim s As String s = ChemDrawCtl1.Data("cdx") ' get the cdx document from the ChemDraw ActiveX control Dim com As ADODB.Command ' create a new ADODB.command Set com = New ADODB.Command Rem now build the sql string step by step, and create the corresponding parameters as well Rem the query data will be passed as an array defined in CsCartridge Rem sql = "Select " + idSelect ' idSelect contains the column name to be selected sql = sql + " from " + TableName ' from table sql = sql + " where CsCartridge.MoleculeContains(" + StructName '1st param is col name of chem struct sql = sql + ", CsCartridge.Xarray(" ' second param is an array of string literals n = Len(s) ' number of characters in the query structure pos = 1 ' starting position i = 0 ' starting index segmentLength = 4000 ' the length of a segment of the query string While pos < n ' there is remaining part of a query string to be passed si = Mid(s, pos, segmentLength) ' get one 4000 character chunk of the query Dim v As Variant v = si ' create parameter expects the value as variant parname = ":xpar" + CStr(i) ' parameter name as a stem and running index Dim par As ADODB.Parameter ' create the parameter Set par = com.CreateParameter(parname, adLongVarChar, adParamInput, Len(si), v) com.Parameters.Append par ' append it to the parameters accompanying the command sql = sql + parname ' the sql command will have a new parameter pos = pos + segmentLength ' move the position If pos < n Then ' if there is data still to be processed sql = sql + "," ' add a comma to separate the parameters End If i = i + 1 Wend sql = sql + "),'FULL=NO')=1" ' finish up the sql text com.CommandType = adCmdText com.ActiveConnection = c com.CommandText = sql ' set the CommandText field of the command object Set r = com.Execute ' and now the command is ready to be executed
Custom Screening
Custom screening is a tool for a database administrator to affect the processing of a SELECT statement. The database administrator can define
any structure to screen the database when processing a substructure search. If a screen structure is a substructure of a query structure, then the processing of that particular query will be faster. There is no recommendation on how to choose
CS Oracle Cartridge237 Custom Screening
custom screens. Choosing them should be based on the particulars of the database and expected interest of the users. Custom screening can be defined by calling the MolScreen procedure.
CALL CsCartridge.MolScreen('schema_name ', 'table_name', 'field_name', 'index_name', 'smiles_or_encoded_cdx', 'second_part');
Optimizing client programs for version 9

Client programs usually use ADO to retrieve data from the database, and in the case of presentationtier programs present the results to the user, or in middle-tier programs, the result set is passed further to the presentation layer. A typical program looks like the skeleton program below:
dim rs as recordset set rs = adoConnection.Execute "SELECT ..." while not rs.eof do rem deposit result from the result set into a placeholder for the presentation layer rs.MoveNext wend rem Do the presentation.....
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where
schema_name is the schema the table is owned
by table_name is the name of the table to be custom indexed field_name is the name of the field containing chemical information field_name is the name of the index used to index the chemical information smiles_or_encoded_cdx is the substructure depicted by a smiles string or an encoded CDX document. second_part is the second 4000 bytes of an encoded CDX document. All of the names must be enclosed by single quotes. The strings are not processed by Oracle, but rather the MolScreen procedure. Optionally an ALTER INDEX ... PARAMETERS('SYNCHRONIZE') statement also may be executed. For example: CALL CsCartridge.MolScreen('MySchema', 'molecule', 'mol', 'mx', 'Oc1ccccc1', ''); COMMIT; ALTER INDEX mx PARAMETERS('SYNCHRONIZE'); This will improve the speed of the substructuresearch of phenol derivatives.
This strategy was the simplest and best possible strategy when version 2 of the cartridge was used. When using version 9 a better user experience can be achieved with somewhat more sophisticated programming. It should be noted, that in version 2 the execution of the adoConnection.Execute statement was slow because the result set was generated during the execution of that statement, and the MoveNext statements were almost instantaneous. In version 9, the execution of the adoConnection.Execute statement is fast, and most of the calculations are postponed until the MoveNext statements are executed. With the programming schema above the user can not communicate with the program until the whole recordset is deposited into the presentation layer. A much better user experience can be created if the client program just executes as many MoveNext statements as many records are presented in one page and data to be presented on the next page is retrieved only when the user hits the Page Down
CambridgeSoft Optimizing client programs for version 9
button, or clicks on the scroll bar pr any appropriate user control. The result is presented much faster than with the simple scheme above. An even better user experience can be achieved if the data retrieval and the presentation is executed in a different thread. Then while the user can manipulate the part
of the recordset already transmitted to the client computer, and the data processing still goes on in a background thread. The program should look like this
dim rs as recordset set rs = adoConnection.Execute "SELECT ..." if not rs.eof Rem display the data in the recordset and store it into a buffer end if docontinue = true while docontinue rem wait for user action requesting next or previous record or finishing process if pagedown then rem if record is already in the buffer, then display, otherwise rs.MoveNext first end if if pageup then rem show previous record already in the buffer end if if home then rem show the first record end if if end then rem display a message, that this will be slow while not rs.eof do rem store data into buffer rs.MoveNext wend rem show the last record end if if cancel then docontinue = false end if wend
Bulk Loading
Previous versions of the Oracle cartridge allowed suspending and resuming the building of the index tables by the cartridge to speed up large inserting large amount of data into an indexed table. From version 9, the cartridge will be always in "suspended" mode. This means, that new data stored into an indexed field will not be immediately
fully processed, but will be stored, made available for searching, and marked for later processing. This processing will take place, when the
ALTER INDEX index_name PARAMETERS('SYNCHRONIZE')
statement is executed. Substructure search will be reasonably fast as long as the number of partially processed records does not exceed about 50000. After that synchronizing is recommended.
CS Oracle Cartridge239 Optimizing client programs for version 9
Executing the statement above is time consuming, but inserting, or updating records in a table will be much faster then in earlier versions of the cartridge. Version 9 also recognizes the
PARAMETERS('SUSPEND') and PARAMETERS('RESUME') clause in an ALTER INDEX
Schema Overview
All the information the cartridge maintains is stored in the CsCartridge schema. For every index created by the cartridge, 8 tables are created in that schema. The names of these tables are generated from the name of the schema the indexed table resides in, and from the name of the index. Table names are maximized at 20 characters, so the cartridge must require, that the name of the schema and the index together can not be longer, than 16 characters.
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statement. The interpretation, though, is different. The setting affects only the current session. When in suspended mode, no insert is executed, but held up in a buffer memory. When the
PARAMETERS('RESUME')
Tables Related to an Index

The following tables are created: In the following list of tables, sch represents the schema name, and ix represents the index name.
sch_ix - stores most data, most frequently used
call is made, then all the upheld data is stored into the cartridge table in one single round-trip to the server, thus improving speed. Using this feature can be reasonable in applications, where data maintenance is not interactive and is performed in waves of batches.
Data Structures
Whenever a new record is stored in a table, is deleted from a table, or an indexed field is modified, by the Oracle Cartridge, Oracle makes a call to the cartridge passing the rowid of the affected record and the value of the indexed field. The cartridge processes this data, and stores the results in tables in the CsCartridge schema to improve search speed. The major steps of this process are:
attempt to interpret the passed binary or
for substructure search sch_ix_XY - where X refers to the screen type, and Y to the kind of data, stores screening dayta sch_ix_E - stores error messages for a longer process sch_ix_O - stores options set by the end user sch_ix_T3 - stores temporary 3d screening data until synchronization
The sch_ix Table

The following fields are part of the sch_ix table:
RID The rowid of the indexed record in the
character stream as a ChemDraw document extract the chemically meaningful part of the ChemDraw document into a ccMolecule and molstorage structure creating screens used in substructure search for the ccMolecule serializing the molstorage structure for storage storing the generated information
original table. This is returned to ORACLE as a result of a search MOLSTGLENGTH the size of the stored molstorage information. MOLSTG1 The first 2000 bytes of the serialized molstorage if it is shorter than 4001 bytes, otherwise empty MOLSTG2 The second 2000 bytes of the serialized molstorage if it is shorter than 4001 bytes, otherwise empty
CambridgeSoft Data Structures
MOLSTG The serialized molstorage created
from the CDX document if it is longer than 4000 bytes, otherwise empty CTEXT The canonical code of the structure in the CDX document FORMULA The chemical formula of the structure MOLWEIGHT The molecular weight of the structure NC number of carbon atoms in the structure NN number of nitrogene atoms in the structure NO number of oxygene atoms in the structure NHAL number of halogenes in the structure NOTH number of other elements in the structure ISNEW either 'Y' for records not synchronized yet, or NULL for synchronized records. SCREENS_NORMAL a binary representation of the regular screens used for substructure search SCREENS_SIMILAR screening bitvector better suited for similarity searches SCREENS_FULLEXACT screening bitvector used when full structure search is executed considering tautomers as well SCREENS_SKELETAL screening bitvector used when substructure search is executed considering tautomers. MOLSTG_REACTANTS The serialized molstorage of reactants if the CDX document is a reaction SCREENS_REACTANTS screens of reactants if the CDX document is a reaction MOLSTG_PRODUCTS The serialized molstorage of products if the CDX document is a reaction SCREENS_PRODUCTS screens of products if the CDX document is a reaction
The RID field stores the rowid of the record indexed by the cartridge. The value for RID is passed to the cartridge by ORACLE. The MOLSTG field contains all the chemically valuable information from the CDX document stored in a row referred to by the RID field. This field is used when the cartridge has to do atom by atom matching during substructure search. It's a highly compressed format for better retrieval speed. The CTEXT field is the canonical code of the chemical structure, and used for identity search. Identity search is much faster than full structure search. The FORMULA, NC, NN, NO, NHAL and NOTH fields are used for formula search. the MOLWEIGHT field is used for molecular weight searches. Any one of the SCREENS_NORMAL, SCREENS_SIMILAR, SCREENS_FULLEXACT and SREENS_SKELETAL columns may be missing if during index creation the particular feature was not requested. When a program executes a SQL statement referring to the MoleculeContains operator, the cartridge generates its own screening statement retrieving the molstg information from the sch_ix table. The subset of records are selected by using the screenbits of the query and one of the screens from the sch_ix table. The sch_ix_NR or other inverted screen table also may be used if exist to increase speed of the retrieval of screening data. The generated SQL statements can be found in the CsCartridgeHistory.txt file located in the system temporary directory.
The sch_ix_NR Table

That table is the inverted screen table for regular screens. It consists of the following columns:
BIT screen bit number RID rowid of the indexed record
This table is partitioned by the bit column. It has 256 partitions related to each of the screen bits generated by the screening algorithms.
CS Oracle Cartridge241 Data Structures
The sch_ix_NC Table

This table contains the cardinalities of the particular screen bits. It consists of the columns as follows:
sch_ix_O table, the cartridge might not throw an exception, but instead continues operation and stores the reason of the error into the TEXT field.
BIT screen bit number COUNTS cardinality of the screen bit
The sch_ix_3 Table

The following fields are part of the sch_ix_3 table:
ATOMPAIR is a string of 2 or three element
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This table has 256 rows.
The sch_ix_NX Table

Screen cross reference table for regular screens. It has the following columns:
BIT1 screen bit number BIT2 screen bit number COUNTS cardinality of the screen bit
This table has 64K rows for each possible combination of BIT1 and BIT2 values.
The sch_ix_SR, sch_ix_SC, sch_ix_SX Tables

Same contents as the tables above for screens for similarity search.
symbols RIDSVAL nested table containing the rowids and distance or angle information of the indexed records. This table contains information used for fast 3d screening. The ATOMPAIR field contains two element symbols in a string for distances, and three element symbols for angles. The RIDSVAL nested table contains all the rowids and values for the particular ATOMPAIRs. For a two element ATOMPAIR the values are the distances in Angstroms, and for three element ATOMPAIRs, the angle value in radians is stored in the value field.
The sch_ix_O Table

The following fields are part of the sch_ix_O table:
ID this field is a string containing one of a few
The sch_ix_FR, sch_ix_FC, sch_ix_FX Tables

Same contents as the tables above for screens for tautomer full exact search.
The sch_ix_KR, sch_ix_KC, sch_ix_KX Tables

Same contents as the tables above for screens for tautomer substructure search.
predefined keywords VALUE this field contains the corresponding value. In most cases the accepted values are YES and NO. The list of accepted keywords follows:
RAISE_ERROR to control if the cartridge
The sch_ix_E Table

The following fields are part of the sch_ix_E table:
RID rowid of the indexed record TEXT explanation of the error
This table is supposed to be empty. If an error is detected by the cartridge it usually throws an exception. Depending on the content of the
should raise an error when encountering an illegal input, or store the information in the _E table CACHE_RESULTS controls whether the cartridge saves results of substructure searches. If the same query is repeated, then the cartridge can return the existing hit list much faster. This cache is emptied fully if the table changes, so it is mostly recommended for readonly databases.
REACTION_SEARCH to direct the cartridge
whether reactions should be evaluated when screens are generated. NORMAL to direct the cartridge whether maintain normal screens SIMILAR to direct the cartridge whether to maintain screens for similarity search. FULLEXACT to direct the cartridge whether to maintain screens for full structure search considering tautomers. SKELETAL to direct the cartridge to maintain screens for substructure search considering tautomers. THREE_D to direct the cartridge to maintain screens for 3d screening. For the NORMAL, SIMILAR, FULLEXACT, SKELETAL keywords the acceptable values are NO, YES and INDEX. In the case of NO no screens of that particular kind are stored at all. In the case of yes a bitmap field is stored for the screen, and in the case of INDEX an inverted table is maintained for that kind of screen. SYNCHRONIZATION controls if the index is synchronized all the time or if it needs occasional manual synchronization. THREE_D_RESOLUTION can be NO or YES, and LOW or HIGH. If it is low, then less data is stored. REACTION_SCREENING controls if the cartridge keeps screening information for the starting reactants and the final products of a reaction separately from the main screen. It can be useful in a reaction database, when queries are regularly restricted to reactants and/or products. There is one record in the sch_ix_O table for every keyword. It is not recommended to edit this table any way manually. The contents of the table should be changed using the ALTER INDEX command.
Administrative Tables
ALL_CSC_INDEXES Table
The ALL_CSC_INDEXES table lists all the indexes created by the cartridge.
OWNER name of the owner's schema INDEX_NAME name of the index TABLE_NAME name of the table COLUMN_NAME name of the indexed
column COLUMN_TYPE 'CLOB' or 'BLOB'
CUSTOM_SCREENS Table
The CUSTOM_SCREENS table contains the list of custom screens applied to every new created index. After installation, this table contains the SMILES string for benzene and cyclohexane. The administrator can add new items to this list, or remove the ones there.
SMILES the smiles string of the custom
screen.
GLOBALS Table
The GLOBALS table contains information globally representative to the cartridge.
ID identifier of an entry VALUE value of an entry Currently the following identifiers are stored in
the GLOBALS table: ID VALUE VERSION current version number LIBRARY_DIRECTORY the directory the CsCartridge shared library is stored USE_THREADS YES or NO (default YES) The cartridge generates threads in an attempt to improve the speed of substructure search. On some platforms that resulted in worse
performance. The administrator can control the behavior of the cartridge by the USE_THREADS parameter. STORE_INPUT_DATA YES or NO (default NO) If the STORE_INPUT_DATA parameter is set to yes, then the cartridge stores the data being processed into a file. The file's name is CsCartridgeData, and it is stored normally in the C:\WINNT\TEMP directory on Windows systems, and into the /tmp directory on UNIX systems. TRACING YES or NO or string (default NO) If the TRACING parameter is set to YES, then the cartridge keeps a log in the CsCartridgeTrace.txt file, which is located in the C:\WINNT\TEMP directory on Windows systems, and into the /tmp directory on UNIX systems. These files can be used for troubleshooting. The value of this parameter must be changed directly by an UPDATE CsCartridge.Globals SET value = 'YES' WHERE id = 'TRACING'; statement. The value of the string depends on the version and build number of the cartridge. The string is a concatenation of different trace selector. The tracing settings select certain features for tracing. The most commonly used is likely the 'Statement::Execute' trace selector selecting trace for every SQL statement executed. Other selectors: Statement::LobWrite DMLClass::ProcessInsert::data DMLClass::ProcessDelete CStack::push If TRACING=YES is set, the program execution slows down dramatically. MONITORING YES or NO (default YES)
monitoring is set, then program execution can be monitored by the MonitorCartridge.exe program, which is a stand-alone program running on Windows platforms, which shows the "call stack" of execution. QUIT_INDEX_CREATE number (default 10) The number of attempts the cartridge makes when creating an index and a crash is detected. Normally a cartridge creation ends in an error message and no data structures stored if there were more than number crashes. A "crash" may happen if a document can not interpreted any way at all. The cartridge catches and registers those exceptions, and continues building the cartridge tables. Those exceptional documents are rare, that's why the small default number. This default number is also a protection against an error if an index is to be built on a column, which does not contain any meaningful chemical structures. SYNCHRONIZE_BUFFER number (default 1000) this number instructs the cartridge about the number of rows processed in one step during synchronization. This number has profound effect on the speed of synchronization. Though it can not be increased without concerns to Oracle's inherent limitations, which may vary from installation to installation. With 1000 records processed in one step, the cartridge uses about 45MB of memory. With 200 records it uses only 11MB.
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Data stored outside of Oracle

The cartridge stores some auxiliary information outside of the Oracle database. It creates files in the "/tmp" directory on UNIX systems, and in the directory the GetTempDir() Windows system call returns on WIndows machines.
The CsCartridgeData file

This file contains the data being processed while storing, updating or deleting a record from a table. If the program crashes, it might be useful to open an analyze the ChemDraw document to help with troubleshooting the problem.
CS ChemFinder Custom Elements.txt CS Isotopes Table.txt StructureToName.dat These files are located in the $ORACLE_HOME/bin/instance_name directory on Windows computers and in the $ORACLE_HOME/lib/instance_name for UNIX computers, where instance_name is "CsCartridge", or the name entered at the instance name field on the installer dialog.
Program files
The cartridge consists of the following files: CsCartridge.dll (Windows), CsCartridge.sl (HPUX), CsCartridge.so (all other UNIX systems)
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246CS Oracle Cartridge CambridgeSoft Data Structures
Scientific Databases
CambridgeSoft offers a library of chemical information databases, containing compounds and chemical reactions. Users may search over the databases with tools provided in the ChemOffice software suite. The Scientific Databases bring a wealth of chemical information to your desktop. Searching through these databases by chemical names, structures, physical data, suppliers, safety data, and literature references becomes as easy as clicking a mouse. All of the databases are available to the user on CD, for individual use. Section VI: Sourcing and Safety Data Chapter 16: ChemACX Chapter 17: ChemMSDX Chapter 18: Sigma-Aldrich MSDS Chapter 19: EH&S Enterprise Section VII: Reaction and Synthesis Data Chapter 20: ChemRXN Chapter 21: ChemSynth Chapter 22: ChemReact
Available Formats
Subscriptions and ChemOffice Enterprise Based Databases
The following databases are available as a ChemOffice Enterprise application and/or webbased subscription as well as on CD: The Merck Index Ashgate Drugs Traditional Chinese Medicines ChemACX ChemINDEX NCI AIDS MediChem ChemReact ChemSynth The databases available through a subscription or the ChemOffice Enterprise applications use the same technology as other WebServer applications.
ChemFinder.Com Gateway
The ChemFinder.Com Gateway allows users to search all of CambridgeSoft's Scientific Databases in one easy step. Searchable fields include Structure, Sub-structure, Chemical Name and CAS Number. The search results will contain the number of search results, which databases the results are found in, and present hyperlinks to the appropriate database record for review.
Database Offerings
Section V: Reference Data Chapter 9: The Merck Index Chapter 10: MediChem Chapter 11: Traditional Chinese Medicines Chapter 12: Ashgate Drugs Chapter 13: ChemINDEX Chapter 14: NCI Chapter 15: AIDS
Scientific Databases247 ChemFinder.Com Gateway
For more information about general ChemOffice Enterprise application concepts, please see ChemOffice Enterprise on page 191.
CD Based Databases
The following chemical databases, available on CD, are described in this section:
The Merck Index Ashgate Drugs Traditional Chinese Medicines ChemACX ChemSCX ChemMSDX ChemINDEX ChemRXN NCI AIDS ChemReact68 ChemSynth The chemical Databases work with ChemOffice, an integrated suite of software tools for chemists with personal computers. The ChemOffice applications, ChemFinder, ChemDraw, and Chem3D, help ChemInfo deliver information. ChemOffice includes the following: ChemFinderThe primary application used by ChemInfo. It provides the engine for searching the data the forms and tables for viewing it. Relational databases are supported by ChemFinder. ChemDrawThe chemical drawing standard allows structures to be drawn and edited in ChemFinder. It can represent individual structures or chemical reactions, complete with atom-to-atom mapping and absolute or relative stereochemistry, for detailed structure-based queries.
Chem3DA molecular modeling and computations application offers molecular mechanical and quantum mechanical computational capability. Featuring an intuitive graphical user interface, it displays molecules as three-dimensional models that you can rotate and translate to reveal details of a structure not evident in two dimensions.
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Installation
The databases do not have to be installed; they can be accessed directly from the CDs. If the databases are accessed from a CD, they are Read-only. If you have sufficient hard disk space, you can copy the databases from the CDs. This not only makes searching faster but allows you to edit the databases, except ChemACX, ChemSCX, The Merck Index, Ashgate Drugs, and Traditional Chinese Medicines.
Using Scientific Databases

The CD based databases use ChemFinder to deliver data to the user. ChemOffice Enterprise on page 191 contains a tutorial that gives an overview of using ChemFinder with CambridgeSofts Scientific Databases. ChemFinder Tips Some databases are provided with customized applications. If the database you are using does not include such an application:
1. Insert one of the ChemInfo CD-ROMs into
your CD drive.
2. Start ChemFinder. 3. From the File menu, select Open and select a
form for one of the databases. Alternatively, you can explore the CD-ROM with the Windows Explorer and open ChemFinder by double-clicking one of the ChemFinder form icons.
248Scientific Databases
CambridgeSoft Available Formats
Help Additional sources of help for using ChemInfo include the following: Quick Reference Card ChemFinder and ChemDraw online help ToolTips Status Bar CambridgeSoft Technical Support Online Help Access to online help is provided from the ChemFinder and ChemDraw help menus. To learn about using the online Help: From the Help menu, choose How to Use Help.
To access online Help: From the Help menu, choose Contents. ToolTips ChemFinder and ChemDraw provide ToolTips as an additional form of online Help. Rest your pointer on a tool to display a message box with a brief description of the tool.
Status Bar The bottom left corner of the ChemFinder and ChemDraw Status Bars display a slightly more detailed description of the tool icons.
Scientific Databases249 Available Formats
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250Scientific Databases CambridgeSoft Available Formats
Section V: Reference Data

This section provides information about CambridgeSofts Reference Data Chemical Databases. The following databases comprise CambridgeSofts Reference Data Offerings:
The Merck Index MediChem Traditional Chinese Medicines Database Ashgate Drugs ChemINDEX NCI AIDS
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Chapter 9: The Merck Index

The Merck Index is a one-volume encyclopedia of chemicals, drugs and biologicals that contains more than 10,000 monographs. The entries are not a listing of Merck & Co., Inc. products, but rather cover a wide range of compounds that have been selected by the editors on the basis of present or historic importance and interest. Since the publication of its Twelfth Edition in 1996, over 5,000 monographs have been significantly revised and updated. Each monograph is a concise description of a single substance or a small group of closely related compounds. The information provided includes chemical, common and generic names, trademarks and their associated companies, Chemical Abstracts Service (CAS) Registry Numbers, molecular formulas and weights, physical and toxicity data, therapeutic and commercial uses, citations to the chemical, biomedical and patent literature, and chemical structures. other attributes can also be used in the search. As with the other ChemInfo databases, The Merck Index also allows searching by structure, substructure, and similarity, all of which are virtually impossible when using the printed edition alone. Organic Name Reactions, and Additional Tables are also available to search through.
How Is It Useful?
For more than 100 years, the printed edition of The Merck Index has been the premier reference for validated data about many compounds of general interest. The subjects covered include human and veterinary drugs, biologicals and natural products, agricultural chemicals, industrial and laboratory chemicals, and environmentally significant compounds. The electronic version includes all of the information in the printed edition, and enhances it by allowing direct and rapid searching over all data fields. Where the printed edition offers indexes of names and CAS Registry Numbers, the electronic version allows the user to enter them as search terms, and takes you directly to the relevant monographs without having to flip through a bulky printed volume. Physical properties as well as many
About The Merck Index

Availability:
CD-ROM Internet Subscription Intranet using ChemOffice Enterprise
The Merck Index253 How Is It Useful?
Number of Monographs
Included in 13th Edition: 10,250 Added since 13th Edition: 230
Compound Searching
The Compound Searching section allows searching for compounds by physical properties, compound attributes, and structure. The Merck Indexs compound searching form acts much like the other search forms found in ChemOffice Enterprise applications. For more information about searching, please see Searching ChemOffice Enterprise Applications on page 194. To access the Compound Searching section: Click on the Compound Search Tab found at the top of the page. The Compound Search Form appears
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Archived from 12th Edition: 540
Using The Merck Index Online

The Merck Index is split into 5 tabs:
Introduction Compound Searching Organic Name Reactions Additional Tables System Requirements
To search for compounds: The Introduction and System Requirements tabs deliver important information about The Merck Index, compatibilities, and how to navigate the site. Each of the other tabs allow the user to access three major sections of The Merck Index: Compounds, Organic Name Reactions, and Additional Tables.
1. Enter the desired information into the fields
provided in the Compound Searching Form. To search without using the structure search, click on the Click Here for Non-Plugin Searching link.
2. Click
Search.
254The Merck Index
CambridgeSoft Using The Merck Index Online
A list of search results appears
are meant to be informative, but not comprehensive. The descriptions are composed of the following:
name(s) associated with the reaction the original and/or primary contributor(s)
connected with the discovery and/or development of the reaction

a concise description of the transformation a reaction scheme key references cross references to other ONR based on
To view the contents of a particular record in the list, click Show Details. The complete contents of the chosen record is displayed.
commonalities. Useful abbreviations can be found on the mainpage of this section. To access the Organic Name Reactions section: Click on the Organic Name Reactions Tab found at the top of the page. The Organic Name Reactions homepage appears.
Organic Name Reactions

The Organic Name Reactions (ONR) section contains a list of reactions which have come to be recognized and referred to by name within the chemistry community. The reaction descriptions
The left frame of the homepage contains 2 tabs: Browse and Search. The Browse Tab lists all reaction names included in the Merck Index. To view the contents of a record, scroll to the appropriate reaction and click on the link.
The Merck Index255 Using The Merck Index Online
The Reaction details appear in the right frame
Click on the Additional Tables Tab found at the top of the page. The Additional Tables homepage appears.
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The Search Tab allows the user to enter a free text search for the appropriate reaction. To search for a reaction:
3. Enter keywords into the text box available. 4. Click
Search. A list of matches is returned.
5. Click on the link for the appropriate reaction.
The Reaction details appear in the right frame. For tips about entering a free text search, click on the Tips for Searching link found below the free text search textbox under the Search Tab.
To view a particular table, click on the link provided. All tables are available in PDF format and therefore require the Adobe Acrobat Reader to view. If you do not have the Adobe Acrobat Reader installed, click on the link provided to obtain a free copy.
Logging Off
You can end your session with The Merck Index at anytime by logging off. To log off:
Click
Log Off.
Additional Tables
The Additional Tables section lists multiple tables available to view by the user in PDF format. To access the Additional Tables section:
256The Merck Index
CambridgeSoft Using The Merck Index Online
Chapter 10: MediChem

Curated by GVK Biosciences, MediChem contains information on over 600,000 compounds selected from top medicinal chemistry journals. Each compound has been evaluated in the literature for some medicinal property. Included are literature references along with biological activity information such as bioassay and target, activity. The compounds selected for inclusion in MediChem have been evaluated in the literature for important biological and or medicinal properties. The database consists of chemical information (2D structure, molecular weight, formula, name, SMILES), literature reference (authors, affiliations, title, journal, volume, page, etc.), and biological activity information (bioassay, target, activity, etc.).
About Medichem
Availability: Internet Subscription Number of compounds: >650,000
Using MediChem Online

MediChem is a unique medicinal chemistry database containing over 500,000 compounds in more than 650,000 records selected from the top 25 medicinal chemistry journals published since 1959.
Types of assays included in MediChem are ADME (A), binding to a target (B), binding to a mutant target (B/M), functional assays using either a cell based or in vivo animal model (F), toxicity (T), and others (O). Data records are also identified by target platforms, such as Kinase, G-Protein-coupled Receptor (GPCR), Protease, Ion Channel, Nuclear
MediChem257 About Medichem
Hormone Receptor (NHR), and more. These database fields are easily populated via drop down selections for easy querying. Other database fields include compound name, molecular formula (range search enabled), molecular weight (range search enabled), protein name, company name, journal reference fields (title, author, article title, journal, year, volume, etc.), PubMed ID, activity type and more. On the result pages, PubMed IDs are hyperlinked to the online PubMed record.
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258MediChem
CambridgeSoft Using MediChem Online
Chapter 11: Traditional Chinese Medicines

Compiled by NiceData, TCM has monographs for over 10,000 chemicals isolated from 4,636 natural sources used in traditional Chinese remedies. The monographs feature bio-activity data for many of the compounds, effects and indications of the medicines, English, Latin, and Chinese names for the natural sources, and over 2,000 references. Searching by chemical structure requires the use of ChemDraw or the ChemDraw ActiveX/Plugin, which is available for free from CambridgeSoft for the Internet subscription version, and is included with the runtime software on the CD-ROM and ChemOffice Enterprise versions. sources database. The enhanced search interface allows users to choose one or both methods. Users need to simply click the desired check box on the search form and then search away! (Note: The CDROM version allows the user to perform both searches independently.) The chemical substructure search shown, drawn in the ChemDraw Active X control, has a ring locant with the [N,O,S] label which allows for any of the three elements nitrogen, oxygen, or sulfur at that position.
About TCM
Availability:
CD-ROM Internet Subscription Intranet with ChemOffice Enterprise SD-File
Number of compounds: 10,458 Number of natural sources: 4,636
Using TCM with ChemOffice Enterprise

The Traditional Chinese Medicines database is designed to allow users to choose different views of the dataset, which can be called "Chemistry Space" and "Natural Sources Space". Some might wish to search over the chemical information database. Others will prefer searching over the natural The search found 165 records in "Chemistry Space", or 165 chemical compounds that contain the substructure that was searched. The search also found 175 records in "Natural Sources Space",
Traditional Chinese Medicines259 About TCM
which means that there 175 natural sources that contain a chemical compound with the substructure that was searched.
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The view of the search results are selected by the user by choosing the radio button next to the in the view results section of the screen. Selecting the Natural Sources radio button will display the results in Natural Sources Space. Search results from either view may be expanded. For example, selecting Show Details for the sixth record from the "Chemistry Space" result list will display the monograph for that record.
260Traditional Chinese Medicines CambridgeSoft Using TCM with ChemOffice Enterprise
The monograph contains chemical information about the compound, including when available, CAS numbers, synonyms, and physical properties. Also in the monograph is a list of all the natural sources containing the compound (in this case there is only one), along with the uses, effects and indications, English, Latin and Chinese names, and bio-activity when available. The bottom part of the monograph contains the references. All of the "Chemistry Space" monographs are cross referenced with the "Natural Sources Space" monographs. Clicking on the View Details hyperlink found after the natural sources section of the monograph will bring up the "Natural Sources Space" monograph for that particular source. This view repeats the information found about found in the "Chemistry Space" monograph, and then includes a list of all active chemical compounds that have been isolated from the source.
Each of the chemical compounds are cross referenced back to the "Chemistry Space" monographs, and can be accessed by clicking on the associated View Details hyperlink.
Traditional Chinese Medicines261 Using TCM with ChemOffice Enterprise
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262Traditional Chinese Medicines CambridgeSoft Using TCM with ChemOffice Enterprise
Chapter 12: Ashgate Drugs

Ashgate Drugs is fully searchable database created from the popular book, Drugs: Synonyms and Properties, published by Ashgate The online database has 7,922 drugs which are currently in common use worldwide. It includes all drugs approved by FDA prior to 2004. These drugs all have recognized applications, and are classified into one or more of 201 therapeutic categories. Each entry is accompanied by:
The CAS Registry Number and, as available, The Merck Index (13th Edition) monograph
About Ashgate Drugs

Availability:
CD-ROM Internet Subscription Intranet on ChemOffice Enterprise SD-File
Number of Record: 7,922 Key Fields:

Chemical Structure CAS Number The Merck Index (13th edition) Monograph
number The European Inventory of Existing commercial Chemical Substances (EINECS) number Each field is fully searchable. Thus an entry may be located on the basis of structure or substructure, synonyms, biological activity, physical properties or manufacturer. A key component of this reference is the extensive coverage of synonyms. The electronic version adds almost 70,000 synonyms and trade names that did not fit into print version bring the total number to nearly 100,000. This reference will be invaluable to research chemists, biologists, and physicians and to anyone interested in drugs who, starting with a single synonym for a drug, will be able to quickly find a thumbnail sketch of the essential information concerning that agent.
Number
EINECS Number Chemical name Molecular formula Synonyms, including tradenames Medical application Manufacturer Physical Properties
Using Ashgate Drugs on CD-ROM

When you open Ashgate Drugs in ChemFinder, the application starts in Monograph view. In this view, users can browse records using the navigation buttons on the ChemFinder Menu. To do a search, click on the Search Monographs button
Ashgate Drugs263 About Ashgate Drugs
Using Ashgate Drugs Online or with ChemOffice Enterprise

Ashgate Drugs is split into 4 tabs:
Introduction Compound Searching Browse System Requirements
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Data that can be searched includes chemical structures, synonyms, Chemical Abstracts Service (CAS) Registry Number; the European Inventory of Existing Commercial Chemical Substances (EINECS) Number; The Merck Index (Thirteenth Edition) Number; the physical properties of each compound; and the known biological activity and indicated applications. Search results are displayed in Monograph view and can be browsed using ChemFinders record navigation tools.
264Ashgate Drugs
The Introduction and System Requirements tabs deliver important information about Ashgate Drugs, compatibilities, and how to navigate the site. The Compound Searching and Browse tabs bring the Ashgate Drugs data to the user.
Compound Searching
The Compound Searching section allows searching for compounds by physical properties, compound attributes, and structure. The Ashgate Drugs compound searching form acts much like the other search forms found in ChemOffice Enterprise applications. To access the Compound Searching section:
CambridgeSoft Using Ashgate Drugs Online or with ChemOffice Enterprise
Click on the Compound Search Tab found at the top of the page. The Compound Search Form appears
The complete contents of the chosen record is displayed.
To search for compounds:

1. Enter the desired information into the fields
provided in the Compound Searching Form. for more information about a particular field. To search without using the structure search, click on the Click Here for Non-Plugin Searching link.
2. Click
Browse
The Browse Tab lists therapeutic categories in alphabetical order. Click on a link to view the record for compounds with the listed therapeutic category.
Search. A list of search results appears
To view the contents of a particular record in the list, click Show Details.
Chem & Bio Office Enterprise, Workgroup & Databases 2006 Ashgate Drugs265 Using Ashgate Drugs Online or with ChemOffice Enterprise
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266Ashgate Drugs CambridgeSoft Using Ashgate Drugs Online or with ChemOffice Enterprise
Chapter 13: ChemINDEX

ChemINDEX Ultra is a collection of chemical reference databases composed of the following databases: ChemIndex, BuckyBase, and NCI Cancer, and AIDS databases. The databases are found in the ChemINDEX DVD-ROM, and, except for Buckybase, are also available as Internet Subscriptions and on Intranets using ChemOffice Enterprise.
Supplier Catalog Name Vapor Pressure Synonym CAS Registry Number Boiling Point Melting Point Site ID
How Is It Useful?
This class of databases serves as an extensive chemical reference for finding general information about commonly used compounds, such as structure, name, molecular weight, CAS Registry Number, synonyms, and physical data (melting point, boiling point, vapor pressure, etc.). ChemINDEX Net contains active hyperlinks to WWW sites with further information about the compounds.
Using ChemINDEX Ultra on DVD-
About ChemIndex
Availability:
DVD-ROM as part of ChemINDEX Ultra Internet Subscription Intranet with ChemOffice Enterprise SD-File
Number of compounds: >78, 000 Key Fields:

Structure Formula ACX Number SC Number Molecular Weight
Each data field on this form is labeled. Melting points and boiling points are presented as three fields:
If only a single value is available, it is placed in
the first field. If a range is available, the low and high limits of the range are placed in the first two fields.
ChemINDEX267 How Is It Useful?
The third field is for a note, such as (dec) for
decomposes. Synonyms and hyperlinks are displayed in the subforms on the right side of the form. You must have an internet connection to use the hyperlink features. If you are connected to the internet, the GO button at the upper right connects to CambridgeSofts WWW server for this database. Click the button or one of the hyperlinks, and ChemInfo attempts to start your systems default web browser and direct it to the appropriate URL.
To view any of the buckyballs or building blocks as a 3-dimensional model using Chem3D:
Right-click the structure and select View Model.
Chem3D starts and displays the molecule.
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BuckyBase
The subfolder BUCKYBSE within ChemINDEX contains two databases. BUCKBALL is a file of 132 buckminsterfullerenes, and BUILDING is a file of 99 building blocks which can be joined together to make new or existing buckminsterfullerenes. Directories: buckybse, balls, building Filenames: Buckball.cfw, Building.cfw Number of compounds: 132 buckyballs; 99 building blocks Key Fields:
Structure Formula Molecular Weight Name
ChemFinder.Com
The webserver at www.chemfinder.com, is one of the most heavily used public-access chemical information site on the Internet. ChemINDEX is the ChemFinder database of small molecule information presented at this site. Many of the individual compound records also contain lists of hyperlinks (URLs) to other sites containing additional information about the compound. To go to a site, click its link. The default web browser on your system will be activated and directed to the target URL.
Using ChemINDEX With ChemOffice Enterprise or Online

ChemINDEX, available online through a Subscription uses the same conventions as other webserver applications. For more information about general ChemOffice Enterprise application concepts, please see ChemOffice Enterprise on page 191.
268ChemINDEX
CambridgeSoft BuckyBase
Chem & Bio Office Enterprise, Workgroup & Databases 2006 ChemINDEX269 Using ChemINDEX With ChemOffice Enterprise or Online
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270ChemINDEX CambridgeSoft Using ChemINDEX With ChemOffice Enterprise or Online
Chapter 14: NCI

NCI (National Cancer Institute) is a database of potential screening compounds provided by the National Cancer Institute. The NCI database is provided with CambridgeSoftgenerated 2-dimensional structures.
1. Basic Chemical Information
Using NCI on CD
Availability: Part of ChemIndex
CD-ROM Internet Subscription Intranet on ChemOffice Enterprise
searchable by: Chemical Structure Molecular Formula Molecular Weight NSC Number CAS Number Synonym
2. Human Tumor Cell Line
Number of compounds: >223,000

NOTE: The National Cancer Institutes AIDS database can be accessed through the NCI database. Please see on page 273 for more information.
A box appears under the Basic Chemical
Information tab if data is available.
Using the NCI Forms

The NCI Database ChemFinder form consists of three tabs:
NCI271 Using NCI on CD
3. AIDS Antiviral Screen (Please see on page 273
for more information) A box appears under the Basic Chemical Information tab if data is available.
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Using NCI Online

ChemINDEX, available online through a Subscription uses the same conventions as other ChemOffice Enterprise applications. For more information about general ChemOffice Enterprise application concepts, please see ChemOffice Enterprise on page 191.
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CambridgeSoft Using NCI on CD
Chapter 15: AIDS

AIDS (The National Cancer Institutes AIDS database) is a library of potential HIV screening compounds provided by the National Cancer Institute. The AIDS database is provided with CambridgeSoft-generated 2-dimensional structures.
Using AIDS on CD
The AIDS database is available through the NCI search forms. Please see NCI on page 271 for more information. If AIDS information is available for the substance retrieved, a box appears under the Basic Chemical Information tab.
Using AIDS Online

The AIDS database is available through the NCI search forms online.Please see NCI on page 271 for more information.
AIDS273 Using AIDS on CD
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274AIDS CambridgeSoft Using AIDS on CD
Section VI: Sourcing & Safety Data

This section provides information about CambridgeSofts Sourcing and Safety Data Chemical Databases. The following databases comprise CambridgeSofts Sourcing and Safety Data Offerings:
ChemACX ChemSCX ChemMSDX Sigma-Aldrich MSDS EH&S Enterprise
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276 CambridgeSoft
Chapter 16: ChemACX

ChemACX (Available Chemicals Exchange) is a class of databases available from chemical manufacturers and distributors, featuring complete catalogs of major world suppliers of fine research, specialty, and industrial chemicals. ChemACX is a read-only database.
Supplier ID Property Supplier Name
How Is It Useful?
ChemACX is your guide to commercially available chemicals worldwide. Whether you are planning a bench synthesis, scale-up, or a commercial process, you can search these databases to determine the availability and sources for the chemicals you need. You can search ChemACX by any of the following:
Chemical structure Chemical substructure Compound name Molecular formula CAS Registry Number Molecular weight range Combinations of the above criteria
ChemACX Database
Availability:
DVD-ROM as part of ChemACX Ultra Internet Subscription Intranet with ChemOffice Enterprise SD-File
Number of Catalogs: 405 Number of Unique Chemical Entities: >350, 000 Number of Chemical Products: > 1 Million Key Fields:
Structure Formula ACX Number Product Name Molecular Weight CAS Registry Number Synonym Product ID Catalog Number
For information about searching, see the ChemFinder section in the purple ChemOffice manual.
Using ChemACX with ChemOffice Enterprise

ChemACX allows the user to search for particular chemicals, view a list of vendors providing what was searched for, and save the products desired to a Shopping Cart.
ChemACX277 ChemACX Database
Opening ChemACX
To open ChemACX: Type http://servername into your web browser.
NOTE: Servername is the name of the ChemOffice
Searches for chemicals in ChemACX can include a combination of any of the following fields:
Substance Name (text search) CAS Registry Number ACX Number Mol. Formula (formula search) MW Range (molecular weight search) Catalog Number
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Enterprise machine. For more information about your server, please contact your system administrator. The main ChemOffice Enterprise window appears. Click ChemACX. The ChemACX Query Input Form appears.
To search for information from ChemACX vendors:

1. Open ChemACX. 2. Enter search criteria. 3. Select the appropriate Search:
If you would like to search over all of the
vendors in ChemACX, select Search all vendors. If you would like to search over a previously generated list of favorite vendors, select Search your favorite vendors.
4. Click Search.
The Search Results page appears. The following illustration shows part of the results from a substructure search for cyclohexane.
Searching ChemACX Catalogs

Searching ChemACX is similar to searching all other ChemOffice Enterprise applications. For tips regarding searching ChemOffice Enterprise applications, please see Searching ChemOffice Enterprise Applications on page 194.
278ChemACX
CambridgeSoft Using ChemACX with ChemOffice Enterprise
Searching Without the Plug-in

A ChemDraw plug-in is available from the ChemACX Query Input Form. This plug-in aides in the process of searching by substructure. If searching by substructure is not necessary, searching without the plug-in may be appropriate. Searching without the plug-in allows the user to simplify the search to a chemical name or a CAS number only. To search without the plug-in:
1. From the ChemACX query input form, click Click for Non-Plugin Search.
Vendors
It is possible for the user to search for substances under a shorter list of preferred vendors. This shorted list helps to limit search results to include products from only your favorite vendors. To create or edit a list of favorite vendors available to search under:
1. From the ChemACX Query input form, click Edit Favorite Vendors List.
The Vendor Selector box appears.
The Non-Plug-in Search page appears.
If you want to search
Then
2. Select the checkbox next to any vendor that
by chemical name
in the text box, enter a chemical name. in the text box, enter a CAS number.
should be included in the favorite list. To remove a vendor, deselect the checkbox.
3. Click Save as Preferred List.
by CAS number
A list of favorite vendors is saved and the Vendor Selector box closes.
with the full query click Advanced page, including Query with Plugin. structures and other criteria
3. Click Search.

Similar to other ChemOffice Enterprise applications, search results can be viewed in two major formats: List View and Details View.
List View - lists all results in a compact manner,
The Search Results page appears.
Creating and Editing A List of Favorite
giving only summary information for each result. You are able to register and lookup MSDX data from this view.
ChemACX279 Using ChemACX with ChemOffice Enterprise
Details view allows users to view all
6. In the list, select the checkbox next to Add to
information in the selected record. You are able to register and lookup MSDX data from this view as well as add items to your shopping cart from this view. To view a record's entry:
1. Search for a chemical on ChemACX. For more
Cart and enter a quantity.
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information about searching in ChemACX, see Searching ChemACX Catalogs on page 278. 2. To view vendors for a specific record, click Details. The detailed view appears
The order is added to your Shopping Cart. 7. To view the full catalog listing, click Catalog Details, and a new window will appear displaying catalog information. 8. In the list, select the checkbox next to Add to Cart and enter a quantity. The order is added to your Shopping Cart.
Viewing Search Results in List View

Results of a search are returned in list view by default. The maximum total number of records returned and the number of records returned on each page is controlled by user preferences.
3. Select one of the tabs: Online Vendors, Your
Favorite Vendors, or Other Vendors. 4. Highlighting a vendor name in the list found in the tabs will display a catalog listing to the right. To compare more then one vendor, hold down CTRL when highlighting vendor names. 5. Clicking Catalog View or Compact View will toggle between the two viewing options. Select whichever view you are most comfortable with.
The following functions can be performed from this view:

Zoom in on the structure. List all Synonyms for the substance. Access the record in details view. Mark the record. Register the compound in Registration
Enterprise. Access the MSDX data for the compound.
280ChemACX
To view results in list view, perform a search. Use the browsing buttons to browse through the pages of result.
Add products to your shopping cart.
Browsing Vendor Information
Viewing Search Results in Details View

Clicking on the Details button for a record in List View brings you to details view for that record. Details view makes available all of the tools to browse through vendor catalogs and add products to your shopping cart. The following functions can be performed from this view:
Zoom in on the structure. List all Synonyms for the substance. Return the List View. Mark the record. Register the compound in Registration
Records in details view are displayed with both structure and vendor information. To find the vendor catalog you are looking for:
1. Select one of the tabs: Online Vendors, Your
Favorite Vendors, or Other Vendors depending on your preference.

2. Highlighting a vendor name in the list found in
the tabs will display a catalog listing to the right.
Enterprise. Access the MSDX data for the compound. Browse Vendor information.
Note: To compare more then one vendor, hold down CTRL when highlighting vendor names. 3. Select the appropriate viewing option by clicking on one of the following buttons: Catalog View
For details about using the shopping cart,
please see Using the Shopping Cart on page 283.
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Accessing MSDX Data

MSDX Data, when available, can be accessed from the MSDX link found in list and details view on a substance's record. MSDX data is not available for all substances. By default, when the data is not available, the MSDX link will appear greyed out. To access a substance's MSDX data, click the MSDX link in list or details view.
To view the full catalog listing, click Catalog
Details, and a new window will appear displaying catalog information. Compact View
If there is more then one data sheet for the
substance, an option window appears.
282ChemACX
If there is only one data sheet available, or as a
result of selecting one of the options, the datasheet appears in PDF format.
Viewing Your Shopping Cart

Your Shopping Cart list can be retrieved from the ChemACX Query Input form or the Search Results page. To view your Shopping Cart, click either

OR
Your Shopping Cart list appears.
Using the Shopping Cart

The Shopping Cart is a convenient way to save a list of chemicals to be ordered. For more information, about ordering the chemicals in your shopping cart, see Ordering The Chemicals in the ChemACX Shopping Cart on page 283. You can add items in the shopping cart from details view of any record. To view a record's entry:
1. Search for and access a record in details view. 2. Browse to the product you would like to add to
Removing Items from Your Shopping Cart

To remove an item from your Shopping Cart:
On the Shopping Cart page, click
Remove. To remove all items from your Shopping Cart:

On the Shopping Cart page, click
Remove all.
your shopping cart. 3. In the list, select the checkbox next to Add to Cart and enter a quantity.
Ordering The Chemicals in the ChemACX Shopping Cart

There are three options in saving the ChemACX shopping cart information gathered during a session: Print, Export to Excel, or Export to Word. To print your shopping cart, click on Print.
The order is added to your Shopping Cart.
To export shopping cart data to Excel or Word:

1. Click
Export to
Excel (or Export to Word).
Send Hits to Inventory button (on the shopping cart page) are visible. Otherwise, these tools will not be available. For more information about configuring your system to link to Registration Enterprise and/or Inventory, please see your system administrator.
Administrator
NOTE: Exporting to MS Excel or MS Word
are options configured by your system administrator. See your system administrator for more details. The Requisitioner Information Form appears.
Registering Products in Registration Enterprise

.When this feature is available, a Register link appears in List View.
To register the compound:

1. Click the Register link.
A registration window appears.
2. Enter appropriate information in the space
provided. 3. Click Export to Excel (or Export to Word). Your shopping Cart information is saved to an Excel workbook or Word Document with one sheet for each vendor.
Registering and Creating Inventory Containers

ChemACX can be integrated with Registration Enterprise and Inventory if they are installed. If the system is configured to utilize these features, the Register link (on search results pages) and the
2. Adjust the information as desired.
Change the CAS number in the CAS
textbox. Select a name from the Chemical Name listbox. The names listed are all names associated with the record in ChemACX. 3. Click OK.
284ChemACX
The compound is added to the Temporary Table in Registration Enterprise by default.
3. Click OK.
Creating Inventory Containers in Inventory for Products

When this feature is available, a Send Hits to Inventory button is found on the shopping cart page.
4. From this screen, you are able to commit the
information you have entered or test the commit process before actually committing the data. To test the data before committing, click Test.
To Send the contents of your Shopping Cart to Inventory and make containers for them:
1. Click Send Hits to Inventory.
An Inventory window appears.

To commit the data to Inventory, click
Commit Click View to view your new containers in Inventory.
2. Enter the appropriate information about the
containers being created for each ChemACX product.
Saving Hitlists and Exporting SD Files

ChemACX, being a ChemOffice Enterprise application, uses the hitlist management and SD File Export Features of the ChemOffice Enterprise. See Manipulating Hit Lists on page 208 and Exporting Search Results on page 210 for more information.
If you start your search with the Index form and find some matching compounds:
A list of synonyms in the Synonyms subform
appears. A list of suppliers in the Products subform appears. Search MSDX by clicking the MSDX button. To view product information: On the Index form, click a product name. The Product form appears.
Administrator
Logging Off
You can end your session with ChemACX at anytime by logging off. To log off:
Click
Log Off.
Using the ChemACX Ultra DVD-ROM

If you want to search over the entire database for a chemical, start with the Index form.
To return to the Index form:

Click Index Form.
To view information about the supplier of the chemical:
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Click Supplier Info Form.
The Supplier form appears.
What If My Favorite Supplier Isnt Listed Here?

An updated list of participating vendors can be found on CambridgeSofts corporate website at: http://chemacx.cambridgesoft.com/chemacx/sup pliers.asp CambridgeSoft is always adding new companies to ChemACX. The one you want might be in the next release of ChemInfo,.. Contact your supplier and ask them to participate in ChemACX. To participate, your supplier sends CambridgeSoft its product list. The preferred format for submission is a ChemFinder database with structures. They can also use other electronic formats such as Access databases or Excel spreadsheets. They can use a brochure for short product lists. Send the information to one of the following:
csinfo@camsoft.com ChemACX Data, CambridgeSoft Corporation,
To display a list of products for the displayed supplier:

Click Products.
The Products form appears.
100 CambridgePark Drive, Cambridge, MA 02140 (USA)
ChemACX287 What If My Favorite Supplier Isnt Listed Here?
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288ChemACX CambridgeSoft What If My Favorite Supplier Isnt Listed Here?
Chapter 17: ChemMSDX

CS ChemMSDX is a collection of over 21,000 Material Safety Sheets presented through ChemACX in PDF format.
How is it Useful?
ChemMSDX provides rapid access to comprehensive health and safety information to aid in the safe handling, storage, and transportation of materials, and provides precautionary and emergency medical information. Availability:
DVD-ROM as part of ChemACX Ultra Internet Subscription as part of
ChemACX.com Intranet with ChemACX on ChemOffice Enterprise Number of Compounds: > 21,000
Using ChemMSDX from ChemACX Ultra DVD

Access MSDX data from ChemACX by clicking the MSDS Database button in the records form.
Using ChemMSDX from ChemOffice Enterprise

Access MSDX data from ChemACX on ChemOffice Enterprise by clicking on the blue MSDX hyperlink. If the MSDS is not available, the hyperlink will be grayed out.
ChemMSDX289 How is it Useful?
Selecting View MSDS will cause the MSDS record will appear in a new browser window in PDF format.
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If multiple MSDS records are available, users are able to choose which record they wish to view.
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Chapter 18: Sigma-Aldrich MSDS Collection

Extend the coverage of safety information with this collection of over 130,000 MSDSs for the products of the Sigma-Aldrich family of catalogs (Sigma, Aldrich, Fluka, Supelco, Riedel-de Han) in HTML format. This information is smoothly integrated with CambridgeSoft's Enterprise and Workgroup products. With a click of a hyperlink, users will be able to pull up the Sigma-Aldrich MSDS using their browser. Number of records: >130,000
About the SigmaAldrich MSDS Collection

Availability:
Intranet with ChemOffice Enterprise and ChemACX Enterprise Inventory Enterprise E-Notebook Enterprise CD-ROM with Inventory Workgroup
Sigma-Aldrich MSDS Collection291 About the Sigma-Aldrich MSDS Collection
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292Sigma-Aldrich MSDS Collection CambridgeSoft About the Sigma-Aldrich MSDS Collection
Chapter 19: EH&S Enterprise

EH&S Enterprise is a complete packages for handling Environmental, Health, and Safety Data and Report Management
Key Benefits:
Never again worry about getting a citation
How Is It Useful?
Environmental, Heath and Safety (EH&S) groups are critical to research institutions because they help to ensure compliance with laws, regulations and an organization's own safety policies. As part of the basic function, these groups often play a key role in the procurement, inventory, transport, storage, and disposal of chemicals throughout the organization. EH&S Enterprise is a fully developed and proven system to provide clients with information that allows all departments, from the receiving clerk to the company's waste disposal contractor, to properly segregate chemicals for delivery, storage, handling and disposal. Chemical structure and substructure searching provides intuitive access for chemists. Non-chemists can correctly segregate chemicals using the chemical segregation module. The backbone of EH&S Enterprise is a data system which has been fully developed by a certified industrial hygienist with over 24 years of experience. The data is integrated into the application using CambridgeSoft ChemOffice Enterprise technology.

from OSHA for failure to correctly segregate reactive chemicals Integrated Department of Transportation and IATA regulatory information Deliver in-depth right-to-know information to all employees with a few keystrokes. HMIS/NFPA hazard warning Is the compound a carcinogen or sensitizer? Material Safety Data Sheets A complete DEA regulated compound database Purchases can be pre-approved Comply with shipping and storage requirements OSHA and EPA threshold planning lists Ensure quantities purchased will not exceed the threshold planning quantity No more process safety management reports Integration with Inventory Enterprise and Workgroup Integration with ChemACX Enterprise and Workgroup Integration with the Sigma-Aldrich MSDS collection
EH&S Enterprise293 How Is It Useful?
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294EH&S Enterprise CambridgeSoft Key Benefits:
Section VII: Reaction & Synthesis Data

This section provides information about CambridgeSofts Reaction and Synthesis Data Chemical Databases. The following databases comprise CambridgeSofts Reaction and Synthesis Data Offerings:
ChemRXN ChemSynth ChemReact ChemRXN
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Chapter 20: ChemRXN

ChemRXN is a class of databases of chemical reactions which include literature citations, products, reactants, solvent and catalyst data, yields, and reaction conditions. ChemRXN consists of ChemPrep and ChemSelect. Number of Reactions: 16,761 Key Fields:
Structure (reaction) Reaction Formula Abstract Molecular Weight (components) Atmosphere Reaction text Time Key phrases Pressure Reflux
How Is It Useful?
ChemRXN provides ready access to information useful in planning a chemical synthesis. A reaction query can search for all reactions that:
Yield a particular product Use a particular catalyst or solvent Consume a particular reactant Have been published by a certain author
For example, you can search for reactions which produce benzofurans in greater than 90% yield.
ChemPrep has a principal form or main screen, Chemprep.cfw, and three associated forms:
Reaction.cfw Solvent.cfw Catalyst.cfw
ChemPrep
ChemPrep is a carefully prepared chemical reaction database from the Institute for Scientific Information (ISI). ISI is one of the largest and most reputable providers of scientific information, and has a number of scientific databases available including exhaustive reaction and molecular literature databases. Directory: ChemPrep Filenames: Chemprep.cfw, Catalyst.cfw, Reaction.cfw, Solvent.cfw
Reaction.cfw shows the reaction diagram in a larger window. It is useful in case the reaction is complicated or has large molecules or many components. Reaction.cfw is called from the main screen by clicking the zoom Reaction button. The view Solvents and view Catalysts buttons provide larger views of the solvent (form Solvent.cfw) and catalyst (form Catalyst.cfw) molecules which appear in the scrolling lists on the right of the main screen. Each of these associated forms has a button to return to the main screen.
ChemRXN297 How Is It Useful?
The reactions in ChemPrep were selected by ISI from their larger reaction databases and were provided with full literature references. The reaction centers and atomic transformation matrices were computed with ChemFinder.
Molecular Weight (components) PageNumber Journal Yield Reaction Text Pressure Reflux Literature text Author Type Title Language Volume
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ChemSelect has a main form, ChemSelect.cfw, and three associated forms:
ChemSelect
ChemSelect is a collection of the most commonly cited reactions from the literature, selected by InfoChem GmbH of Germany. The ChemSelect data is taken from the VINITI project of the former Soviet Union, in which over 2 million chemical reactions were compiled. The 13,037 reactions of ChemSelect were obtained using a defined statistical methodology which selects the most representative reactions from the database. All reactions contain full literature citations. Directory: ChemSelect Filenames: ChemSelect.cfw, Catalyst.cfw, Reaction.cfw, Solvent.cfw Number of reactions: 13,037 Key Fields:
Structure (reaction) Reaction Formula Year
Reaction.cfw Solvent.cfw Catalyst.cfw
The associated forms show the data in a larger window. To access Reaction.cfw:
From the main screen, click Zoom Reaction.
To display larger views of Solvent.cfw and Catalyst.cfw molecules:

Click Zoom Solvent(s) or Zoom Catalyst(s).
To return to the main screen:

Click Return or Return to main screen.
InfoChem is a major provider of scientific information, and has also created selections called ChemReact41 (41,000 reactions), ChemSynth (100,000 reactions), and ChemReact (400,000 reactions). These will also be available as ChemFinder databases. For further information, contact CambridgeSoft or InfoChem GmbH.
298ChemRXN
CambridgeSoft ChemSelect
Selection Criteria
For inclusion in ChemSelect, each reaction must typify at least five different reactions. Two reactions are considered to be of the same type if the reaction centers and the groups around the reaction centers
are identical. Each reaction in ChemSelect has been cited in at least five different journal articles, has a yield of at least 50%, and has been published in a generally available journal.
ChemRXN299 ChemSelect
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300ChemRXN CambridgeSoft ChemSelect
Chapter 21: ChemSynth

ChemSynth contains essential information on 180,000 reactions referenced in literature published from 1974-2001. These reactions have been selected from the parent InfoChem database with an eye towards emphasizing those reactions that have been proven to be synthetically useful. All of these reactions have been reported as having greater than 50% yield, and all have been sited in leading journals at least twice. How Is It Useful? When you open ChemSynth in ChemFinder, the application starts in browse view. In this view, users can browse records using the navigation buttons on the ChemFinder Menu. To do a search, click on the Search icon or menu in ChemFinder button
About ChemSynth
Availability:
CD-ROM (ChemFinder database only - no
software is included) Internet Subscription Intranet on ChemOffice Enterprise Number of Record: 178,842 Reactions Key Fields:
Reaction Structure Yield Reaction Conditions Catalyst Structure Solvent Structure Author Title Journal Reference
Data that can be searched includes chemical structures and reactions. You can search for particular templates for starting materials or products by placing an arrow to the left (product) or right (reactant) of the structure you wish to search. Other searchable fields include yield, reference information and comments.
Using ChemSynth on CD-ROM

ChemSynth on CD-ROM is a ChemFinder database. No software is included with the database.
Using ChemSynth Online or with ChemOffice Enterprise

Searching ChemSynth
The Search Page allows searching for by reaction, by product or reactant, by compound, and by literature reference information. The ChemSynth
ChemSynth301 About ChemSynth
searching form acts much like the other search forms found in ChemOffice Enterprise applications.
3. Click
Search.
To search a structure only as a product

1. Enter the structure into ChemDraw box
Administrator
To search for compounds anywhere in the reaction
1. Enter the structure into the ChemDraw
provided in the Search Form. 2. Place an arrow to the left of the structure 3. Click Search. The example shows a search for a structure as a product. When the search is complete, A list of search results appears.
provided in the Search Form.

2. Click
Search.
To search for a complete reaction transformation

1. Enter the reaction into ChemDraw box
provided in the Search Form. 2. Click Search. To search a structure only as a reactant
To view the contents of a particular record in the Show Details. The complete list, click contents of the chosen record is displayed.
provided in the Search Form. 2. Place an arrow to the right of the structure
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ChemSynth303
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304ChemSynth CambridgeSoft
Chapter 22: ChemReact

ChemReact500 contains essential information on almost 500,000 reactions referenced in literature published from 1974-2001. These reactions have been selected from the parent InfoChem database with an eye towards emphasizing those reactions that have been proven to be synthetically useful. All of these reactions have been reported as having greater than 50% yield. ChemReact68 futher refines the selection by adding the criteria that have been sited in leading journals at least 5times.
Using ChemReact68 on CD-ROM

ChemReact68 on CD-ROM is a ChemFinder database. No software is included with the database. When you open ChemReact68 in ChemFinder, the application starts in browse view. In this view, users can browse records using the navigation buttons on the ChemFinder Menu. To do a search, click on the Search icon or menu in ChemFinder button
About ChemReact
Availability:
ChemReact68 CD-ROM (ChemFinder
database only - no software is included) Internet Subscription Intranet on ChemOffice Enterprise Number of Record:
ChemReact500: 445,717 Reactions ChemReact68: 67,926 Reactions
Key Fields:
Reaction Structure Yield Reaction Conditions Catalyst Structure Solvent Structure Author Title Journal Reference
Data that can be searched includes chemical structures and reactions. You can search for particular templates for starting materials or products by placing an arrow to the left (product) or right (reactant) of the structure you wish to search. Other searchable fields include yield, reference information and comments.
ChemReact305 About ChemReact
Using ChemReact Online or with ChemOffice Enterprise

Searching ChemReact
The Search Page allows searching for by reaction, by product or reactant, by compound, and by literature reference information. The ChemReact searching form acts much like the other search forms found in ChemOffice Enterprise applications.
To search a structure only as a reactant

provided in the Search Form. 2. Place an arrow to the right of the structure 3. Click Search. To search a structure only as a product
Administrator
provided in the Search Form. 2. Place an arrow to the left of the structure 3. Click Search. When the search is complete, A list of search results appears.
To search for compounds anywhere in the reaction

1. Enter the structure into the ChemDraw
provided in the Search Form.

2. Click
Search.
To search for a complete reaction transformation

1. Enter the reaction into ChemDraw box
To view the contents of a particular record in the Show Details. The complete list, click contents of the chosen record is displayed.
provided in the Search Form. 2. Click Search.
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ChemReact307
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308ChemReact CambridgeSoft
Appendices
This section contains appendices in the following order:
Appendix A: DocManager Enterprise Free Text Searching - Describes the use of key words and symbols in Free Text Searching Appendix B: BioAssay Actions Menu Commands - Describes the actions available form the Actions button within BioAssay. Appendix C: BioAssay Plate Block Data Files - Indicates how to indicate to BioAssays FIle Import Template Wizard how your plate block data file is formatted. Appendix D: Oracle Cartridge Dependencies by Operating System lists the libraries necessary for the Oracle Cartridge Appendix E: Scientific Databases First Search Tutorial - A tutorial for using the CD based Scientific Databases with ChemFinder.
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Appendix A: DocManager Enterprise Free Text Searching

Understanding Basic Text Searching
You can use basic text searching, or querying, to find information in documents within Documentation Manager. There are a number of special characters used in basic text searching which will help narrow or increase search results. Normally, the more narrow a search, the less ambiguous and more precise search results become, making it easier to find the correct information. As a search gets broader, the longer the search results list becomes. Different types of basic text searching are available, depending on the needs of the search. For example, the following searches really mean:
Searching for Returns documents with
thymidine synthesis
the words thymidine synthesis in that order, with no words between in a documents text. the word cyclohexane in a documents text.
cyclohexane
Wildcard Searching
If a prefix or a suffix for a word is either unknown or variable, wildcard characters become useful in a free text search to return all words with the same word root. Wildcard characters can be used in a basic text search when searching for all documents that contain a part of a word. This kind of search typically returns more matches to search criteria than the exact phrase search.
Exact Phrase Matching

If a search is meant to find only exact matches for the text entered, exact word or phrase matching should be used. This is the most simple search, or query, which returns exactly the information requested.
DocManager Enterprise Free Text Searching311 Understanding Basic Text Searching

NOT (~) OR (|) soundex (!) stem ($)
Administrator
synth*
any word with synth as the first 5 letters in a documents text. Matches include synthesis, synthetic, and syntheses. any word with ethane as the last 6 letters in a documents text. Matches include ethane, and methane.
ABOUT
The ABOUT operator, when used in an advanced text search, or query, retrieves documents that contain information related to a word or phrase. The ABOUT operator is used, by entering the word ABOUT in all capital letters followed by the word or phrase on which to search in parentheses. ABOUT searches are always case-sensitive. The text string inside the parentheses is interpreted with respect to case. For example, the following searches really mean:
*ethane
Understanding Advanced Text Searching

Advanced text searching, or querying, is also available for document searching from within Documentation Manager. Using specific operators in an advanced search allows the user to narrow search parameters dramatically. The following is a list of some of the special operators used in advanced searching:
ABOUT AND (&) EQUIValence (=) fuzzy (?) MINUS (-) NEAR
ABOUT (carbon)
any word with words related to carbon in the documents text. Matches include coal and diamond. any word with words related to carbon biproducts from syntheses at 25 degrees Celcius in the documents text. Matches include coal and diamond
ABOUT (carbon biproducts from syntheses at 25 degrees Celcius)
The ABOUT operator becomes very powerful when coupled with other operators, such as AND or NOT.
312DocManager Enterprise Free Text Searching
CambridgeSoft Understanding Advanced Text Searching


ABOUT (carbon) AND diamond
any word with words related to carbon as well as the word diamond in the documents text. any word with words related to carbon but excluding the word diamond in the documents text.
carbon AND diamond both the words carbon, and diamond, found anywhere within a documents text. carbon & diamond both the words carbon, and diamond, found anywhere within a documents text. all the words carbon, diamond, and graphite, found anywhere within a documents text. both the phrases thymidine synthesis, and carbon dioxide, found anywhere within a documents text.
ABOUT (carbon) NOT ABOUT (diamond)
NOTE: For advanced Oracle users: The word or phrase specified in an ABOUT query does not have to exactly match the themes stored in the index. Oracle automatically normalizes the word or phrase before performing lookup in the Text index.
carbon & diamond & graphite
thymidine synthesis AND carbon dioxide
AND (&)
The AND operator used in an advanced text search or query, finds documents that contain more than one word or phrase. The AND operator is used to search for documents that contain at least one occurrence of each of the query terms. The AND operator, is used by entering the first term, then the word AND in all capital letters (or entering the ampersand (& symbol)), followed by another word or phrase on which to perform a search.
EQUIValence (=)
The EQUIValence operator used in an advanced text search, or query, will allow the user to find documents that contain information about words that can be used in place of each other, alone or in a phrase. The EQUIValence operator is used to specify an acceptable substitution for a word in a query. The EQUIValence operator is used by, entering EQUIV in all capital letters (or enter the equal sign (=)), followed by the phrase on which the search is to be performed.
DocManager Enterprise Free Text Searching313 Understanding Advanced Text Searching


Administrator
graphite EQUIV diamond
the words graphite or diamond found anywhere within a documents text. the words graphite or diamond found anywhere within a documents text. the words carbon dioxide, carbon monoxide, or both terms found anywhere within a documents text.
?boron
any word spelled similarly to boron found anywhere within a documents text. Matches include baron. any words spelled similarly to read found anywhere within a documents text. Matches include read, lead, and real. any words spelled similarly to chemist found anywhere within a documents text. Matches include chemists and chemistry
graphite = diamond
?read
carbon dioxide=monoxide
?chemist
NOTE: The EQUIValent operator has higher precedence than all other operators except the expansion operators (fuzzy, soundex, stem).
Fuzzy (?)
The fuzzy operator used in an advanced text search, or query, will find documents that contain words similar to the word used in a search. For example, the fuzzy operator can be used to expand queries to include words that are spelled similarly to the specified term. This type of expansion is helpful for finding more accurate results when there are frequent misspellings, or alternate spellings in the documents in the database. The fuzzy operator is used by, entering a question mark (?), followed by the word on which to perform a search.
MINUS (-)
The MINUS operator can be used in an advanced text search, or query, to find documents that contain two phrases, with the first phrase taking precedence. The MINUS operator is used to search for documents that contain two query terms, but documents containing the second term are ranked lower than documents without the second term. The MINUS operator is useful for lowering the score of documents that contain a certain term, without eliminating those documents. The MINUS operator is used, by entering the first term, then MINUS in all capital letters (or enter the minus sign or hyphen (-)), followed by another term on which to perform a search.

The NEAR operator is used by, entering the first term, followed by NEAR in all capital letters (or enter a semicolon (;)), followed by the second term on which the search is to be performed. Use the NEAR operator to return documents based on the proximity of two or more query terms.
NOTE: NEAR cannot be used in ABOUT queries.
carbon - diamond
the words carbon and diamond in them, but documents with diamond are listed last. the words carbon and diamond in them, but documents with diamond are listed last. the words diamond and carbon in them, but documents with carbon are listed last.

carbon MINUS diamond
diamond - carbon
carbon NEAR diamond
the words carbon and diamond in them, but only when they appear less than 100 words apart and in no specific order.
NEAR (;)
The NEAR operator is used in an advanced text search, or query, to find documents that contain two phrases that are close together. The maximum distance between the two terms can be specified.
NEAR uses the following defaults:

Search terms are found if they are 100 words
apart or less, unless specified otherwise. Use whole numbers between 1 and 100. Search terms are found in any order, specified otherwise. Use TRUE or FALSE.
The NEAR operator can be used with other operators, such as AND, OR, and EQUIValence. For example, the following searches really mean:
by, entering the term to be found, followed by the word NOT in all capital letters (or enter a tilde (~)), followed by the term to be excluded in the search. Use the NOT operator to search for documents that contain one query term and not another. For example, the following searches really mean:
Administrator
Searching for
Returns documents with
NEAR ((carbon, the words carbon and diamond), 20, FALSE) diamond in them, less than 20 words apart, in no specific order. NEAR ((carbon, the words carbon and diamond), 20, TRUE) diamond in them, less than 20 words apart, in this specific order. NEAR ((carbon, diamond), 10) AND benzene the words carbon, diamond, and benzene in them, but only when carbon and diamond appear less than 10 words apart and in no specific order. the words carbon, diamond, and graphite in them, but only when carbon and diamond or carbon and graphite appear less than 10 words apart and in no specific order.
carbon NOT diamond the word carbon, but not the word diamond anywhere in the documents text. carbon ~ diamond the word carbon, but not the word diamond anywhere in the documents text. the word carbon, but not the word diamond or graphite anywhere in the documents text.
carbon NOT (diamond OR graphite)
NEAR ((carbon, diamond = graphite), 10)
NOTE: The NOT operator does not affect other logical
operators.
OR (|)
The OR operator can be used in an advanced text search, or query, to find documents that contain information about any words in the query, but not necessarily all words in the query. The OR operator is used by, entering the first term, followed by the word OR in all capital letters (or enter the pipe (|)), followed by another term on which the search is to be performed.
NOT (~)
The NOT operator can be used in an advanced text search, or query, to find documents that contain a word or phrase, but only when it appears without a second word or phrase. The NOT operator is used
Use the OR operator to search for documents that contain at least one occurrence of any of the query terms. For example, the following searches really mean:
The soundex operator is used by, entering an exclamation point (!), followed by the word on which to perform a search. Use the soundex (!) operator to expand queries to include words that have similar sounds; that is, words that sound like other words. This function allows comparison of words that are spelled differently, but sound alike in English. For example, the following searches really mean:
carbon OR diamond
the words carbon, diamond, or both anywhere in the documents text. the words carbon, diamond, or both anywhere in the documents text. the words carbon, diamond, graphite, or any combination of the terms anywhere in the documents text. the words thymidine synthesis, carbon dioxide, or both terms anywhere in the documents text.
carbon | diamond
!carben
any words that sound like the word carben in a documents text. Matches include carbon and carboxcylic. any words that sound like the word read in a documents text. Matches include read and lead.
carbon OR diamond OR graphite
!read
thymidine synthesis OR carbon dioxide
Stem ($)
The stem operator is used in an advanced text search, or query, to find documents that contain words similar to the word used in a search. When the stem operator is used, enter a dollar sign ($), followed by the word on which to perform a search. Use the stem operator to search for terms that have the same linguistic root as the query term. Stem expands a query to include all terms with the same stem or root word as the search term.
Soundex (!)
The soundex operator is used in an advanced text search, or query, to find documents that contain words that sound like the word used in a search.

Administrator
$commit
any words with the root commit found in the documents text. Matches include commits, committing, committee, and committed. any words with the root chemist found in the documents text. Matches include chemist, chemistry, and chemists in them.
$chemist
Appendix B: BioAssay Actions Menu Commands

All of the following commands are available from the Actions menu of BioAssay. The commands are only available from the menu when they are relevant. To view a plate format:
1. Select the row defining the plate format to be
Viewing Commands
View Details
The View Details action can be accessed from any Protocol Data table, except from a table found at the bottom of the hierarchy. The View Details action brings about the same result as doubleclicking on a row in the table: the data table holding aggregate data for the current table, is opened. This result makes sense because the data that makes up a particular row in one table is formed by the data calculated in the next lowest table.
viewed. 2. Select View Plate Formats from the Actions menu.
View (from the plates grid)

The View action will populate the cells in the grid with the indicated data. For example, selecting View > Well Contents will populate the cells in the grid with the contents of the well (assigned when defining the plate's format).
View (from the plate formats grid)

The View action will populate the cells in the grid with the indicated data. For example, selecting View > Well Contents will populate the cells in the grid with the assigned contents (e.g. Empty, or Compound). The following options are available from the View action on the plate formats grid:
Well Contents Well Name
View Picklist
The View Picklist action is available from the table containing assay picklist definitions. This action will open a table defining the options available in the chosen picklist. To view a picklist's table:
1. Select the row defining the picklist to be
viewed.
2. Select View Picklist from the Actions menu.
Other Commands
Autofit
The AutoFit action is available from any grid view. If AutoFit is turned on, the grid will automatically resize to fit in the current window. If the window is then resized, the grid will resize accordingly.
View Plate Format

The View Plate Formats action is available from the plate formats table. This action will open a table defining the chosen plate format.
BioAssay Actions Menu Commands319 Viewing Commands
AutoFit On
To change the validity of data in certain rows in the table:

1. Browse to the table holding the appropriate
data. 2. Highlight the rows holding the data. 3. Select Change Validity from the Actions Menu. The Change Validity window appears.
Administrator
AutoFit Off
4. Select the appropriate validity.
Validity Option
Change Validity
The Change Validity action is available from any Data table. By default, all data is assumed to be Not Validated unless otherwise specified. Data which is Not Validated is noted by an N in the leftmost column of the data table. After adjusting the validity of data, it is possible to view only valid data in the tables. It is also possible, in the Security tab of the protocol definition, to specify that Valid data may not be edited or recalculated. Calculations are based on data which is marked with any validity except Invalid.
Not I Validated
no validation Yes decision has been made data is found Yes to be valid data is found No to be invalid
Valid
Invalid
320BioAssay Actions Menu Commands
CambridgeSoft Other Commands
Validity Option
4. Click OK.
Copy
The Copy action is only used in Edit mode. The action will copy any highlighted information.
Request Review
data must be Yes reviewed before making a validation decision
Cut
The Cut action is only used in Edit mode. The action will cut any highlighted information.
Import Data
If you are validating data in a summary table, you can also choose to cascade the validity change to the summary data. Select this box if you would like to apply the new validity to the summarized data. The Import Data Action is available from any Protocol Data table. This action will bring up the File Import Wizard. The wizard assists in importing data through the use of a defined File Import Template.
Coloring Options
The coloring options are used to implement heat maps. The Coloring Options Dialog box will allow the user to select a parameter to base a heat map on, and select what values for that parameter will appear in which colors. To set coloring options:
1. Select Coloring Options from the Actions
Paste
The Paste action is only available in Edit Mode. This action pastes whatever is on the clipboard to the selected area.
Recalculate
The Recalculate action will run all calculations defined in the chosen table again. This is useful if the user changes a key piece of data and is interested to see how the calculations will be effected by the change.
Menu. The Coloring Options dialog box appears.
Save Compound List

The Save Compound List action, available from a data table or search data table, allows the user to save the currently selected rows to a list
Select All
2. Select a parameter to base the heat map on
from the Color based on listbox. 3. Enter maximum and minimum values along with colors that correspond to each.
The Select All action will select all of the rows in a table. This is often helpful when applying a different action to all of the rows in a table.
BioAssay Actions Menu Commands321 Other Commands
Show Coloring
This action shows the heat map coloring. When this action is selected, each cell in the grid will be filled with a color representing a value defined in the coloring options. This is available from all views.
Show Only Valid Data

The Show Only Valid Data will display in any Protocol Data table only the data.
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322BioAssay Actions Menu Commands
CambridgeSoft Other Commands
Appendix C: BioAssay Plate Block Data Files
BioAssay Plate Block Data Files323
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324BioAssay Plate Block Data Files CambridgeSoft
Appendix D: Oracle Cartridge Dependencies by Operating System

In addition to the OCI library. (extension may be .dll, .so, .sl), the following files are a requirement on the specified Operating Systems.
Windows MSVCRT.dll MSVCP70.dll MSVCR70.dll Linux libstdc++.so libclntsh.so libgcc_s.so libpthread.so libdl.so Solaris libclntsh.so libCstd.so libpthread.so libdl.so HP/UX libclntsh.sl libstd_v2.sl libCsup_v2.sl libcl.sl libdl.sl libpthread.sl AIX libclntsh.a libpthreads.a libC.a libc.a libc_r.a libdl.a libodm.a libcrypt.a
Chem & Bio Office Enterprise, Workgroup & Databases 2006Oracle Cartridge Dependencies by Operating System325
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326Oracle Cartridge Dependencies by Operating System CambridgeSoft
Appendix E: Scientific Databases First Search Tutorial

Browsing a Chemical Database
Browsing a database with ChemFinder is intuitive and simple. It requires only two basic steps: 1. Opening a Form (which can be thought of as a viewer for the database) 2. Browsing the database.
Opening a Form in ChemFinder

First, start the ChemFinder application:
From your Windows START menu, select
Program Files >ChemOffice2006 > ChemFinder Net 10.0 5. Click Open.
ChemFinder launches and an empty form appears. To open a database (e.g. CS_demo): 3. Select Open from the File menu or click the Open tool. The open dialog box appears 4. Navigate to \ChemFinder\samples and highlight CS_demo.cfw.
The CS_demo database opens in ChemFinder with the first record displayed.
Switching Between Open Documents

Each time you open a form, a form window appears. If you open more than one form, the form windows are stacked. The front-most form is the active window. All open forms are listed in the Window menu.
Scientific Databases First Search Tutorial327
There are several ways to make another open form the active window:
Select the form from the Window menu. Click any exposed area of the window you want
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to be active. Press CTRL+Tab to switch among the currently open form windows.
Browsing a Database
One option in viewing a ChemFinder database is to browse through the database one record at a time, just as you would turn the pages in a book. The Record Toolbar contains intuitive tools for browsing through the database. Try it!
First record Go to record Last Record
In addition to browsing through the records, you can also go directly to a specific record by using the Go To Record command found in the Record menu. 1. Select Go To Record from the Record menu, Go To Record Tool. or click the The record Number dialog box appears.
Previous record
Next record
By default, the toolbar is docked. If you wish, however, you can grab it with the mouse and drag it anywhere on the screen that is convenient.
2. In the Record Number dialog, enter the record
Alternatively, you can select the corresponding commands from the Record menu, instead of using the toolbar.
number (within the current list) you want to display. 3. Click OK. The specified record is displayed.
The Status Bar

As you browse through records, counters in the lower right corner of the ChemFinder window change to indicate the current record, the current list size, and the total number of records in the database. The lower left corner of the same window displays help for menu items and other information.
328Scientific Databases First Search Tutorial
CambridgeSoft Browsing a Database
When a form is first opened, the current list size will equal the total database record count. If you do a search (see : Scientific Databases First Search Tutorial) to find a subset of the entries in the database, the current list size will change to indicate the number of hits in the search.
A list window, containing the fields and records in the form, appears.
To the left of these counters are three other indicators that show the general status of the database. The first will display the word READ when you are using. The second indicator will display the word ADD when you are entering a new record. The third will display QRY when you are entering a query.
NOTE: The ADD indicator is not applicable to CD-
To display a particular record in the form:

Click the records entry in the list window.
ROM-resident or Read-only databases.
To resize the column widths in the Data Table: 4. Place the cursor on the dividers in the top header. The cursor changes. 5. Click and drag to adjust the column width.
To hide/show the Status Bar:

Uncheck Status Bar in the View menu.
The Data Table

Sometimes browsing through a data record set is more convenient if the data are presented in tabular format. To display data in a table:
Select Data Table from the View menu. You
can change the current window or open a new one.
To resize the row heights in the Data Table: 6. Place the cursor on the dividers in the left header. The cursor changes. 7. Click and drag to adjust the row height.
Scientific Databases First Search Tutorial329 Browsing a Database
12.Select Tile from the Window menu.
The form selected in step 2 appears in the upper half of the ChemFinder window, and the data table is in the lower half.
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By default, the fields in the data table are displayed in the order they were created. To reorder the columns in the Data Table: 8. Click one of the column headers to select the column. 9. Drag that header to a new position.
Another convenient method of viewing data is by displaying a form and data table simultaneously in Tile layout. 10.If you havent done so, open a Data Table view in a separate window. 11. Click on the Form view to activate it.
NOTE: If the Data Table view window is active (i.e. its title bar is highlighted), some menu options are not available. To access these options, first click on the Form view window.
Closing a Form
To close the form you have opened, select Close from the File menu.
CambridgeSoft Browsing a Database
Searching a Chemical Database

Browsing is often a less efficient way to locate specific information when databases become large. In such cases it is better to search the database for a record or data item. Searching a database is like using the index of a book. It is easy to quickly focus on the few pages you are interested in when using an index. Similarly, when searching a database, you enter search parameters and only those records that match that criteria are returned. Once you have this smaller collection (often called a hit list with each record found termed a hit), you can browse it much more efficiently than you could the whole database. In this tutorial you will learn how to perform the two basic types of searches: Text search Structure search You will also do a combined search. The form is cleared to allow you to enter your search terms. The status indicator in the status bar is changed to show you have switched to query mode.
2. Click in the Mol Formula data box, and enter
the query C6N1-2, without the quotation marks, in the Formula box.
This entry specifies a molecular formula having 6 carbon atoms and 1 or 2 nitrogen atoms.
3. Click the Find tool or the Search button.
ChemFinder begins searching. The progress of the search is indicated by counters in the status bar at the bottom of the window. When the search is complete, the number of hits is displayed in the Current List Size window of the Status Bar, and the form displays the first hit. NOTE: If a search returns no hits, an alert appears. After the alert is cleared, the screen is left in query mode with the last query shown to allow you to modify it and try again.
Performing a Text Search

Searching by Formula
For our first text example, were going to perform a Formula search:
1. To clear your query form select Enter Query from the Search menu or click on the
4. Select Data Table from the View menu to
Enter Query tool on the Search toolbar.

Find Enter Query Find current molecule Save list Over current list Find list Retrieve all Previous query Restore previous list Restore list
display the hits and verify that the formulas are correct.
Scientific Databases First Search Tutorial331 Performing a Text Search
Searching by name
For our next example, well perform a text search to find all compounds with molecular names starting with benz. To perform this text search:
1. Click in your form to activate it. 2. Click the Enter Query button to clear the
3. Click the Mol Weight box and enter the query
90-100 without the quotation marks.

4. Click the
Find icon or the Search button.
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5. Verify that the molecular weights are correct by
checking the Data Table.
query form.
3. Click in the Product Name data box, and enter
Performing a Structure Search

To perform a structure search of a ChemFinder database, a query is entered by drawing the target structure using the ChemDraw ActiveX control. Structure searches may be used to find compounds which: contain the drawn structure as a substructure (the default setting) are identical to the drawn structure are similar to the drawn structure In this tutorial you will search to find all molecules containing the propane-2-one (acetone) skeleton as a substructure.
the query benz, without quotation marks, in the data box.

4. Click the
5. Select Data Table from the View menu to
display the hits and verify the molecular names are correct. NOTE: Notice that this search returned benzene but not bromobenzene. The query entered is an anchored substring and thus will only return strings starting with the indicated substring. For more information regarding how to specify text queries, see Text Searching in ChemFinder Help (press the F1 key).
Using the ChemDraw ActiveX Control

The first step in performing this substructure search is to draw a structure query using the ChemDraw ActiveX control. Begin as you did for the text search To clear your form: select Enter Query from the Search menu or click on the Enter Query tool on the Search toolbar. Now that the form has been cleared: Double-click in the Structure/Substructure box.
Searching by Molecular Weight

When performing a numerical search, you can use exact values or ranges of values to target desired information. This exercise searches for compounds whose molecular weights fall within a specified range. To search for compounds with molecular weights between 90 and 100:
1. Click in the form to make it active. 2. Click the Enter Query button to clear the
form.
CambridgeSoft Performing a Structure Search
A blue outline appears around the structure box, and the ChemDraw ActiveX control appears. NOTE: If the ActiveX control does not appear, or if you should accidentally close it, right-click in the structure box and select View > Show Main Tools.
3. Drag the mouse diagonally upwards to the right
at an angle of about 30 degrees (a message in the lower left corner of the document window shows the angle) and release the mouse button when you have extended the bond to its fixed length.
2. point
3. drag
NOTE: Right-click in the structure box and select the Object menu. Fixed Lengths and Fixed Angles should be checked, as shown below. If either is not checked, select it in the menu to place a check beside it.
Next, draw acetone in the Structure window.

1. Click on the solid bond tool in the toolbar.
Next, add a bond:

4. Point to the right atom of the bond. 5. Click the atom to add a bond.
A second bond is automatically deposited at a 120-degree angle between the bonds.

2. Position the pointer (which appears as a cross
when a bond tool is selected) anywhere in the empty Structure/Substructure window and hold down the mouse button.
Scientific Databases First Search Tutorial333 Performing a Structure Search
4. point
5. click
11. Double-click the atom.
Next, add a second bond:
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6. Continue pointing to atom C2. 7. Click the atom to add a bond.
10.point
11. double-click
12.Type a capital O in the textbox that appears. 6. point 7. click
Now, change the single bond into a double bond:

8. Point to C2 and hold the mouse button down. 9. Drag from C2 to C4 over the existing single
To close the textbox, click in an empty area of the window, press Enter, or click the ActiveX control to select another tool.
bond. Release the mouse button. 12. type

13.Click outside the Structure box to complete the
structure drawing. Now that you have drawn acetone in the structure box, you are ready to perform a search.
8. point 9. drag
Next, add labels to the structure. Atom labels can be added in several ways. One way is illustrated below.
10.Point to the atom shown below.
NOTE: See the Tutorials in the ChemDraw Users Guide for more information on drawing in ChemDraw.
Searching for the Structure in ChemFinder

The Search menu offers a number of options. Since you would like to view all records in the database containing molecules that have a propane substructure, you should make sure that the Substructure option is selected in the Search menu, and the Similarity option is not selected. These
CambridgeSoft Performing a Structure Search
menu items are toggles; each time they are selected them, the check mark is removed if it was there already, or added if it wasnt previously visible. So, before you commence the search:
1. Enable Substructure from the Search menu. 2. Disable Similarity form the Search menu.
You can also conveniently view the database in tabular form. Select Data Table from the View menu. Open a Data Table in a separate window. The Data Table appears and displays all records in the current list in tabular form.
NOTE: See Similarity Searching in ChemFinder Help (press the F1 key) for more information. The Search menu should now look like this:
Click a record in the Data Table to display its records in your form window. It is possible to sort records on any field. To sort on the ItemNumber field: Double-click on the ItemNumber table header in the Data Table. To search for structures containing propane: Select Find from the Search menu, or click the Find tool. In the case of a substructure search, the matched portion of each molecule is highlighted in red. All hits are structures that contain a acetone substructure. Now, you can browse through these hits. Use the Record menu or the Record toolbar to browse the hitlist (see Browsing a Chemical Database on page 327). After a short pause, the table is sorted by number. Close the Data Table by selecting Close from the File menu. You can return to the full database at any time. To retrieve all the records in your database: Select Retrieve All from the Search menu or click the Retrieve All tool. NOTE: After a search, you do not need to retrieve all your records before conducting another search; you can perform another search at any time. Each search will search over all records in the database.
Scientific Databases First Search Tutorial335 Performing a Structure Search
Performing a Combined Search

In some cases, you may wish to combine more than one type of search to find a specific class of compounds. For example, you may want to find all compounds in the database that have a benzene substructure and that have a molecular weight greater than 400. The procedure for this search is similar to the ones performed previously:
1. With the database open, click in your form to activate it, then click the Enter Query button. 2. Double-click on the Structure/Substructure
a. Click on the Benzene Ring tool.
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b. Click in the Structure/Substructure box. 4. Click in the query form somewhere outside the Structure/Substructure box to complete the
structure.
5. Click the Mol Weight databox and type >400
without the quotation marks.

6. Click the
databox.
3. Draw benzene in the window by doing the
following:
7. Browse your hit list to verify your hits.
CambridgeSoft Performing a Combined Search
Index
A
About button definition 195 server information 213 About, ChemOffice WebServer 2001 191 Administration 147 Audit report, aggregate 160 Audit report, printing 113 Audit report, standard 159 Audit trail, analyzing 112, 159 Audit trail, viewing 112 Avery labels, selecting 105 viewing search results 283 ChemACX-SC 263 Chemical Registration adding a batch 165 adding a compound 164 defining password 179 deleting a record 168 editing a record 168 identifiers 170, 171 importing sdfiles 182 Log in 164 Log off 187 MatchDatabase 182 new experiments 179 notebooks 174 opening 163 Overview 163 parameter type 181 people 176 printing records 187 projects 173 registering records 169 result type 180 reviewing a record 167 salts 177 searching records 171 sites 177 structure comments 174 temporary table 164 vewing experiment spreadsheets 172 Chemical registration defining passwords 147 Chemical synthesis database 257, 259, 273, 291, 293, 297 Chemicals database 263, 277
B
Backup see Database 111 Browsing search records 204 Buckminsterfullerenes 268 BuckyBase 268
C
CAS registry number 267 Changing password for Documentation Manager 12 Changing passwords 108 Changing quantities in containers 100 Changing quantities, and other shortcuts 99 Changing, results views 203 Check-in/Check-out 99 ChemACX 263, 277 opening 278 ordering chemicals 283 removing from shopping cart 283 saving search results 279 searching 278 using 277, 287
ChemIndex 267 ChemInfo 248 ChemMSDX 289 ChemOffice 249 ChemPrep 297, 298 ChemRXN 257, 259, 273, 293, 297, 301 ChemSelect 298 Clear Form button 196 Clearing marked records 205 Client requirements 191 Combination searching 202 Commonly cited reactions 298 Conflict resolution 97 create duplicate 98 edit 98 select 98 Container grid 111 Containers 92 definition 90 editing 92 new 92 Creating a plate map location 144 daughter plates by target plate 143 new containers 98 new locations 93 new substances 95 new user accounts 159 plate maps 143, 144 Custom fields 110
containers 99 favorite vendors list 279 locations 94 substances 98 EHS data 100 EHS help file 101 Element counts 201 Environmental, Health, and Safety see EHS data 100 Exiting web applications 213 Exporting search results 210
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F
Form view, results 203 Form, see Query Input Form Forms 92 Formula searching 201
H
Hits, exporting 210
I
Importing sdfiles into Chemical Registration 182 Index form ChemACX 286 Input form, see Query Input Form Installation 3, 249 Installation requirements 191 Inventory GUI 91 Inventory terminology 89 Inventory, non-chemical 98
D
Database, backup and restore 111 Deleting locations 94 plates 146 Display preferences settings 195 Documentation Manager overview 7, 9 password 12 submitting documents 10 Drag-and-drop of containers 99 Duplicating a container 99
L
Labels, EHS 106 Labels, printing 104 List View, results 203 Location definition 89 Location tree 93 Location, creating 93 Locations 92 editing 92 new 92 Locking records 111 Log off button 196 web applications 213
E
Editing
ii Index
CambridgeSoft
Logging in 115
Q
Query see also Searching combination 202 different methods 198 formula 201 molecular weight 202 structure 199 text 198 Query Input form accessing 278, 311 components 195 opening 278, 311 using 195 Quitting web applications 213
M
Macintosh system requirements 191 Managing containers 98 locations 93 substances 95 the container list display 111 users and roles 108, 147 Marking records 205 MatchDatabase 182 Molecular weight searching 202 Moving locations 94 plates 145 Moving containers 99 Moving containers, with drag-and-drop 99 MSDS database 289 Multi-select 100
R
RAM 3 Record locking 111 Records clearing marked 205 marking 205 unmarking 205 viewing all 204 marked 205 Refining search results over current records 210 Refreshing the location tree 94 Removing ChemACX shopping cart 283 Reports EHS 107 matching fields 107 printing 106 Reports, printing 104 Requirements RAM 3 system 3 Requirements, installation 191 Restore see Database 111 Results changing views 203 exporting 210 form view 203
N
National Cancer Institute database 271
O
Online help 249 Opening ChemACX 278 server information 213 Ordering chemicals through ChemACX 283 Overview Chemical Registration 163 Documentation Manager 7, 9
P
Passwords, defining 108 Plates retiring 146 Preferences button 195 display 211 search 212 Printing 104 labels 104 reports 106 template Wizard 105 Product form ChemACX 286
Index
Index
iii
list view 203 Roles, assigning users to 109 Roles, managing 108 Roles, nesting 109
S
Safety data see EHS data 100 Saving ChemACX search results 279 to Shopping cart 279 sdf file 210 Search button 196 Search Type list 197 Searches simple 102 Searching 101 advanced techniques 102 ChemACX 278 combination search 202 for containers 101 for substances 103 formula search 201 molecular weight search 202 preferences 103 query methods 198 similarity 201 structure search 199 text search 198 using query input form 195 viewing all records 204 more records 204 results 203 Selecting multiple containers 100 Server information 213 Settings display preferences 211 search preferences 212 Shopping cart removing entries 283 saving to 279 viewing 283 Similarity searching 201 SQL queries, editing 101 Status, of containers 100
Structure searches exact 103 identity 103 similarity 103 substructure 103 Structure searching 199 Submitting documents 10 Substance definition 90 Substances 92 new, form 93 select, form 93 Substructure Search see Structure searches Supplier form ChemACX 287 Supplier Information Form 279 Supplier list, abbreviating 110 Suppliers, adding from ACX link 96 Suppliers, adding to ChemACX 287 Synthesis database 257, 259, 273, 291, 293, 297 System requirements 3, 191
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T
Table view, search results 203 Tables, managing 110 Text Searching 198 ToolTips 1, 249
U
Unmarking records 205 Users, assigning to roles 109 Users, managing 109 Using ChemACX 277, 287 query input form 195 Shopping cart 279
V
Version information 213 Viewing all search records 204 ChemACX shopping cart 283 marked records 205 more search records 204 search results 203 Views, changing 203
iv Index
CambridgeSoft
W
Web application logging off 213
quitting 213 Windows system requirements 191
Index
Index
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vi Index CambridgeSoft
CambridgeSoft Solutions
D ESKTOP S OFTWARE E NTERPRISE S OLUTIONS C HEMICAL I NFORMATICS B IOLOGICAL I NFORMATICS K NOWLEDGE M ANAGEMENT S CIENTIFIC D ATABASES
CAMBRIDGESOFT
ChemOffice Desktop to
KNOWLEDGE MANAGEMENT CHEMICAL INFORMATICS Desktop
E-Notebook Enterprise
CombiChem Enterprise
Registration Enterprise
E-Signatures IP Protection Enterprise
21CFR11 Compliance
GxP Validation
WebServer
DESKTOP TO ENTERPRISE
Chem & Bio Office ChemOffice Workgroup ChemOffice Enterprise
Just as Chem & Bio Office supports the daily work of the individual scientist, ChemOffice Enterprise, with Oracle Cartridge, and ChemOffice Workgroup, based on SQL Server, help organizations from small workgroups to large enterprises collaborate and share information more effectively.
KNOWLEDGE MANAGEMENT
E-Notebook Enterprise Reaction Explorer CombiChem Enterprise E-Signatures 21CFR11 Compliance
Research organizations thrive when information is easily captured, well organized, and readily available. E-Notebook Enterprise streamlines record keeping with rigorous security and efficient archiving, and facilitates text and structure searching. Reaction Explorer can display the ancestors and descendants of a particular batch in seconds, while CombiChem Enterprise provides the power of combinatorial chemistry. E-Signatures provides intellectual property protection and 21CFR11 Compliance implements an organizations regulatory compliance process.
CHEMICAL INFORMATICS
Inventory Enterprise GxP Validation Registration Enterprise DocManager Enterprise Oracle Cartridge
Managing huge data streams is a key challenge. Registration Enterprise organizes information about new compounds according to an organization's business rules, while Inventory Enterprise provides complete management of chemical and biological inventories, including GxP validation. DocManager Enterprise is an important part of collaborative research data management. Oracle Cartridge adds chemically intelligent searching to Oracle, integrating with ChemOffice Enterprise applications.
SOLUTIONS
Enterprise Solutions
BIOLOGICAL INFORMATICS SCIENTIFIC DATABASES
DocManager Enterprise
BioAssay & BioViz
ChemACX Database
The Merck Index
Oracle Cartridge or SQL DB
BioSAR Enterprise
Sigma-Aldrich MSDS
BIOLOGICAL INFORMATICS
BioAssay Enterprise BioViz BioSAR Enterprise BioDraw
Finding structural determinants of biological activity requires processing masses of biological assay data. Scientists use BioAssay Enterprise and BioSAR Enterprise to set up biological models and visualize information, to generate spreadsheets correlating structure and activity, and to search by structure. The BioViz application allows you to create graphical representations of data.
DESKTOP SOFTWARE
ChemDraw & Chem3D ChemFinder & ChemInfo BioAssay & BioViz BioDraw Inventory & E-Notebook
Success begins at the desktop, where scientists use ChemDraw, ChemOffice, and BioOffice to pursue ideas and communicate with the natural language of chemical structures, biological pathways, and models. Scientists organize information and manage data with E-Notebook and Inventory. Chem3D provides modeling, ChemFinder aids searching, while BioOffice adds BioAssay, BioViz and BioDraw. Integrated with Microsoft Office to speed research tasks.
SCIENTIFIC DATABASES
The Merck Index Scientific Databases ChemACX Database Sigma-Aldrich MSDS Development Training & Support
Good research depends on reference information, starting with the structuresearchable ChemACX Database of commercially available chemicals and SigmaAldrich MSDS. The Merck Index and other scientific databases provide necessary background about chemicals, their properties, and reactions.
PROFESSIONAL SERVICES
CambridgeSoft's scientific staff has the industry experience, and chemical and biological knowledge to maximize the effectiveness of your information systems.
Av ai la bl e
Includes *ChemDraw Ultra *ChemDraw Pro *ChemDraw Std
ETh Ch C N Ch In Bi e Bi em Che hem Ch ot ve em oO Bio M oA em Che eb m Bi O Dr Dr er nt m ffi O oV AC ffi oo Dr ck or aw ssa aw ffi ce ce aw 3D iz X k y y ce In Su Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul de ite Pr Pr tra tra tra tra tra tra tra tra tra tra x o o s
Win/Mac Win/Mac Win/Mac Win/Mac Win Win Win Win Win Win Win Win Win Win Win Win Win Win Win Win/Mac Win/Mac Win/Mac Win/Mac Win/Mac Win/Mac Win/Mac Win/Mac Win Win Win Win Win Win/Mac Win Win Win
*ChemDraw ActiveX/Plugin Pro *Chem3D Ultra Software Applications & Features Databases *Chem3D ActiveX Pro *Chem3D & E-Notebook Pro Chem3D & E-Notebook Std ChemFinder Pro ChemFinder Std *BioDraw Pro (Pathworks) *BioAssay Pro *Inventory Pro *E-Notebook Ultra BioViz/Chem & Bio Finder CombiChem/Excel ChemFinder/Oracle ChemFinder/Office ChemDraw/Excel Struct<=>Name ChemNMR & ClogP Stoichiometry Grid TLC PLate Tool Mass Fragmentation Tool Structure Clean Up Polymer Draw LabArt & BioArt Tinker/Chem3D MOPAC Client GAMESS Client Gaussian Client Jaguar Client The Merck Index *ChemACX Ultra (1 Year) *ChemINDEX Ultra ChemRXN, NCI & AIDS *Available Separately
Chem & Bio Office

the ultimate software suite for scientists the standard achieves the ultimate
Software Standard for Scientists
ChemOffice is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and ChemACX for chemists, BioOffice, BioAssay, BioViz, and BioDraw for biologists, and Inventory, E-Notebook and The Merck Index for scientists. ChemOffice and BioOffice are available for Microsoft Windows. ChemDraw includes Struct <=> Name, ChemDraw/Excel and ChemNMR. Create stereochemically correct structures from chemical names, and get accurate IUPAC names for structures. Estimate NMR spectra from a ChemDraw structure with direct atom to spectral correlation. The ChemDraw ActiveX/ Plugin adds chemical intelligence to your browser for querying databases and displaying information. Chem3D provides visualization and display of molecular surfaces, orbitals, electrostatic potentials, charge densities and spin densities. Chem3D utilizes MOPAC, Gaussian, GAMESS and extended Hckel to compute molecular properties. ChemProp computes Connolly surface areas, molecular volumes and properties, including Tinker, ClogP, molar refractivity, critical temperature & pressure. ChemFinder is a chemically intelligent database manager and search engine. ChemDraw/Excel creates searchable spreadsheets. ChemFinder/Word searches documents, spreadsheets, and files for chemical structures and references. ChemFinder includes CombiChem/Excel for combinatorial library generation in chemical spreadsheets. ChemFinder/Oracle provides enterprise solution integration. BioOffice is the ultimate suite for management, analysis and visualization of biological data using BioAssay and BioViz. Use BioDraw for drawing pathways. Includes Chem3D, Inventory and E-Notebook. BioDraw, formerly called Pathworks, makes drawing and annotating your biological pathways straight-forward and quick, adding a level of uniformity and detail which is unmatched. BioAssay manages both high and low throughput biological screening data. Designed for complex lead optimization experiments, the software supports the quick set-up of biological models. BioViz offers automated calculations, curve fitting, and customized structure activity reports, including a user friendly interface for importing, viewing, validating & plotting biological assay data. Inventory manages your reagent and biological tracking needs. Using MSDE as the desktop database, you organize, store and search over your inventory. Inventory integrates with the ChemACX database of available chemicals and ChemMSDX safety data providing chemical sourcing and purchasing. E-Notebook is the efficient, accurate way to write lab notebooks. It stores MS Office documents, ChemDraw structures and reaction drawings, and related data in a notebook searchable by text or chemical structure. Organize pages by project, experiment, or in your own style. Use CombiChem/Excel to build libraries. Databases include The Merck Index and ChemINDEX, including the NCI and AIDS databases. The ChemACX Database contains nearly 400 catalogs from leading suppliers and ChemMSDX Database contains over 20,000 material safety data sheets for commonly used laboratory chemicals.
computational chemistry made easy desktop to enterprise searching ultimate suite for biologists draw pathways screening data visualize data handle reagent tracking efficient notebook keeping access info with ease
ENTERPRISE &
Chem & Bio Office Workgroup

Integrated Research, Discovery, Development,
Research & Discovery - Search for Products
Since the companys founding, CambridgeSofts desktop software, starting with its industry-leading ChemDraw, has been the cornerstone application for scientists who draw and annotate molecules, reactions, and pathways. The suite of applications has developed and CambridgeSoft now provides solutions in virtually all areas of discovery. Researchers can record and share their experimental information using E-Notebook, while protecting intellectual property with digital signatures and 21CFR11 compliance. They can design both single experiments or design combinatorial libraries of compounds. They find and purchase reagents in ChemACX database, store
and use them from Inventory, record newly made compounds within a proprietary Registration system, record the results from biological testing in BioAssay, analyze the results with BioViz, and generate reports linking activity and structure with BioSAR. Virtually every aspect of discoveryfrom synthesis planning, library enumeration, reagent selection, primary and secondary screening, in vivo testing, through to analysis of results and reporting is covered by this integrated application suite.
Development - Converting Leads into Testing
Building on productivity software, CambridgeSoft created enterprise applications to meet the needs of an
En ter
W W W or or or kg kg kg pr ro ro ro ise up up up Ul Std Pr Std tra o
ChemOffice
Includes
En
ter
pr Ul ise tra
En
ter
pr is Pr e o
E-Notebook Enterprise or Workgroup BioAssay Enterprise or Workgroup BioSAR Enterprise BioViz Desktop Registration Enterprise Inventory Enterprise or Workgroup ChemACX Database ChemINDEX Database Oracle Cartridge SQL Server Compatible ChemFinder Ultra
All specifications subject to change without notice.
US EU 1 800 3157300 00 800 875 20000 INTL 1 617 5889300 UK +44 1223 464900 FAX JP 1 617 5889390 0120 731 800 EMAIL WWW info@cambridgesoft.com www.cambridgesoft.com
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005
WORKGROUP
and Enterprise Solutions

Trials and Manufacturing Workflow
ever expanding research and development community that relies on data sharing across scientific disciplines, research campuses, and even oceans as globalization has increased demands. Since it is web-based, the software is deployed readily throughout a research and development organization. Using Registration, ENotebook, BioAssay, and BioViz, in conjunction with DocManager and DrugDeg, scientific teams are well armed to solve the daily challenges of development. These teams include scientists who scale up and design manufacturing procedures, toxicologists who determine the metabolic fate of drug candidates, formulation scientists who determine drug dosing and delivery systems, as well as many others.
Trials & Manufacturing - Last Steps to Success
The handling of materials, including chain of custody requirements, material documentation, material workflow, such as availability states and recertification dates, are tracked and handling by the system. The systems meet these requirements and provide the basis to manage materials and records during clinical trials. Clinicians can design and record results from protocols, and all of these web based software systems provide the access required by clinicians who are removed from the sponsoring company.
ChemOffice Enterprise is a comprehensive
A suitable drug candidate is one that has the desired activity to provide disease therapy while still meeting drug safety requirements, can be manufactured in a cost effective and reproducible fashion under 21CFR11 and GMP guidelines, and is stable under normal formulation and storage conditions. With a drug candidate in hand, the final challenge is to determine safety and efficacy, beyond the laboratory, in a patient population. Manufacturing requires the hand off of data and batch process records from the pilot plant studies using Inventory, E-Notebook, and Registration systems under Good Laboratory and Manufacturing Processes (GxP).
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knowledge management and informatics solution, covering electronic notebooks, biological screening, chemical registration and more over your intranet. Enterprise Ultra includes E-Notebook for record keeping, BioAssay for low and high throughput screening with integrated plate inventory, BioSAR for SAR reports, Registration system, Inventory for reagents and ChemACX database of available chemicals. Technologies include ChemDraw ActiveX and Oracle Cartridge.
ChemOffice Workgroup is a comprehensive
knowledge management and informatics solution, covering electronic notebooks, biological screening and more over your intranet. Workgroup Ultra includes E-Notebook for record keeping, BioAssay for low and high-throughput screening, BioViz for visualization, Inventory for reagents and ChemACX database of available chemicals. Technologies include SQL Server for affordability and ease of administration.
EMAIL WWW
info@cambridgesoft.com www.cambridgesoft.com
KNOWLEDGE
E-Notebook, Reaction Explorer,

Electronic Journal and Record Keeping
E-Notebook E-Notebook provides a smooth web-based interface designed to replace paper laboratory notebooks, with a fully configurable, secure system for organizing the flow of information generated by your organization. You can enter reactions, Microsoft Word documents, spectra and other types of data, and search this data by text, substructure or meta data. You can organize your electronic pages by projects, experiments or any other classification that conforms to your workflow. E-Notebook Enterprise E-Notebook Enterprise edition integrates notebook keeping at group and enterprise levels to promote lab productivity and information sharing. Oracle Cartridge manages chemical structures in a common data repository with detailed security and 21CFR11 Compliance. The enterprise edition also works with procurement and inventory management systems to save time locating chemicals and entering structures. E-Notebook Workgroup E-Notebook Workgroup, intended for use with a medium number of users, offers much of the functionality delivered in E-Notebook Enterprise while using SQL Server as the database. Learning to use and administer the application is quick and straightforward. E-Notebook applies various data types to suit different disciplines with an unlimited number of workflows.
E-Notebook offers custom organization of notebook pages at personal or enterprise levels Quick access to important data by searching on keywords, dates, chemical structures and more Reaction Explorer can display the ancestors and descendants of a batch in seconds
E-Notebook Ultra E-Notebook Ultra is the efficient, accurate way to write lab notebooks entries as you work. It stores Microsoft Office documents, ChemDraw structures and reaction drawings, and related data in an electronic notebook you can search by text or chemical structure. Organize pages by project, experiment or your own style with the MSDE database. CombiChem/Excel builds combinatorial libraries. Reaction Explorer Reaction Explorer is a powerful application that assembles a vast amount of information into a lucid synthesis map. The map provides reaction information, as well as quick access to experiments. Reaction Explorer displays two types of relationships between compounds: relationships grouped by batch and those grouped by compound. Both types of displays are configurable, allowing scientists to create a look and feel that they are comfortable with.
MANAGEMENT
E-Signatures & 21CFR11 Compliance

Property Protection and Regulatory Compliance
The batch display tracks the history of a particular entity through several subsequent reactions and experiments. This might be of interest to a chemical auditor or patent attorney needing to track down the original source of material. The compound display is more general, and shows all possible pathways to and from a compound. This is ideal for chemists working to optimize a process, or a patent attorney trying to link a product to discovery, or a scientist trying to compile work done by several other scientists. Process Chemistry The objective of process research is to identify efficient processes for the synthesis of active pharmaceutical agents at the scale required for clinical trials and commercial use. It is necessary to provide precise descriptions of these processes so that they can be executed by different groups in different locations. E-Notebooks process chemistry modules are designed to support these dual workflow and regulatorycompliance needs of process chemists. After the steps in a synthesis have been optimized, either individual steps or the entire synthesis must be scaled.
E-Notebook also provides the capability to scale reactions by virtually any parameter from reagent amount to vessel size. Individual reactions may be scaled as well as total syntheses. Batch procedures created with E-Notebook can be used to produce automatically batch record worksheets.
Display Ancestors
Authenticate Work
KNOWLEDGE
E-Notebook, Reaction Explorer,

Electronic Journal and Record Keeping
CombiChem Enterprise Combinatorial chemistry, in particular the technique of parallel synthesis, has become an essential element of the drug discovery process. By using parallel synthesis techniques, chemists are able to multiply their productivity by a factor of between 5 and 100. CombiChem Enterprise has been developed to provide the tools required by the combinatorial chemist to manage and document parallel synthesis experiments. Flexibility is the key when dealing with databases of chemical compounds. CombiChem Enterprise can use reagent lists from a variety of different sources: SD files, ChemFinder databases, ChemFinder hit lists, ChemACX Database, or directly from the user via ChemDraw. Regardless of the source, CombiChem produces a list of reagents which match a particular generic reactant. E-Signatures IP Protection E-Signatures provides data storage and access functions for electronic records. It is used in conjunction with E-Notebook as a long-term storage system. While E-Notebook is intended to capture and record data as the experiments are carried out, E-Signatures serves as the repository for finished experiments and other documents. Electronic records must be available indefinitely, and their authenticity must be verifiable independently of the E-Notebook system. In addition to the record, E-Signatures long-term archive includes a digital signature, a timestamp, and
Highly flexible and configurable to match an organizations workflow Consulting teams analyze and adapt existing procedures to comply with new regulations Systems include authentication and digital signatures and adapt to changing regulations and demands for intellectual property protection
associated metadata. Managers, patent attorneys, and scientists can retrieve records based on searches over the metadata. E-Signatures also manages the signature workflow for electronic records and documents in process. Digital signatures are captured at the time of record creation, which can later serve to prove the authenticity of the stored electronic records. Reviewers, witnesses, and other individuals can countersign records for various business purposes, including witness records necessary to meet the needs of 37 CFR and similar regulations worldwide. 21CFR11 Compliance Large and growing enterprises are facing a challenge to their core missions of developing and producing new products including food, therapeutic pharmaceuticals, medical devices, cosmetics or other health

MANAGEMENT
E-Signatures & 21CFR11 Compliance

Property Protection and Regulatory Compliance
enhancing items. The complexity lies in complying with government regulations designed to protect public health and safety. The most notable of these is Title 21 of the Code of Federal Regulations governing Electronic Records and Signatures (21CFR11). Once you have determined how your enterprise will comply with these new regulations, implementing those decisions needs to be done quickly, efficiently and with the understanding that the rules for compliance are in flux. In order to succeed, you must be able to respond to change. CambridgeSofts 21CFR11 Compliance consulting has both the tools and the expertise to provide complete solutions, carry out integration with existing systems, and help execute the process as quickly as your organization demands.

CHEMICAL
Inventory, Registration,
Chem and Bio Inventory and Registration
Chem & Bio Inventory Inventory is an application designed to manage the chemical and reagent tracking needs of laboratories and research centers. The system manages data associated with both commercially procured and internally produced chemical substances from procurement or initial production through depletion and disposal. To meet the needs of institutions of all sizes, Inventory comes in an Enterprise edition, a Workgroup edition and two Desktop editions. Inventory Enterprise is an Oracle-based, ChemOffice Enterprise product. Designed for large organizations, it comprises a number of features not included in the desktop or workgroup versions. Inventory Enterprise conveniently manages plate information. In addition to storing, moving, and deleting plates, the application allows users to create daughter plates and reformat plates. Inventory Enterprise can be tightly integrated with Registration Enterprise and ChemACX Database. Inventory Workgroup is a thick-client SQL Serverbased product. This version is suitable for larger organizations that do not have the interest or desire to maintain an Oracle server. Inventory Ultra is the same MSDE based product, while also including the ChemACX Database, CambridgeSofts collection of nearly 400 catalogs from suppliers of chemical reagents.
Inventory offers plate handling for highthroughput experimentation Inventory is GxP Compliant with validated audit trails Registration has flexible business rules for registration, salt handling, and batch fields with chemical intelligence that includes advanced stereochemistry
Inventory Pro is an all-inclusive desktop product. It includes Microsoft SQL Server Desktop Edition (MSDE ), the re-distributable database for SQL Server. No additional licensing is required. Registration Enterprise Registration Enterprise includes a robust data model for pure compounds, batches, salt management, automatic duplicate checking and unique ID assignments. Compounds may be entered individually or through the use of a batch loader. The data model resides entirely in Oracle and uses Oracles security and transaction framework. Registration is easily adapted to any workflow. New compound chemical and non-chemical data is entered into a temporary storage area through a web form. When the compound is registered, it is compared for uniqueness via a configurable, stereoselective duplicate check, and assigned a registry
I N F O R M AT I C S
DocManager & Oracle Cartridge

Document Searching and Enterprise Infrastructure
number. All information about the compound, including its test data and other syntheses, is tracked by the registry number. When a compound is registered, the structure is checked for novelty. If a duplicate already exists in the database, the user can elect to register the information as a new batch of the existing compound, or assign it a unique registry number. Registration Enterprise is the only true n-tiered application of its kind that is designed around thin clients and thin servers. This translates into ultimate flexibility on both the client and server side. Oracle is supported on a variety of platforms and operating systems. Using Oracle keeps your proprietary data secure through the use of Oracles role based security and allows all chemical and non-chemical data to be stored directly in the Oracle tables. Formulations & Mixtures Formulation scientists face different challenges from those working with individual molecules, yet many of the tools they are forced to use emerge from the drug-discovery world, where single-molecule research is the norm. Take an essential task such as compound registration and you will find that most
systems are designed for registration of single molecules, with little thought for the world of formulations and mixtures. CambridgeSoft has developed a system specifically designed for this registration need called Formulations & Mixtures.
Index Documents
Manage your Inventory
CHEMICAL
Inventory, Registration,
Chem and Bio Inventory and Registration
DocManager Enterprise Web browser based, DocManager Enterprise extends the capability of standard search engines to include full free text searching and chemically intelligent structure searching of electronic documents including Text, Microsoft Word, Excel, PowerPoint, and Adobe PDF. The DocManager Enterprise interface allows users to easily submit documents through a series of simple to navigate web forms. When a new document is submitted, DocManager builds a free-text index of the document, and extracts chemical information into a chemically-aware, substructure searchable database. Chemical information can originate from either ChemDraw or ISIS Draw. DocManager Enterprise includes a batch loading utility for administration level users to load multiple documents at one time. The system can be configured to submit a batch of documents as one event, or as a reoccurring submission to be executed daily. The administrator simply specifies a time for the submission to take place and the location of the files. DocManager Enterprise utilizes the searching intelligence of the ChemOffice Enterprise suite. In addition to standard textual and numerical searching, DocManager searches the submitted documents for chemical structure or reaction.
DocManager parses Word, Excel and PowerPoint documents, including free text DocManager has a web based interface and a file drop folder for quick submissions Oracle Cartridge is compatible with Linux, Solaris, AIX and Windows and includes structure searching, property predictions and nomenclature
Oracle Cartridge The CambridgeSoft Oracle Cartridge is used by all ChemOffice Enterprise applications for storing, searching over, and analyzing chemical data. It can also be used in the development of your custom Oracle applications. Chemical structure information is difficult to manipulate without utilizing special software. Oracle data cartridges define new, recognized datatypes. CambridgeSofts Oracle Cartridge utilizes this technology making it possible to manipulate chemical structure and reaction data from within Oracle, improving portability and consistency in applications. Since the Oracle Cartridge is accessed through Oracle, this allows the programmer to interact with chemical structure data directly in Oracle. The CambridgeSoft Oracle Cartridge supports CDX , CDXML , MolFile, RXN , and SMILES formats making it flexible enough to be included with both new and legacy data, without the need for conversion.
DocManager & Oracle Cartridge

Document Searching and Enterprise Infrastructure
ChemFinder Enterprise ChemFinder Enterprise is a multiple-user system designed for sites with heavy-duty chemical and biological data needs. ChemFinder Enterprise contains its own engine for working with local and shared databases and it is also delivered with the CambridgeSoft Oracle Cartridge, the powerful Oracle-hosted structure engine based on ChemFinder search technology. So, the face of ChemFinder Enterprise is the same friendly form-oriented interface as the desktop version, but underneath is a fast direct connection to Oracle and the robust, scalable Oracle Cartridge running on the server.

BIOLOGICAL
Assay Screening and Visualization

BioAssay Biological assay data comes in many forms, from a scientists observations to output from a plate reader. Software designed to store and analyze this data must provide a solution for both the ultra-high volume laboratories, including laboratory automation, calculation, and statistics, as well as the very complicated low and medium throughput assays such as animal models and in vivo experiments. Organizing, analyzing, and sharing data can be a challenge for screening biologists, regardless of the amount of automation or manual data manipulation employed. BioAssay was designed to tackle the needs of high and low throughput screening biologists alike by providing an application flexible enough to model any assay, regardless of complexity, while robust enough to provide an easy to use interface for importing, storing and analyzing the data. The software supports the quick set-up of biological models, automated calculations and curve fitting, data validation, and the creation of customized structure activity reports. BioAssay Enterprise offers a scalable, flexible biological screening solution utilizing Oracles role based security and the Oracle Cartridge. As part of ChemOffice Enterprise, BioAssay is easily integrated with Inventory Enterprise for plate tracking and management, Registration Enterprise for the registration of new compounds and BioSAR Enterprise for customized reporting.
BioAssay, BioViz,
BioAssay effectively manages data from complex biological assays involved with lead optimization BioViz provides a flexible reporting and plotting engine for your scientific data BioViz integrates with BioSAR for one step indepth data analysis from a BioSAR report
BioAssay Workgroup, intended for single site deployment, uses SQL Server as a database, instead of Oracle. This solution offers affordability and ease of maintenance, but still remains a robust solution suitable for a smaller groups needs. Organize and share your biological screening data with minimal administrative costs. BioAssay Ultra is designed to deliver much of the functionality of our enterprise level applications, without a widespread roll out. MSDE database compatible, BioAssay Ultra, coupled with BioViz, offers a user friendly interface for importing, viewing, validating, and plotting your biological assay data from your desktop.
BioSAR & BioDraw

BioViz BioViz, with ChemFinder, transforms the numbers in your database into graphics on your screen. Retrieve or search for a set of compounds, choose the data you want to see, whether it is biological test results in Oracle tables, physical property values calculated automatically or prices in a catalog, and BioViz will generate an interactive window showing a scatterplot, histogram, or other useful data graphic. The Plot Window, the key to data visualization in BioViz, shows two variables plotted against each other in a scatterplot with each point representing a structure from the current hit list. If you modify the list, for example by performing a search, the plot updates to show the new set of points. You can drag a rectangle around a set of points to select them, or zoom in to see them more closely.
Data Mining and Pathway Drawing
Draw Biological Pathways
Plot Assay Data

BIOLOGICAL
Assay Screening and Visualization

BioSAR BioSAR Enterprise, a strategic must for any discovery organization interested in serious data mining, is a data-dictionary driven structure-activity analysis program. Users may choose among assays registered in the dictionary or search for assays of interest. The power of BioSAR lies in the researchers freedom from dependence on IT support. Once an assay is registered into the data-dictionary, it is automatically included in the powerful analysis framework. By reducing the time between question and answer, BioSAR gives researchers the ability to explore new ideas, the bottom line for discovery information systems. Systems that provide answers after questions have become irrelevant are of no use. BioSAR avoids this issue by placing application development in the researchers control. BioSAR Enterprise allows the researcher to create custom reports and views of their data. You decide what is displayed, and BioSAR takes care of the rest. While most SAR tools provide only a table-based interface, BioSAR provides a both a form view and table view. The form view provides highly detailed information about one compound, whereas the tabular view makes viewing comparisons between compounds more feasible. There is often a tradeoff between power and simplicity, and most SAR tools opt for the former at the expense of the latter. BioSAR, however, merges the sophistication of a powerful data catalog technique with knowledge gained through years of
BioSAR is a catalog driven data mining and structure- activity analysis program BioSAR provides both form and table views within a simple and powerful web interface BioDraw makes it easy to draw and annotate biological pathways including common elements such as membranes, enzymes, receptors and DNA
BioAssay, BioViz,
working closely with users. The result is a SAR application that is as intuitive as it is powerful. Security within BioSAR Enterprise is highly granular. Different roles exist for administrators, publishers, and browsers. Administrators may add assays to the data catalog engine, publishers may create reports and publish them, and browsers may use data query and analysis. Most data mining tools provide a mechanism to store queries, but the interface for creating queries is too complex. With BioSAR, each set of assays is a complete report with a query form, a view form, and a table view, combining the convenience of a ChemFinder or ISIS application with the power and flexibility of a data catalog-driven mining program.

BioSAR & BioDraw

BioDraw Reporting on and presenting findings is a task familiar to every biologist. Making this process easier and more effective benefits everyone involved. BioDraw, formerly called Pathworks, is doing for biologists what ChemDraw has done for chemists for years saving time, and resulting in a more professional representation of the science at hand. BioDraw makes drawing and annotating biological pathways quick and easy, adding a level of uniformity and detail which is unmatched. Typical drawings of biological pathways include many elements that are difficult to draw with the standard presentation and word processing software that is on the market. Common pathway elements such as membranes, enzymes, receptors, DNA and reaction arrows are built into the BioDraw toolbar. BioDraw also allows users to import images in GIF, PNG or JPEG format. Keeping data organized is of utmost importance in any lab. BioDraw reflects that importance by allowing users to store annotations for each element in a drawing. Annotation data ranges from manually entered text to attached documents, restriction maps, microarrays, sequence information, literature references, or links. Any data, regardless of format, is stored side-by-side with the drawing for future retrieval.
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Data Mining and Pathway Drawing

The drawing and data organization offered by BioDraw gives any biologist an advantage. Sharing this advantage assists the community as a whole. BioDraw offers many ways to share your drawings and accompanying data. Users can export data to Microsoft Office applications for inclusion in presentations and grant proposals or save data as an image file for use in journal article submission.
DESKTOP
Structure Drawing and Molecular Modeling

ChemDraw Ultra adds Struct<=>Name, ChemDraw/Excel, ChemNMR, CLogP, tPSA and ChemFinder/Word to ChemDraw Pro. With rich polymer notation, atom numbering, BioArt templates, and modern user interface, ChemDraw is more powerful than ever before. Create tables of structures, identify and label stereochemistry, estimate NMR spectra from a ChemDraw structure with structureto-spectrum correlation, obtain structures from chemical names, assign names from structures, and create multi-page documents and posters. ChemDraw Pro will boost your productivity more than ever. Draw publication-quality structures and reactions. Publish on the web using the ChemDraw Plugin. Create precise database queries by specifying atom and bond properties and include stereochemistry. Display spectra, structures, and annotations on the same page. Use the Online Menu to query ChemACX.Com by structure and identify available vendors. Struct<=>Name contains the leading comprehensive methods for converting chemical structures into chemical names and names to structures. It can be used for many types of compounds, including charged compounds and salts, highly symmetric structures and many other types of inorganic and organometallics. Struct<=>Name is available in two forms: a batch application, and an interactive version that is also available in ChemDraw Ultra.
ChemDraw, Chem3D,
ChemDraws improved Struct<=>Name feature produces names for more types of compounds Live ChemDraw window embedded in Chem3D application allows simultaneous 2D and 3D editing Chem3D brings workstation-quality molecular graphics and rigorous computational methods to your desktop
ChemDraw/Excel allows the user to create chemically knowledgeable spreadsheets within the familiar Microsoft Excel environment. You can build and manipulate chemical structures within Excel, compute chemical properties and perform database searches. ChemNMR can be used to accurately estimate 13C and 1H (proton) chemical shifts. The molecule and the spectrum appear in a new window. The chemical shifts are displayed on the molecule and the spectrum is linked to the structure so that clicking on a peak in the spectrum highlights the related fragment on the molecule.
S O F T WA R E
ChemFinder & ChemInfo

Structure Searching and Scientific Databases
Chem3D Ultra includes a number of molecular modeling capabilities such as molecular overlay, conformational searching and dihedral driver support. It also includes interfaces for optional use of MOPAC , Gaussian and GAMESS . The user can also compute advanced physical properties such as CLogP and ChemProp. These properties can be used to create SAR tables. ChemSAR/Excel can then be used to explore structure activity relationships. High quality Chem3D graphics can be viewed on the web using the Chem3D ActiveX. Chem3D Pro brings workstation quality molecular visualization and display to your desktop. Convert ChemDraw and ISIS/Draw sketches into 3D models. View molecular surfaces, orbitals, electrostatic potentials, charge densities and spin densities. Use built-in extended Hckel to compute partial atomic charges. Use MM2 to perform rapid energy minimizations and molecular dynamics simulations. ChemProp estimates physical properties such as logP, boiling point, melting point and more. Visualize Connolly surface areas and molecular volumes. MOPAC is a semi-empirical quantum mechanics package which can be applied to the study of chemical properties and reactions.
It can also be used to predict a number of chemical and physical properties. Chem3D contains an interface to the MOPAC package. Gaussian is a collection of semi-empirical and ab initio molecular orbital (MO) computational methods which can be used to predict energies, molecular structures, molecular properties, as well as molecular spectra. Chem3D enables the user to transparently create input and analyze output resulting from Gaussian.
Molecular Modeling
Estimate Spectra
DESKTOP
Structure Drawing and Molecular Modeling

ChemFinder Enterprise is a multiple-user system designed for chemical and biological data management. ChemFinder Enterprise contains its own engine for working with local and shared databases and it is also delivered with the CambridgeSoft Oracle Cartridge, the powerful Oracle-hosted structure engine based on ChemFinder search technology. So, the face of ChemFinder Enterprise is the same friendly form-oriented interface as the desktop version, but underneath is a fast direct connection to Oracle and the robust, scalable Oracle Cartridge running on the server. BioViz, included in ChemFinder Enterprise, provides a new set of data visualization features. These features allow you to plot structural and biological data in a variety of styles, filter plots based on your criteria, highlight lists and intersecting sets on plots, generate histograms of data distributions, and more. ChemFinder Pro is a fast, chemically intelligent, relational database search engine for desktop, workgroup or enterprise applications. Extended integration with Microsoft Excel and Word adds chemical searching and database capability to spreadsheets and documents. Today, an ever-increasing number of chemical databases are available in ChemFinder format. Compatibility with MDL ISIS databases is provided by SDfile and RDfile import/export. ChemFinder provides network server workgroup functionality when used with ChemOffice Workgroup and Enterprise.
ChemDraw, Chem3D,
ChemFinder offers improved searching and hitlist management, along with new property generation ChemFinder is tightly integrated with CambridgeSofts Oracle Cartridge Search ChemACX and other CambridgeSoft databases for important chemical information
The Merck Index is an encyclopedia of chemicals, drugs and biologicals, with over 10,000 monographs covering names, synonyms, physical properties, preparations, patents, literature references, therapeutic uses and more. ChemACX Database includes 500,000 chemical products from nearly 400 supplier catalogs, searchable with a single query by structure, substructure, name, synonym, partial name, and other text and numeric criteria. ChemSCX is a compilation of searchable catalogs from leading screening compound suppliers. ChemMSDX Database provides material safety data sheets for 7,000 pure compounds. ChemINDEX Database includes 100,000 chemicals, public NCI compounds, AIDS data, and more.
S O F T WA R E
ChemFinder & ChemInfo

Structure Searching and Scientific Databases
NCI Database contains over 200,000 compounds with anti-cancer drug dose-response data. AIDS Database is an NCI compiled database for AIDS anti-viral compounds. ChemRXN Database is a collection of 30,000 fully atom-mapped reactions selected and refined from the chemical literature. It includes reactions from InfoChems ChemSelect database and ISIs ChemPrep database. ChemFinder.Com is the award-winning web site with information and WWW links for over 100,000 chemicals. Users can search by name or partial name, view structure drawings, or use the ChemDraw ActiveX/Plugin for structure and substructure searches. In addition, users can view live ChemDraw files on Windows and Macintosh clients.

DESKTOP
BioDraw, BioAssay, BioViz

BioAssay Ultra BioAssay Ultra, the cornerstone of BioOffice, provides flexible storage, retrieval, and analysis of biological data. BioAssay easily manages both high and low throughput biological screening data. Designed for complex lead optimization experiments, the software supports the quick set-up of biological models, automated calculations and curve fitting, and the creation of customized structure activity reports. BioAssay brings all of this functionality to your desktop. BioAssay Ultra, compatible with MSDE database, offers a user friendly interface for importing, viewing, validating and plotting your biological assay data. BioViz Combining biological data with the chemical structure is of utmost importance in any drug discovery environment. BioViz allows you to analyze structurerelated data combined with biological data visually. BioViz, within ChemFinder, provides a graphical representation of the data loaded into a ChemFinder form. Users can search over data and construct a scatterplot, histogram, or other useful data charts. Plots are interactive to allow you to select subsets of your data. BioDraw BioDraw, formerly called Pathworks, makes drawing and annotating your biological pathways quick and easy, adding a level of uniformity and detail which is unmatched. Typical drawings of biological pathways include many elements that are difficult to draw with
Pathways, Biological Assay and Visualization

BioAssay offers flexible storage, retrieval and analysis of biological data BioViz provides a graphical representation of the data loaded into a ChemFinder form BioDraw allows for quick and easy drawing and annotating of biological pathways, including importing of images in GIF , PNG or JPEG format
the standard presentation and word processing software on the market. Common pathway elements such as membranes, enzymes, receptors, DNA and reaction arrows are built into the BioDraw toolbar and including them in your document is as easy as including a rectangle. Click on the toolbar shortcut and drop the element into your document. Resize and move elements by clicking and dragging and create an accurate and concise drawing in minutes. BioDraw allows the import of images in GIF , PNG or JPEG format. ChemDraw users are also able to include ChemDraw structures in drawings without difficulty. Keeping data organized is of utmost importance in any lab. The BioDraw application reflects that importance by allowing you to store annotations for each
S O F T WA R E
Inventory & E-Notebook

element in your drawing. Annotation data ranges from manually entered text to attached documents, literature references, or links. Any data, regardless of format, is stored side-by-side with the drawing for future retrieval. The drawing and data organization offered by BioDraw gives any biologist an advantage. Sharing this advantage assists the community as a whole. BioDraw offers many ways to share your drawings and accompanying data.
Materials Management and Electronic Journal
Notebook Pages
Data Visualization

DESKTOP
BioDraw, BioAssay, BioViz

Inventory Ultra Inventory is an application designed to manage the chemical and reagent tracking needs of laboratories and research centers. The system manages data associated with both commercially procured and internally produced chemical substances from their procurement or initial production through their depletion and disposal. Inventory Ultra is an MSDE based product and includes the ChemACX Database with nearly 400 catalogs of chemical reagents. The three primary entities in an Inventory system are locations, containers, and substances. Users or administrators configure a network of locations, which represent locations within an organization. Containers are created to represent actual containers in your facility. Each container is assigned a unique barcode, which can be printed, using a customized template, from the Inventory interface. Each container stores a substance. Additional text fields are available to track other chemical contents such as the solvent, and custom fields may also be defined. To keep track of substances, the system maintains its own internal chemical structure database containing unique substances that can be associated with inventory containers. Advanced duplicate checking is incorporated in the system. Every field in a record, including chemical structure, molecular formula and molecular weight are searchAll specifications subject to change without notice.
Pathways, Biological Assay and Visualization

Inventory manages the chemical and reagent tracking needs of laboratories and research centers Inventory maintains its own internal chemical structure database with advanced duplicate checking E-Notebook stores Microsoft Office documents, ChemDraw structures, reaction drawings and related data in a convenient, searchable format
able. The application includes a number of specially designed inventory search forms. Search results are returned in list form and can be exported into a document (PDF , RTF , HTML ) using the report engine. The Inventory interface allows for printing labels as well as generating elaborate reports. Inventory uses a report application that incorporates wizards that allow for the quick creation of simple report and label templates that can be shared across an organization. Inventory Pro Inventory Pro contains the same features as Inventory Ultra without the ChemACX Database. E-Notebook Ultra E-Notebook Ultra is the efficient, accurate way to write lab notebooks entries as you work. It stores
S O F T WA R E
Inventory & E-Notebook

Microsoft Office documents, ChemDraw structures and reaction drawings, and related data in an electronic notebook that is searchable by text or chemical structure. You can organize pages by project, experiment, or in your own style with the MSDE database . CombiChem/Excel builds combinatorial libraries. E-Notebook is configured exactly like a chemist would like his or her own notebook to be. Reactions can be easily drawn into the reaction template by either selecting from the generous list of preloaded reagents or by entering or drawing ones own chemicals. Commonly used reagents can be stored in a separate folder for easy access. Another fantastic feature is the procedural section. This section contains prewritten procedural sentences with the ability to easily drop in the specific names of reagent chemicals present in the reaction. One can also easily add other data to the notebook page such as spectra and Word or Excel documents. CombiChem/Excel CambridgeSoft provides you with the tools to effectively plan combinatorial chemistry experiments in Excel. The CombiChem/Excel add-in introduces additional functionality for handling combinatorial chemistry. Users can generate products from a reaction and lists of reagents, you can view all the products arising from a given reagent or all the reagents of a given product, and you can lay out reagent and reaction plates.
Materials Management and Electronic Journal
SCIENTIFIC
The Merck Index, NCI, AIDS,

Scientific Reference, Chemical Reactions and Patents
The Merck Index Among printed chemical reference works, one that stands out for its integrity, detail and longevity is The Merck Index. The Merck Index database is a structuresearchable encyclopedia of chemicals, drugs, and biological agents which includes the complete 10,250 monographs of the 13th edition, 230 new monographs unavailable anywhere else, as well as 540 monographs retired from the 12th Edition. The Merck Index is available in many forms to suit the various needs of both individuals and institutions. Personal subscriptions are available in one-year and one-month time periods. A stand-alone package, requiring no other applications, is also available for personal use. The subjects covered include human and veterinary drugs, biological agents and natural products, industrial and laboratory chemicals, and environmentally significant compounds. In addition to the standard searches, compound monographs can be searched by ChemDraw structure as well as substructure. Traditional Chinese Medicines Many of todays well-known drugs have their origins from natural sources. Access to this wealth of knowledge is now available with the Traditional Chinese Medicines database. The database consists of monographs for 10,458 chemicals isolated from 4,625 natural sources used in traditional Chinese remedies. The monographs feature bio-activity data for many
The Merck Index offers encyclopedic reference for over 10,000 chemicals, drugs and biological agents Traditional Chinese Medicines provides chemical information and their biological effects of complex compounds isolated from natural sources All electronic databases are updated, contain information unavailable in print, and are searchable by structure, as well as text and numeric range
of the compounds, effects and indications of the medicines, English, Latin, and Chinese names for the natural sources, and over 2,000 references. This information is also available as an SD file to facilitate in silico research. ChemINDEX The ability to quickly look up data such as chemical properties, biological assay results and toxicological information is no longer a luxury item, but instead a requirement. Scientists have used the award-winning ChemFinder.Com database since 1995. Now, the data on ChemFinder.Com is integrated into ChemOffice as ChemINDEX. ChemINDEX contains data on over 75,000 compounds including structures, names and synonyms, physical properties, and Internet links.
D ATA B A S E S
ChemACX & Sigma-Aldrich MSDS

Available Chemicals and Material Safety Data Sheets
NCI, AIDS & Cancer Three informative databases have been integrated into one powerful application with the NCI and AIDS database collections. The application starts with a collection of over 200,000 molecules collected by the National Cancer Institute. Searchable fields include structure, synonym, CAS RN, formula, and molecular weight. ChemRXN ChemPrep and ChemSelect are the two reactions databases that make up ChemRXN. ChemPrep is a reaction database assembled by the Institute for Scientific Information (ISI). This reaction database is designed to help organic chemists find reactions easily. It includes full literature citations. ChemSelect, licensed from InfoChem GmbH, is a reaction database containing 13,000 important organic reactions. ChemSynth ChemSynth, from InfoChem GmbH, is a database of sample reactions comprising essential information on 180,000 reactions. These reactions have been selected because they have greater than 50% yield and have been sited in leading journals more than once. The database consists of reaction information and literature reference.
ChemReact68 ChemReact68, from InfoChem GmbH, is a database of sample reactions comprising essential information on 68,000 reactions. These reactions have been selected because they have greater than 50% yield and have appeared in more than five example reactions. The database consists of reaction information and literature references.
REFERENCE DATA
The Merck Index Traditional Chinese Medicines ChemINDEX Database NCI, AIDS & Cancer Drugs: Synonyms & Properties Medicinal Chemistry
SOURCING & SAFETY DATA
11,000 monographs 10,000 substances 75,000 substances 270,000 substances 8,000 drugs 540,000 substances 380 catalogs 23,000 MSDSs 130,000 MSDSs 28,000 reactions 178,000 reactions 68,000 reactions
ChemACX Database ChemMSDX Database Sigma-Aldrich MSDS

REACTION & SYNTHESIS DATA
ChemRXN Database ChemSynth ChemReact68
PROFESSIONAL
Development, Deployment,
Custom Development and System Deployment
With custom development, CambridgeSoft works collaboratively with your team to create a system that meets your needs while executing our quality driven software development process. We deliver what you need, on time and within budget, without surprises.
In order to provide our customers with a total solution for scientific informatics, CambridgeSoft offers the following services to assist our clients in maximizing the productivity of their research and discovery organizations. Informatics Planning
Strategic and Operational Planning
A formal analysis is conducted to provide a roadmap for successful technology utilization. This process includes: An analysis of the current state of the science technology environment, including architecture and operational processes A view of the strategic goals and the barriers to achievement The delivery of a phased technology transition plan
Requirements Analysis & Proof of Concept
Project Readiness Assessment
Is your project set up for success? Is it well defined into measurable deliverables? Are the roles of project members clearly defined? CambridgeSofts Project Readiness Assessment has one goal in mind to create or assess current plans and make recommendations to ensure that results are achieved.
21CFR11 Compliance
CambridgeSoft consultants can create or refine requirements to produce an environment that will ensure success. With years of experience meeting the needs of the scientific community, CambridgeSoft understands the user. The prototyping process allows definition and testing of the functional and technical feasibility of potential technology solutions. The process provides a baseline for the future development and deployment of a tailored solution. Users gain valuable first hand knowledge in experiencing how the system can help achieve individual and workgroup goals.
Successfully implemented, a traceable and usable system is essential to any organization involved in the creation and management of data in a regulated environment. As an integral part in creating 21CFR11 and GxP validated applications, CambridgeSoft offers services to: Audit the software and process Create conforming systems design specifications Generate test plans and validation matrices Insure systems compliance with functional guidelines
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SERVICES
Training & Support

Product Development
Data Conversion and Integration
Educational Training and Technical Support

but would like to customize it for a unique environment. Our professional services teams can provide those specific features by making custom modifications that will be supported in the future. Systems Deployment
Installation and Configuration
When developing a new system, the process of converting existing data and creating interfaces with other data systems is an essential part of the process. CambridgeSofts professional services staff is equipped to seamlessly incorporate existing data into the development of a new enterprise system. Organizations will be able to capitalize on historical scientific data while setting the platform for future success.
Custom Development
CambridgeSoft will install and configure applications to meet the needs of your user community. For unique environments, we build custom installers that allow us to productively deploy software across an enterprise.
DEVELOPMENT Data Integration DEPLOYMENT Installation & Configuration Systems Optimization Pre-Release Programs Software Evaluations Training Services MANAGEMENT Managed Informatics
You have discovered a unique application need in your organization, but cannot find a solution that will meet your functionality or cost requirements. With custom development, CambridgeSoft works collaboratively with your team to create a system that meets your needs, while executing our quality driven software development process. We deliver what you need, on time and within budget, without surprises.
Systems Integration
PLANNING Strategic/Op Planning Requirements Analysis Proof of Concept Project Readiness 21CFR11 Compliance
Custom Application Development
Ultra Services Plans
The ability to integrate core applications with other systems in the technology environment is a competency required to deliver the functionality of a new application.
Product Tailoring
Systems Integration
Technical Support
Your organization can see the benefit from implementing a CambridgeSoft application,
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Product Tailoring
Remote DBA Services
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PROFESSIONAL
Development, Deployment,
Custom Development and System Deployment
Managed Informatics allows your organization to focus on science, allowing CambridgeSoft to plan, implement and manage your technology environment. Systems Optimization
CambridgeSofts systems deployment team will work with you to make sure that your computing environment has been optimized for high performance. Your systems, networks, applications and databases are assessed and designed to deliver maximum achievement.
Beta and Pre-Release Programs
CambridgeSoft is committed to maximizing your productivity through the use of our products, as well as exposing you to the newest technologies. Our beta and pre-release programs provide you with that knowledge, allowing CambridgeSoft to improve applications with your customer feedback.
Pilot Software Evaluations
sional services staff supporting your systems environment On-site formal classroom training Webinars for multi-location instruction Off-site at CambridgeSoft facilities Systems Management
Managed Informatics
It often makes sense to pilot an application before a major commitment for an enterprise wide implementation is made. CambridgeSoft will work closely with you to plan the evaluation, deploy the application, and gather critical feedback regarding systems design, APIs and technology specifications.
Training
Effective user, administrator and help desk training is often an afterthought in many systems deployments. However, the productivity returns generated by an investment in systems training can provide dramatic returns. CambridgeSoft offers training in the following ways: On-site real time training through our profesAll specifications subject to change without notice.
There is no longer a need to worry about licensing fees, maintenance contracts, systems administration work or database support. Informatics Outsourcing provides the people, processes and technology to develop a unique level of service for your organization. For a monthly fee, CambridgeSoft will deliver the informatics applications and the technology staff required to maximize productivity. This service allows your organization to focus on science, while CambridgeSoft plans, implements and manages your technology environment.
Ultra Services
The Ultra Services program is CambridgeSofts personalized, premium service for supporting our
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SERVICES
Training & Support

customers. Organizations can take advantage of both telephone and electronic access to CambridgeSofts support scientists who can address: Usage and installation questions Product compatibility and interoperability questions Diagnostic review to help isolate the cause of a problem Configuration assistance Planning information for software updates and upgrades Assistance with problem resolution
Technical Support & Remote DBA Services
Educational Training and Technical Support
To complete our Management Services offerings, Technical Support and Remote DBA Services, for Oracle and SQL Server, are also available.

Chem & Bio Office

KNOWLEDGE MANAGEMENT CHEMICAL INFORMATICS BIOLOGICAL INFORMATICS SCIENTIFIC DATABASES
Desktop Software to Enterprise Solutions
Desktop
E-Notebook Enterprise
CombiChem Enterprise
Registration Enterprise
DocManager Enterprise
BioAssay & BioViz
ChemACX Database
The Merck Index
E-Signatures IP Protection Enterprise
21CFR11 Compliance
GxP Validation
Enterprise
Oracle Cartridge or SQL DB
BioSAR Enterprise
Sigma-Aldrich MSDS
Research, Discovery, Development, Trials & Manufacturing

Enterprise Solutions include ChemOffice, with Oracle Cartridge, and ChemOffice Workgroup, based on SQL Server to help organizations from small workgroups to large enterprises collaborate and share information more effectively. Desktop Software includes ChemOffice, a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and ChemACX for chemists, BioDraw, BioAssay and BioViz for biologists, and Inventory and E-Notebook. Knowledge Management with E-Notebook, including Reaction Explorer, CombiChem, E-Signatures for intellectual property protection and 21CFR11 Compliance, streamlines daily record-keeping with rigorous security and efficient archiving. Chemical Informatics, including Registration, organizes new compound information. Inventory provides complete management of chemical and biological inventories including GxP Validation. DocManager indexes chemical structures in documents. BioIogical Informatics scientists use BioAssay, BioViz, BioSAR and BioDraw to set up biological models and visualize information, generate spreadsheets correlating structure and activity, search by structure, and draw and annotate pathways. Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS. The Merck Index and other scientific databases provide information about chemicals, their properties, and reactions. Professional Services includes custom development, system deployment, educational training, and technical support for pharmaceutical, biotechnology, and chemical customers, including government and academia, by experienced staff.
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DETAILS OF THE PROBLEM
SYSTEM CONFIGURATION
SOFTWARE
Application Name Please cut here or photocopy page. Version Number Serial Number
SYSTEM
Windows (version) MacOs (version) Web Browser(s) (version)
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ChemBioOfce.Com
CS BioAssay
for Windows
SCREEN ELEMENTS
Quick Reference
Protocols Protocol Folders Project Protocol Compound Lists Plate settings; Define Picklists
LOGGING IN
Server Name where BioAssay database is located Login information Database file
Server where BioAssay data is located
Database where BioAssay data is located
PROTOCOL QUICK START

1. Decide whether you can reuse an existing protocol. If so, duplicate, if not, create a new one. 2. Create the fields you will need to store your raw data. 3. Create the calculation fields you will need to produce your results. 4. Define a file import template to describe the format of your raw data. 5. Define any graph templates you may need. 6. Import your data using the file import template you have set up.
PROTOCOLS DATA TAB

Click to import a file
Click to recalculate this plate
Filter or reload the data Plate and multi plate tabview the plates in this table in the plate viewer
Make this window the active window Graph tab-select a graph template to plot the data in the table
DEFINITIONS TAB
Tables and fields which define the data tables in your protocol Details about the highlighted entity Templates which define how data is imported into the data tables from a file
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ChemBioOfce.Com
CS ChemInfo
for Windows
Main Tool Bar
Quick Reference
CHEMFINDER SCREEN ELEMENTS

Text Editing Toolbar Quit Box Close Box Maximize Button Minimize Button Search Tool Bar Record Tool Bar Scroll Bar
Structure Data Box
Status Bar
Table View
Total Database Size Current Record Current List Size
TOOLBARS
New Save Copy Undo Print Layout Mode Switch Views First Record Go To Last Record Record Undo Changes Delete Record
Open
Cut
Paste
Redo
About ChemFinder
Layout Tool
Previous Record
Next Record
Add New Changes
Commit Changes
Omit Record
Enter Query Find
Find Current Save Current Hit List Restore Previous List Molecule
Find List Restore Saved Over Current List Retrieve All Records Hit List Display Previous Record
CHEMINFO DATABASES
ChemINDEX contains compound reference databases including structures, physical constants and synonyms. ChemRXN contains reaction reference databases indexed from the literature. ChemACX contains available chemicals data from the worlds leading chemical catalogs. ChemMSDX contains a collection of materials safety datasheets. NCI contains the National Cancer Institute database of potential screening compounds. AIDS contains a library of potential HIV screening compounds provided by the National Cancer Institute.
CHEMINFO QUICK START

To Start 1. Launch ChemFinder. 2. Choose Open from the File menu. 3. Locate the database you want to use (*.cfw extension). 4. Click the Open button. To Search 1. From the Search Tool bar, click the Enter Query button. (The form is cleared.) 2. To enter a structural query: right-click on a Structure Data Box and choose Edit Structure. Draw your query in ChemDraw and click on the ChemFinder window when you are done. 3. To enter an alphanumeric query: click the Data Box you want to search and type the query in the Data Box. 4. From the Search menu, choose the type of search (e.g. Similarity) you want. 5. From the Search tool bar, click the Search button. 6. Click the Retrieve All button from the Search tool bar to browse the full database. 7. To abort a query search, press the Escape key. NOTE: You can only abort structure, molecular weight or formula SQL searches.
Display the rst record in the opened database. Display the preceding record in the database. Display the next record in the opened database. Display the last record in the database. Specify a record number to display in the database. Add a new record to the current database. Make a copy of the current record and add it to the database. Permanently remove the current record. Register changes to the current record Undo unsaved changes to the current record. Remove current record from list.
To Perform a Combined Search 1. Enter information in more than one eld. The search is assumed to be a Boolean AND search. 2. Use raw SQL to perform and OR or NOT Boolean search. To Browse 1. Use Record Tools toolbar or Record menu to navigate forward or backward by one record at a time or to go to the beginning or end of the database. To View Records as a Table 1. From the View menu, choose Data Table. 2. Sort elds by clicking on a column heading. To View a Structure as a 3D Model in Chem3D 1. Right-click over a structure databox. 2. From the Context menu, choose View Model. 3. Use the tools in Chem3D to manipulate the model.
Clear active form for entering search query. Execute search query. Stop current search. Display previous search query. Select current molecule as the structure in a search query. Restrict structural query to an exact match. Save current query results to a le. Retrieve stored list of query results for current database. Restore hit list before last search. Specify preferences for how searches are performed and results are displayed. Search current hit list. Restore all records in the opened database back into the active form. Search for the current structure according to the restrictions chosen below. Restrict structural query to a substructure match.
C H E M D R AW S C R E E N E L E M E N T S
Application Control-menu Menu bar Title bar Magnification Control Minimize button Maximize button Close box Tool bar Scroll box Tools palette Rotation handle Vertical scroll bar Resize handle Drawing area Document window Selection rectangle Resize handle Text box Application window
Status bar
Horizontal scroll bar
Scroll arrow
TOOLS PALETTE
Lasso Structure Perspective Solid Multiple Dashed Marquee Mass Fragmentation Eraser Text Pen Arrows Orbitals Drawing Elements Brackets Chemical Symbols Query Tools TLC Plate Templates Cyclobutane Cyclohexane Cyclooctane Cyclohexane Chair (2) Benzene
Bond Tools
Hashed Hashed Wedged Bold Bold Wedged Hollow Wedged Wavy Table Acyclic Chain Cyclopropane
Ring Tools
Cyclopentane Cycloheptane Cyclohexane Chair (1) Cyclopentadiene
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DRAWING QUERY STRUCTURES IN CHEMDRAW

If you want to
Draw a rst bond Add a bond to a structure Label an atom using a bond or ring tool Label an atom using the Text tool Label an atom using a HotKey Draw a double bond (solid, dashed, bold only) Draw a triple bond (solid only) Reduce bond order using Eraser tool Change double bond alignment Change double bond type Move an atom Change bond type Change bond layering using bond tool Draw a ring Create a spiro-linkage Create a fused ring Change size of non-bond object Draw a Structure Arrow Automatically map atoms in a reaction Manually map atoms in a reaction Remove reaction mapping Indicate Stereochemistry Apply Atom Properties Apply Bond Properties Search for product(s) of reaction Search for reactant(s) Search for reaction intermediates(s)
Heres how
Drag to draw the bond. Click an atom or drag from an atom. Double-click an atom (triple-click to repeat last label). Click an atom (double-click to repeat last label). Point at an atom and press a HotKey (e.g., c). Drag over a single bond using a bond tool. Drag over a double bond using a bond tool. Click center of a multiple bond. Click center of double bond using any bond tool. Click center of double bond using different bond tool. SHIFT+drag an atom using a bond or selection tool. Click center of bond using different bond tool. Double-click center of bond you want forward. Click or drag using a Ring tool. Click or drag from an atom using a Ring tool. Click a bond using a Ring tool. SHIFT+drag starting point of object (e.g., arrowhead). Choose from the Arrows palette and drag tail to head. Select All. Choose Map Reaction Atoms (Structure menu). Click Reaction Atom-Atom Map tool. Drag atom to atom. Select All. Choose Clear Mapping (Structure menu). Use Wedged and Hashed bond tools. Select atoms. Choose Atom Properties (Structure menu.) Select bonds. Choose Atom Properties (Structure menu.) Draw reaction arrow in front of query structure. Draw reaction arrow following query structure. Draw arrows before and after query structure.
TEXTUAL AND NUMERICAL SEARCHING IN CHEMFINDER

Search a range of values To nd an exact match Combined search terms in one eld Search a subform Query using straight SQL
Use inequality operators < and >. Put an equals sign = in front of value. Use Boolean operators OR and AND. Select subform, choose Enter Query, search as usual. Begin query with backslash \ and use SQL syntax.
Chem & Bio Office Desktop Software to Enterprise Solutions
Desktop Software to Enterprise Solutions
Research, Discovery, Development, Trials & Manufacturing

Enterprise Solutions include ChemOffice, with Oracle Cartridge, and ChemOffice Workgroup, based on SQL Server to help organizations from small workgroups to large enterprises collaborate and share information more effectively. Desktop Software includes ChemOffice, a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and
ChemACX for chemists, BioAssay, BioViz and BioDraw for biologists, and Inventory, E-Notebook and The Merck Index.
Knowledge Management with E-Notebook, including Reaction Explorer, CombiChem, E-Signatures for intellectual property
protection and 21CFR11 Compliance, streamlines daily record-keeping with rigorous security and efficient archiving.
Chemical Informatics, including Registration, organizes new compound information. Inventory provides complete management of
chemical and biological inventories including GxP Validation. DocManager indexes chemical structures in documents.
BioIogical Informatics scientists use BioAssay, BioViz, BioSAR and BioDraw to set up biological models and visualize
information, generate spreadsheets correlating structure and activity, search by structure, and draw and annotate pathways.
Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS.
The Merck Index and other scientific databases provide information about chemicals, their properties, and reactions.
Professional Services includes custom development, system deployment, educational training, and technical support for
pharmaceutical, biotechnology, and chemical customers, including government and academia, by experienced staff.
Web America Europe Japan
MAE 09156 0512
www.cambridgesoft.com
1 800 3157300 00 800 875 20000 0120 731 800
info@cambridgesoft.com
+44 1223 464900 +49 69 2222 2280 +33 1 70 71 98 80

Chem Office Enterprise 2006

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Chem & Bio Office Enterprise 2006

Chem & Bio Office

Enterprise, Workgroup and Databases

A Guide to CambridgeSoft Manuals

em En te & rp Bi an ris e o d W Da O ffi ta ork gr ba ce ou se p s

ChemOffice Enterprise and Workgroup Solutions . . . . . . . . . . . . . . . . . . . . . . . . 3

Section I: Knowledge Management . . . 5

Manage Users and Roles . . . . . . . . . . . . . . . . . . . 12

Section II: Biological Informatics . . . 13

Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Viewing Protocols in the Navigator . . . . . . . . . . 19

Chem & Bio Office Enterprise, Workgroup & Databases 2006

Chapter 4: BioSAR Enterprise . . . . . . . . . 61

Section III: Chemical Informatics . . .87

Managing Tables . . . . . . . . . . . . . . . . . . . . . . . . 110 Custom Fields . . . . . . . . . . . . . . . . . . . . . . . . . . 110

Inventory Enterprise . . . . . . . . . . . . . . . . 115

Chapter 6: Registration Enterprise . . . . . 163

Chem & Bio Office Enterprise, Workgroup & Databases 2006

Section IV: ChemOffice Enterprise . 189

Chapter 8: CS Oracle Cartridge . . . . . . . 215

Chapter 7: ChemOffice Enterprise . . . . . 191

Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . .248 Using Scientific Databases . . . . . . . . . . . . . . . .248

Section V: Reference Data . . . . . . . . .251

Chapter 10: MediChem . . . . . . . . . . . . . . 257

Chapter 11: Traditional Chinese Medicines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

Chapter 12: Ashgate Drugs . . . . . . . . . . . 263

Chapter 13: ChemINDEX . . . . . . . . . . . . 267

Chapter 14: NCI . . . . . . . . . . . . . . . . . . . . 271

Chapter 15: AIDS . . . . . . . . . . . . . . . . . . . 273

Scientific Databases . . . . . . . . . . . . . 247

Section VI: Sourcing & Safety Data . 275

Chem & Bio Office Enterprise, Workgroup & Databases 2006

Chapter 22: ChemReact . . . . . . . . . . . . . . 305

Section VIII: Appendices . . . . . . . . .309

Chapter 17: ChemMSDX . . . . . . . . . . . . . 289

Chapter 18: Sigma-Aldrich MSDS Collection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

Appendix B: BioAssay Actions Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 319

Chapter 19: EH&S Enterprise . . . . . . . . . 293

Section VII: Reaction & Synthesis Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295

Chapter 21: ChemSynth . . . . . . . . . . . . . . 301

Chem & Bio Office Enterprise, Workgroup & Databases 2006

About the Manual

Helpful CambridgeSoft Links

http://www.cambridgesoft.com/ services/documentation/manuals _enterprise.cfm

Chem & Bio Office Enterprise, Workgroup & Databases 2006

About the Manual 1 Manual Organization

ChemOffice Enterprise and Workgroup Solutions

Section I: Knowledge Management

ChemFinder, and E-Notebook manual for more details) DocManager Enterprise

Chem & Bio Office Enterprise, Workgroup & Databases 2006

Chapter 1: E-Notebook Enterprise

Chem & Bio Office Enterprise, Workgroup & Databases 2006

Chapter 2: DocManager Enterprise