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The National Center for

Biotechnology Information
Introduction to NCBI
• The National Center for Biotechnology Information
advances science and health by providing access to
biomedical and genomic information
• It is part of the United States National Library of
Medicine (NLM), a branch of the National Institutes of
Health (NIH).
• The NCBI is located in Bethesda, Maryland
• It was founded in 1988 through legislation sponsored
by Senator Claude Pepper
Mission of NCBI
• Background
– Understanding nature's mute but elegant language of living cells
is the quest of modern molecular biology.
– From an alphabet of only four letters representing the chemical
subunits of DNA emerges a syntax of life processes whose most
complex expression is man.
– The unraveling and use of this "alphabet" to form new "words
and phrases" is a central focus of the field of molecular biology.
– The staggering volume of molecular data and its cryptic and
subtle patterns have led to an absolute requirement for
computerized databases and analysis tools.
– The challenge is in finding new approaches to deal with the
volume and complexity of data and in providing researchers
with better access to analysis and computing tools to advance
understanding of our genetic legacy and its role in health and
disease.
Mission of NCBI
• Creating NCBI
– The late Senator Claude Pepper recognized the importance
of computerized information processing methods for the
conduct of biomedical research and sponsored legislation
that established the National Center for Biotechnology
Information (NCBI) on November 4, 1988, as a division of
the National Library of Medicine (NLM) at the National
Institutes of Health (NIH).
– NLM was chosen for its experience in creating and
maintaining biomedical databases, and because as part of
NIH, it could establish an intramural research program in
computational molecular biology.
– The collective research components of NIH make up the
largest biomedical research facility in the world.
Mission of NCBI
• Basic Research
– As a national resource for molecular biology information, NCBI's
mission is to develop new information technologies to aid in the
understanding of fundamental molecular and genetic processes
that control health and disease.
– More specifically, the NCBI has been charged with creating
automated systems for storing and analyzing knowledge about
molecular biology, biochemistry, and genetics
– Facilitating the use of such databases and software by the
research and medical community; coordinating efforts to gather
biotechnology information both nationally and internationally;
and performing research into advanced methods of computer-
based information processing for analyzing the structure and
function of biologically important molecules.
Mission of NCBI
• To carry out its diverse responsibilities, NCBI:
– conducts research on fundamental biomedical problems at the
molecular level using mathematical and computational methods
– maintains collaborations with several NIH institutes, academia,
industry, and other governmental agencies
– fosters scientific communication by sponsoring meetings, workshops,
and lecture series
– supports training on basic and applied research in computational
biology for postdoctoral fellows through the NIH Intramural Research
Program
– engages members of the international scientific community in
informatics research and training through the Scientific Visitors
Program
– develops, distributes, supports, and coordinates access to a variety of
databases and software for the scientific and medical communities
– develops and promotes standards for databases, data deposition and
exchange, and biological nomenclature
NCBI organizational structure
•Is a branch of geology, which deals with study of rocks (Petro=rock, Logos=study)

NCBI

Computational Biology Information Engineering Information Resources


Branch (CBB) Branch (IEB) Branch (IRB)
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NCBI organizational structure
• Computational Biology Branch (CBB)
– Conducts basic and applied research in computational,
mathematical, and theoretical problems in molecular biology
and genetics, including genome analysis, sequence
comparisons, sequence search methodologies, macromolecular
structure, dynamics and interaction, and structure/function
prediction
– Establishes collaborative research projects in computational
molecular biology with biologists, chemists, mathematicians,
and computer scientists in NIH intramural laboratories, other
government agencies, academia, and industry
– Consults and advises governmental agencies and research
laboratories in the application of computer-based analytical
tools for studying molecular biology
– Interacts with molecular biology groups to enhance wet-bench,
laboratory-based research through the application of
computational and theoretical approaches
NCBI organizational structure
• Information Engineering Branch (IEB)
– Performs applied research in data representation and
analysis, including the development of computer-
based systems for the storage, management, and
retrieval of knowledge relating to molecular biology,
genetics, and biochemistry
– Designs database schema and specifications for
representation of various forms of molecular biology
information, including nucleic acid, protein, and
structural information. These databases serve as
national resources.
– Designs and develops distributed software systems
from the prototype to operational phase, which
provides researchers with both local and remote
computational services
NCBI organizational structure
• Information Engineering Branch (IEB)
– Coordinates public access to sequence, genetics,
structural, and bibliographic information by building
curated and integrated databases and, when possible,
establishes linkages to external databases
– Establishes collaborative informatics research projects
with NIH intramural laboratories as well as extramural
academic groups
– Consults with and advises other governmental
agencies and research laboratories on advanced
methods of software and database design
– Develops and promotes standards for databases, data
exchange, and biological nomenclature
NCBI organizational structure
• Information Resources Branch (IRB)
– Plans, directs, and manages the technical operations of
NCBI, including the computer systems used for research
and development as well as the computer systems used to
access public databases
– Provides technical assistance to NCBI staff and provides
support for external users of NCBI network services
– Supervises network operations for the NCBI and
coordinates with other government agencies for both
national and international access to NCBI services
– Organizes educational demonstrations and workshops for
the biomedical community to foster the use of NCBI's
information services
NCBI organizational structure
• Information Resources Branch (IRB)
– Plans, develops, and manages government contracts and
cooperative agreements to procure equipment and services in
support of NCBI information functions
– Serves as liaison for user support services to agencies involved
in genome projects
– Performs applied research and development, provides technical
consultation and direction, and identifies user needs.
– Conducts surveys to evaluate the use of NCBI-developed
software in the biology user community.
– Coordinates with other governmental agencies and biology
information resources to facilitate the development of data
repositories at the NCBI
NCBI News & Blog
• KEEPING UP WITH THE NCBI
– NCBI Twitter Feed
– NCBI Facebook Page
– NCBI LinkedIn
– NCBI News Archive
– NCBI ListServs & RSS Feeds
– NCBI Education & Outreach
• KEEPING UP WITH THIS BLOG
– Posts
– Comments
Features of NCBI
• NCBI Home • PubMed
• Resource List (A-Z) • Bookshelf
• All Resources • PubMed Central
• Chemicals & Bioassays • BLAST
• Data & Software • Nucleotide
• DNA & RNA • Genome
• Domains & Structures • SNP
• Genes & Expression • Gene
• Genetics & Medicine • Protein
• Genomes & Maps • PubChem
• Homology
• Literature
• Proteins
• Sequence Analysis
• Taxonomy
• Training & Tutorials
• Variation