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Introductory Overview

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The National Institutes of Health

Bethesda, MD

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edThe National Center for

Biotechnology Information

Created in 1988 as a part of theNational Library of Medicine at NIH

– Establish public databases– Research in computational biology– Develop software tools for sequence analysis– Disseminate biomedical information

Bethesda,MD

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What does NCBI do?

• NCBI accepts submissions of primary data

• NCBI develops tools to analyze these data

• NCBI uses these tools to create derivative databases based on the primary data

• NCBI provides free search, link, and retrieval of these data, primarily through the Entrez system

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The National Center for Biotechnology Information

• Created as a part of NLM in 1988– Establish public databases– Perform research in computational biology– Develop software tools for sequence analysis– Disseminate biomedical information

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What is Entrez?

• A system of 31 linked databases

• A text search engine

• A tool for finding biologically linked data

• A retrieval engine

• A virtual workspace for manipulating large datasets

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The Entrez System at NCBI

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Number of Users and Hits Per Day

0

50,000

100,000

150,000

200,000

250,000

300,000

350,000

400,000

450,000

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sers

1997 1998 1999 2000 2001 2002 2003

Christmas &New Year’s

Days

NCBI, Currently averaging15,000,000 to 50,000,000

hits per day!

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PubMed Hits for March 2005

Saturday &Sunday ~6 million

hits/day

PubMed averages10,000,000 to 13,000,000

hits per day!

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Countries of Origin

U.S.U.S.(.com, .net, (.com, .net, .org,.org,

..govgov, .us), .us)40%40%

Japan 6%Italy 4%

Canada 3%

Germany 3%

United Kingdom3%

Netherlands 2%

Spain 2%

Brazil 2%Sweden 1%Switzerland 1%Belgium1%

OtherOther14%14%

U.S.U.S.(.com, .net, (.com, .net, .org,.org,

..govgov, .us), .us)40%40%

Japan 6%Italy 4%

Canada 3%

Germany 3%

United Kingdom3%

Netherlands 2%

Spain 2%

Brazil 2%Sweden 1%Switzerland 1%Belgium1%

OtherOther14%14%

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edThe (ever expanding) Entrez System

EntrezEntrez

PopSet

Structure

PubMed

Books

3D Domains

Taxonomy

GEO/GDS

UniGene

Nucleotide

Protein Genome

OMIM

CDD/CDART

Journals

SNP

UniSTS

PubMed Central

Gene

HomoloGeneHomoloGene

Gene

NLM CatalogPubChem

BioAssaysCompounds

Substances

Cancer Chromosomes

GenSat GenomeProjects

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Literature Databases

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A part of the NCBI Bookshelf

Part 1. The Databases

Part 3. Querying and Linking the Data

Part 2. Data Flow and Processing

Part 4. User Support

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PubMed Central

PubMed Central is a digital archive of life sciences journal literature. Integrated into the Entrez retrieval system, PMC provides free and unrestricted access to the full text of over 160 life sciences journals, with more to come.

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NCBI Journal Database

Detailed journal information

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OMIM - A catalogue of genes involved with human disease processes - Detailed clinical and reference information - Curated and maintained by Johns Hopkins - Links to PubMed and sequence databases

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“Global Entrez Query”

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NM_000249: PubMed

Books

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Books Link

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OMIM: Human Disease Genes

Conserved Domain

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HINARI

• The Health InterNetwork Access to Research Initiative (HINARI) is part of the United Nation’s Health InterNetwork (HIN) project,

• Coordinated by the World Health Organization (WHO) as the lead agency.

• Collaboration between the WHO, publishers and other health care content owners intended to provide biomedical and health care research and guideline information to non profit academic and research institutions, governmental and policy making departments in low income countries.

• Access to this information will generally be provided at low cost or in most cases free by the Publisher, to institutions in many countries with a Gross National Product (GNP) per capita of US $1000 or less according to the World Bank Report, December 1999 (HINARI Phase 1)

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HINARI License Agreement

• http://www.who.int/entity/hinari/about/Licence%20Agreement%20Phase%201%20(free%20access).pdf

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HINARI Do’s

• Material owned by the Publishers made available through HINARI may only be used by Authorised Users or Walk-in Users.

• An Authorised User: an institution’s or government department’s employee, permanent or visiting faculty, or student.

• Walk-in User: Anyone who comes to the Institution’s premises and is permitted by the Institution to access services there.

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HINARI Do’s

• The Publisher’s Material (for HINARI Phase 1) may also be placed in electronic reserves for students to access in specified education courses. Delete after the end of the course.

• Document Supply: Institution may supply printed or digital materials only to the Institution’s employees, faculty members, or another Authorised User.

• Remote access from computer owned personally by employees or by Institution.

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HINARI Don’ts• Downloading: Do not download complete journal

issues or books.• Printing: Do not print complete issues of books or

journals.• Course Packs: Academic and teaching staff may

make copies in print or digital form of the Publisher’s Material for course packs (recover the cost of producing such course packs from the the students). Cannot make a profit from the Publisher’s Material.

• Document supply: Do not distribute documents obtained through HINARI to any other individuals or organisations outside the Institution.

• Document Fees: The Institution may not supply the document for a fee except to recover cost of compiling course pack or other teaching materials.

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HINARI Don’ts• Do not modify, adapt, transform or create any

derivative work from the Publisher’s Material. Consequence: Immediate termination of the contract between the Publisher and the Institution.

• Do not modify, adapt, transform or create any derivative work or version from the Publisher’s access software or that of his hosting agent. Do not tamper or amend the Publishers access software.

• Uploading: Do not upload the Material to or post to a publicly available website or elsewhere. Do not add to the Publisher’s Material without express permission of the Publisher including notices, advertisements, comments, or other information.

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HINARI Don’ts

• Do not give the Publisher’s Material to other individuals or institutions.

• Do not access HINARI while traveling outside the country.