Introductory Overview

The National Institutes of Health Bethesda, MD

The National Center for Biotechnology Information Bethesda,MD Created in 1988 as a part of the National Library of Medicine at NIH Establish public databases Research in computational biology Develop software tools for sequence analysis Disseminate biomedical information

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

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

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

The Entrez System at NCBI

Number of Users and Hits Per Day 1997 1998 1999 2000 2001 2002 2003 NCBI, Currently averaging 15,000,000 to 50,000,000 hits per day! The number refers to NCBI, the bulk of the hits and users just uses PubMed Christmas & New Year’s Days

Sunday ~6 million hits/day PubMed Hits for March 2005 PubMed averages 10,000,000 to 13,000,000 hits per day! 1113507870.graph_hits.png Bar chart shows data from last month Line graphs show historical data for comparisons:  2 months ago (thick solid line); 3 months ago (solid line); 4 months ago (dashed line); 5 months ago (dotted line) Saturday & Sunday ~6 million hits/day

Countries of Origin

The (ever expanding) Entrez System PubChem NLM Catalog Entrez PopSet Structure PubMed Books 3D Domains Taxonomy GEO/GDS UniGene Nucleotide Protein Genome OMIM CDD/CDART Journals SNP UniSTS PubMed Central Gene HomoloGene Protein Sequence/Structure Compounds BioAssays Genome Sequence/Structure Substances Literature Organism Expression Sequence Nucleotide HomoloGene Based on key word searching (MESH terms, author names, gene names, accession or gi numbers, or just recognized patterns in the records). 15 database are included…. Gene GenSat GenomeProjects Cancer Chromosomes

Literature Databases

A part of the NCBI Bookshelf Part 2. Data Flow and Processing Part 1. The Databases Part 3. Querying and Linking the Data Part 4. User Support A part of the NCBI Bookshelf

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.

Detailed journal information NCBI Journal Database Detailed journal information

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

“Global Entrez Query”

NM_000249: PubMed Books

Books Link

OMIM: Human Disease Genes Conserved Domain

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)

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

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.

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.

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.

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.

HINARI Don’ts Do not give the Publisher’s Material to other individuals or institutions. Do not access HINARI while traveling outside the country.