Entrez, dbSNP, GEO, OMIM & LinkOut JanPlan 2012

Entrez Distributed by NCBI in 1991 on CD-ROM Included linked nodes: GenBank & PDB Translated GenBank, PIR, SWISS-PROT, PDB & PRF MEDLINE

Entrez Purpose: To enhance computation As data sets get bigger, the problem remains tractable or may even inprove because of better statistics Computational approaches often produce god results more objectively and efficiently

Entrez Discovery system: A data-retrieval system succeeds when you can retrieve the same data you put in. A discovery system is intended to let you find more information than appears in the original data. By making links between selected nodes and making computed associations within the same node, Entrez is designed to infer relationships between different data that may suggest future experiments or assist in interpretation of the available information, although it may come from different sources.

Entrez Now includes Taxonomy, Structure, Genomes, OMIM, PopSet, and BookShelf

dbSNP The Single Nucleotide Polymorphism database (dbSNP) is a public-domain archive for a broad collection of simple genetic polymorphisms. Includes: Singe-base nucleotide substitution (SNPs) Small-scale multi-base deletions or insertions (DIPs) Retroposable element insertions and microsatellite repeat variations (short tandem repeats or STRs)

dbSNP Physical mapping: Where is the SNP, DIP or STR? Functional analysis: How does the SNP, DIP or STR change protein function? Association studies: Complex phenotypes Evolution studies: Population genetics Null results are important

GEO Gene Expression Omnibus Initiated at NCBI in 1999 in response to the growing demand for a public repository for data generated from high-throughput microarray experiments Gene expression overview: What is it good for?

OMIM Emerged from a project at Johns Hopkins University last published in Still curated at JHU School of Medicine Provides authoritative free text overviews of genetic disorders and gene loci Provides many rich connections to relevant primary resources such as bibliographic, sequence, and map information.

LinkOut Designed to provide Entrez users with links from database records to a wide variety of relevant online resources, including full-text publications, biological databases, consumer health information, and research tools. The goal of LinkOut is to facilitate access to relevant online resources beyond the Entrez system to extend, clarify, or supplement information found in the Entrez databases. By branching out to relevant resources on the Web, LinkOut expands on the theme of Entrez as an information discovery system.