Entrez genes
Entrez Gene is a metasearch engine operated by the National Center for Biotechnology Information (NCBI) that enables simultaneous access to multiple biochemistry databases and thus wide-ranging searches. It also offers a whole range of tools for data analysis and special search operations.
Networked databases
- 3D Domains: Contains protein domains from the Entrez structure database.
- Books: A growing collection of biomedical books that can be searched directly.
- Cancer Chromosomes: Is composed of the NCI / NCBI SKY / M-FISH & CGH, the NCI Mitelman database and the NCI Recurrent Aberrations in Cancer.
- Conserved Domains: database of protein domains ; The sources for this data are Pfam , Smart and COG.
- GDS: "GEO DataSets" is a collection of data sets from the "Gene Expression Omnibus (GEO) repository".
- Genes: contains genes from RefSeq genomes which are identified either by sequence, position in the NCBI Map Viewer or both.
- Gensat: Project to map the expression of genes in the mouse CNS using in situ hybridization techniques and via transgenic mice.
- Genomes: provides views of various genomes, complete chromosomes, sequence maps, and integrated genetic and physical maps.
- GEO: serves as a public data collection for a large number of high-throughput experiments .
- Journals:
- Nucleotide (consists of GenBank , RefSeq, PDB ):
- OMIA : database of genes, hereditary diseases and traits in animals (excluding mice)
- OMIM : Catalog of Human Genes and Genetic Disorders. The database contains text information, references and numerous links to MEDLINE and NCBI databases.
- Pop Set: Set of DNA sequences that have been put together for the analysis of the evolutionary relationships of a population.
- Protein (consists of SwissProt , PIR, PRF, PDB):
- PubChem (-BioAssay, -Compounds and -Substance): Provides information about the biological activity of small molecules.
- PubMed (scientific literature):
- PubMed Central (scientific literature, fully accessible free of charge):
- SNP:
- Structure: the “Molecular Modeling Database” ( MMDB ) contains 3D structures of macromolecules, including proteins and polynucleotides.
- Taxonomy: contains the names of all organisms that are represented in the NCBI gene database by at least one nucleotide or protein sequence.
- Uni Gene : experimental system for the automatic division of gene bank sequences into a non-redundant system of gene-oriented clusters.
- Uni STS: Integrates marker and mapping data from various public sources.
- Homologs : a system for the automatic detection of homologies within eukaryotic gene sets.
construction
Entrez brings together all networked databases under one user-friendly interface. In doing so, one does not select the individual databases, but rather topics in which several databases are sometimes combined. For each of these subject areas there is a search mask which enables the search in only this area and the databases it contains. A brief description can be called up for all areas on the main page, which provides information about the databases summarized under this point and the data contained therein.
The "Site Map" button on the main page provides links to the individual databases and Entrez tools.
Quality of results
The quality of the results strongly depends on the database used and thus on the information sought. Search queries in PubMed Central or OMIM are usually of high quality, since the information here is always based on a paper, in the case of OMIM even a book. Search queries for nucleotide or polypeptide sequences are also usually very good because they are based on data from BLAST , which is also operated by the NCBI . These entries almost always contain cross-references to the PubMed papers in which the results were published and are therefore easy to check.