Gene: a gene-centered information resource at NCBI

By Garth R. Brown, Vichet Hem, K. Katz, M. Ovetsky, Craig Wallin, O. Ermolaeva, I. Tolstoy, Tatiana A. Tatusova, Kim D. Pruitt, Donna R. Maglott and 1 more. Nucleic Acids Res., 2014

654 citations recorded by the source corpus.

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP.

Subfields: Molecular Biology

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Citations in the corpus

g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, positive): “Information about genome variants is retrieved from dbSNP (31) and mapped to NCBI Genes (32).”
DGIdb 3.0: a redesign and expansion of the drug–gene interaction database (2017, neutral): “The enhancements to the online updaters have also been applied to Entrez Gene, from which 99% of all gene claims made by the DGIdb constituent sources were grouped (Supplementary Figure S2) (3).”
Genenames.org: the HGNC and VGNC resources in 2021 (2020, background): “This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. nloaded from https://aca”
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs (2016, background): “This involved selection of the most pertinent gene annotations by means of programmatic access to Ensembl MySQL (http://ensemblgenomes.org/info/access/mysql) and UniProt SPARQL (http://sparql.uniprot.org/) services, and from NCBI by FTP downloads.”
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts (2020, methodology): “Of the 41 sources in DGIdb, 12 sources are now imported using the online updater format, including Entrez (28), the core source of gene concepts for gene grouping in DGIdb, and Ensembl (29), a key source of gene aliases.”
Genenames.org: the HGNC and VGNC resources in 2019 (2018, background): “HGNC symbols are displayed in all major databases containing human gene and protein data including Ensembl (1), NCBI Gene (2), UniProt (3), GeneCards (4) and the UCSC genome browser (5), as well as resources focused on human disease and phenotypes such as Decipher (6), OMIM (7), Locus Reference Geno”
The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses (2016, methodology): “Gene unification is achieved by comparing gene locations and annotation from two sources (Ensembl and NCBI’s Entrez Gene) and combining genes with overlapping locations (Coordinators, 2015; Cunningham et al., 2015; Rosen et al., 2003).”
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins (2015, methodology): “Genes that did not meet our selective criteria for inclusion in Tmito but which had some evidence of mitochondrial localization from the MitoP2 database (20) or the NCBI GO database (17,21) (downloaded 2/19/2014) were grouped into a Tpossible mito gene set, not used for training.”
PubChem 2019 update: improved access to chemical data (2018, neutral): “The PubChem Target View page for a given target can be accessed via a web unique resource locator (URL) that contains the corresponding NCBI Gene ID or Gene Symbol.”
DGIdb 2.0: mining clinically relevant drug–gene interactions (2015, background): “These updaters have been built for the most actively updated existing sources (Figure 1), including DrugBank (10) (drug–gene interactions), Gene Ontology (26) (druggable gene categories), Entrez (30) (genes), and PubChem (31) (drugs).”
SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping (2018, positive): “0) (19) and NCBI gene (version 2018) (20) databases.”
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016, methodology): “We created gene set libraries from HumanCyc (15), a Nucleic Acids Research, 2016, Vol. 44, Web Server issue W91 metabolic pathway resource stored in BioPAX format (16); gene and small-molecule perturbations from the LINCS L1000 data set; NCI-Nature pathways (17); protein complexes from the NURSA pro”
Genenames.org: the HGNC and VGNC resources in 2017 (2016, background): “Hint text is provided within the search box to indicate some of the accepted search terms, which include approved gene symbols, keywords likely to be found within a gene name such as kinase or pseudogene, as well as gene identifiers from VGNC, NCBI Gene and Ensembl.”
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (2015, background): “The external databases include KEGG (3), Meta-Cyc (4), Reactome (27), HMDB (21), RCSB PDB (28), Model SEED (29) and Entrez Gene (30).”
Database resources of the National Center for Biotechnology Information (2014, background): “Gene (28) provides an interface to curated sequences and descriptive information about genes with links to a wide variety of gene-related resources.”