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HGNC : Human Gene Nomenclature Database
We have already approved over 24,000 symbols;
the vast majority of these are for protein-coding genes, but also
include symbols for pseudogenes, non-coding RNAs,
phenotypes and genomic features (see HGNC Search).
Our current priority is assigning nomenclature to genes submitted to us
from...
Learn more about HGNC : Human Gene Nomenclature Database »
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6 Bioinformatics database from Banff Manifesto topics matching:
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GO : Gene Ontology
Biologists currently waste a lot of time and effort in searching
for all of the available information about each small area of research.
This is hampered further by the wide variations in terminology that may
be common usage at any given time,...
Database schema:
Identifier example:
- GO:0046703 ,
- 0006915
Provider homepage:
- http://www.geneontology.org/
Replaces:
- Identifier from Gene Ontology Database. (e.g. GO:1234) ,
- Gene Ontology Evidence Codes ,
- A namespace to represent any entity within the Gene Ontology ,
- Gene Ontology Database references
References:
- Conserved Domain Database ,
- OMIM : Online Mendelian Inheritance in Man ,
- AgBase resource for functional analysis of agricultural plant and animal gene pr ,
- Arabidopsis Genome Initiative (TAIR, TIGR, MIPS)
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- EMBL nucleotide sequence database ,
- GO : Gene Ontology ,
- [bm:lsrn]
Freebase Topic:
Link From:
- Affymetrix : Alliance for Cellular Signaling ,
- GoPubMed : Search PubMed and get results sorted by GO and MeSH
Reserved namespace:
- go
URL pattern:
- http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=GO:0004396 ,
- http://godatabase.org/cgi-bin/go.cgi?query=GO:0046703 %s ,
- http://www.ebi.ac.uk/ego/QuickGO?query=GO:%s&mode=search&entry=&querytype=protein&showcontext=false ,
- http://godatabase.org/cgi-bin/go.cgi?query=GO:%s
Description:
- pThe objective of GO is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them. The controlled vocabularies of terms are structured to allow both attribution and querying to be at different levels of granularity.ppGO is a database independent of any other. GO itself is not populated with gene products of any organism, although tools can be built which allowGO to be displayed as if it were (e.g. http:www.fruitfly.organnotgo). Databases external to GO collaborate with GO in three ways: by makingdatabase cross-links between GO terms and objects in their database (typically, gene products, or their surrogates, genes), and then providingtables of these links to GO (and hence the community), second by supporting queries that use these terms in their database, and third bycontributing to the development of the GO database itself expanding the vocabularies and refining the terms.p ,
- Gene ontology consortium database
UniProt : The Universal Protein Resource
The Swiss-Prot, TrEMBL, and PIR protein database activities have united to form the Universal Protein Resource (UniProt), which provides a central resource on protein sequences and functional annotation with three database components, each...
Bioinformatics tag:
View entire collection »Identifier example:
- UniProt:P51587
Provider homepage:
- http://www.uniprot.org/
Replaces:
- The Universal Protein Knowledgebase, a central repository of protein sequence an ,
- section of the UniProt Knowledgebase, containing computationally analysed record ,
- section of the UniProt Knowledgebase, containing annotated records, which includ ,
- Namespace for UniProt gene symbol status: depreciated alias.
References:
- UniGene gene-oriented nucleotide sequence clusters ,
- EchoBASE - an integrated post-genomic database for E. coli ,
- Escherichia coli strain K12 genome database ,
- EMBL nucleotide sequence database
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- [bm:lsrn] ,
- [bm:nar] ,
- [bm:srs]
Freebase Topic:
Link From:
- Affymetrix : Alliance for Cellular Signaling ,
- ChEBI : Chemical Entities of Biological Interest database of small molecules ,
- DBpedia
Reserved namespace:
- uniprot
URL pattern:
- http://www.uniprot.org/uniprot/%s
Description:
- The Swiss-Prot, TrEMBL, and PIR protein database activities have united to form the Universal Protein Resource (UniProt), which provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKBSwiss-Prot section and the automatically annotated UniProtKBTrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations, and literature-based evidence attribution enable scientists to analyze proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90), or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. The UniProt databases continue to grow in size and in availability of information. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division, and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon.
National Center for Biotechnology Information, Bethesda
Bioinformatics tag:
- bm:Prefix. ,
- bm:General sequence databases ,
- bm:Taxonomy and identification ,
- bm:Viral genome databases
Provider homepage:
- http://www.ncbi.nlm.nih.gov/
References:
View entire collection »Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- GO : Gene Ontology ,
- [bm:nar]
Reserved namespace:
- ncbi
Description:
- The NCBI Entrez Protein database comprises sequences taken from a variety of sources, including SwissProt, the Protein Information Resource, the Protein Research Foundation, the Protein Data Bank, and translations from annotated coding regions in the GenBank and RefSeq databases. Protein sequence records in Entrez have links to pre-computed protein BLAST alignments, protein structures, conserved protein domains, nucleotide sequences, genomes, and genes. ,
- The NCBI Taxonomy Database includes names and classifications for all of the organisms that are represented in the protein and sequence databases. The taxonomy browser is a convenient way to navigate and search the classification; it is updated continuously as new taxa are added to the database. The taxonomy browser includes a rich set of links to other NCBI resources (sequences, structures, genomes, literature &c.) as well as externally curated links to outside resources (LinkOut links). The taxonomy database is also represented as a domain of Entrez (a href=http:www.ncbi.nlm.nih.goventrezquery.fcgi?db=Taxonomyhttp:www.ncbi.nlm.nih.goventrezquery.fcgi?db=Taxonomya) and is available as a set of ftp files (a href=ftp:ftp.ncbi.nih.govpubtaxonomyftp:ftp.ncbi.nih.govpubtaxonomya) that are updated every two hours. ,
- The NCBI Viral Genomes Resource (a href=http:www.ncbi.nlm.nih.govgenomesVIRUSESviruses.htmlhttp:www.ncbi.nlm.nih.govgenomesVIRUSESviruses.htmla) provides sequence information, as well as precomputed comparative analyses and Web tools, for all viruses and viroids for which (nearly) complete genomic sequences have been established and deposited to DDBJ, EMBL, or GeneBank. The collection currently contains over 2200 reference sequences (RefSeq) and about 6,500 additional complete sequences for more than 1,500 different viral species. The reference sequences are maintained in separate records that are further curated and updated. Whenever more than one complete genome for a species is available, a pairwise global alignment of a reference sequence with each additional sequence is provided. Precomputed clusters of related proteins (VOG) from the reference sequences help navigate among viral proteomes and summarize available functional information for most major virus groups. The data are accessible via Entrez as well as from specialized Web pages offering visualization of the sequence information at various levels of detail.
![[bm:lsrn]](http://img.freebase.com/api/trans/image_thumb/en/bm_lsrn?pad=1&maxheight=110&mode=fillcropmid&maxwidth=110)
![[bm:nar]](http://img.freebase.com/api/trans/image_thumb/en/bm_nar?pad=1&maxheight=110&mode=fillcropmid&maxwidth=110)
![[bm:srs]](http://img.freebase.com/api/trans/image_thumb/en/bm_srs?pad=1&maxheight=110&mode=fillcropmid&maxwidth=110)
