Gene Ontology Annotation (UniProt-GOA) Database

The UniProt GO annotation program aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). The assignment of GO terms to UniProt records is an integral part of UniProt biocuration. UniProt manual and electronic GO annotations are supplemented with manual annotations supplied by external collaborating GO Consortium groups, to ensure a comprehensive GO annotation dataset is supplied to users.

UniProt-GOA is a member of the GO Consortium.

For fast access to the Gene Ontology terms and annotations, please use our QuickGO browser.

Release cycle

All UniProt-GOA Gene Association Files are released approximately every four weeks and can be accessed from our Downloads page. We aim to coordinate our release with the UniProtKB releases. In addition, we release our human and chicken Gene Association Files every two weeks to enable the GO Consortium Reference Genome project to use our most up-to-date annotations for curation of orthologous species. These interim releases can be downloaded from our ftp site.

Latest UniProt-GOA news

UniProt-GOA News Feed

All the latest news and information relating to UniProt-GOA.

Date	UniProt-GOA News
10 January, 2012	Improvements to the HAMAP2GO annotation set We are very pleased to announce that this UniProt-GOA release contains an improved set of HAMAP2GO annotations. The previous HAMAP2GO pipeline was unable to use the full complexity of the manually-curated UniProtKB HAMAP rules, however this has changed due to recent developments. The HAMAP source now predicts 3,458,519 GO annotations.
13 December, 2011	Scheduled change to the references applied by UniProtKB Keyword and UniProtKB Subcellular Location 2 GO annotations We would like to alert users to an intended change in the references supplied in annotations from two UniProtKB automatic annotation pipelines. Annotations created from mappings between GO and the UniProtKB keywords and UniProtKB Subcellular Location controlled vocabularies currently cite the GO reference GO_REF:0000004 and GO_REF:0000023, respectively. However, terms from these UniProtKB controlled vocabularies are applied differently to UniProt Swiss-Prot and TrEMBL entries; UniProtKB terms are manually annotated to UniProtKB/Swiss-Prot entries, whereas UniProtKB/TrEMBL entries are annotated from data supplied by the underlying nucleic acid databases and/or by the UniProt automatic annotation program. We intend to change the cited references in the supplied GO annotations to highlight these differences. Therefore, from the February 2012 release onwards, the UniProt-GOA annotation set will use: GO_REF:0000037 or GO_REF:0000038 instead of GO_REF:0000004 for UniProtKB keyword annotations GO_REF:0000039 or GO_REF:0000040 instead of GO_REF:0000023 for UniProtKB Subcellular Location annotations Further descriptions all of these references are available at: http://www.geneontology.org/cgi-bin/references.cgi
20 September, 2011	UniProt-GOA are delighted to announce that we now supply more than 100 million annotations to over 11 million proteins. All annotations are available in the 100th release of the UniProt-GOA 'UniProt' file. The vast majority of the annotations (99%) are created by automatic annotation methods, including InterPro to GO and Swiss-Prot Keyword to GO mappings. For more information on the automatic annotation methods that we incorporate, please see http://www.ebi.ac.uk/GOA/ElectronicAnnotationMethods.html. For details on our manual annotation practices, please see http://www.ebi.ac.uk/GOA/ManualAnnotationEfforts.html. UniProt-GOA would like to thank all of the contributing groups that have helped us reach this milestone. Links to our collaborating groups are displayed on our website, http://www.ebi.ac.uk/GOA.
24 August, 2011	In this release, the UniProt GO annotation files contain a greatly reduced number of protein binding GO annotations from the IntAct database. A subset of presumed reliable interactions is now extracted from the IntAct dataset with export determined using a simple scoring system developed by IntAct, coupled to a score threshold that has been deliberately chosen to exclude interactions supported by only one experimental observation. Further details of how interactions are scored can be found at the IntAct website (http://www.ebi.ac.uk/intact/pages/faq/faq.xhtml#4). This simple score-based filter is used in combination with a set of defined rules that excludes certain types of data, such as interactions that have been inferred but not experimentally proven. UniProt-GOA are pleased to announce the inclusion in their database of electronic GO annotations created by EnsemblPlants/Gramene. The annotations are created by projection of GO annotations from Arabidopsis thaliana or Oryza sativa proteins onto proteins from one or more target species based on gene orthology obtained from Ensembl Compara. This first release contains almost 230,000 annotations to over 50,000 proteins covering 16 taxonomies including; poplar, maize, sorghum, grape and Physcomitrella. We hope this will be a valuable resource for the non-model plant species community. The annotations can be viewed and downloaded from the QuickGO browser here.
28 July, 2011	1. With the imminent closure of the International Protein Index (IPI), we would like to alert users of the Human, Mouse, Rat, Zebrafish, Chicken and Cow UniProt GO annotation files (files named: gene_association.goa_[species], e.g., gene_association.goa_human) that our July GO annotation release now uses UniProt Complete Proteome sets to determine the protein composition of these files. Further information on UniProt Complete Proteome sets is available here. This change has had a dramatic affect on the gene_association.goa_human file, which has increase in annotation count by 43.7% , as the file now includes GO annotations both to reviewed (Swiss-Prot) and unreviewed (TrEMBL) UniProtKB accessions. Any user wishing to only identify the reviewed (Swiss-Prot) UniProt protein annotation subset will be able continue to do so using the information supplied in the gp_information.goa_uniprot file, which can be found here. Alternatively, users can download the reviewed UniProtKB human GO annotation set from the UniProt QuickGO browser using this link. Users of the Zebrafish species-specific gene association file will, however, notice a decrease in annotations this release, caused by major changes to the Ensembl Zebrafish ENSP identifier set that has resulted in a decreased set of electronic GO annotations obtained from the application of Ensembl Compara orthology data, as well as a decrease in ZFIN manual GO annotations caused by differences in the set of UniProtKB accessions selected for the Zebrafish UniProtKB proteome set and those currently mapped to ZFIN identifiers. 2. An additional restriction on the HAMAP2GO electronic GO annotation pipeline, filtering out all HAMAP2GO predictions for proteins in the Metazoan kingdom, has enabled us to remove incorrect GO annotation predictions for a number of species. 3. Species-specific UniProt GO annotation gene association files that include a filtering step to remove redundant electronic GO annotation predictions are now available from the GOA ftp site for the UniProt Complete Proteome sets of Dictyostellium discoideum (gene_association.goa_dicty.gz), Canis familiaris (gene_association.goa_dog.gz), Drosophila melanogaster (gene_association.goa_fly.gz), Caenorhabditis elegans (gene_association.goa_worm.gz), Saccharomyces cerevisiae (gene_association.goa_yeast) and Sus scrofa (gene_association.goa_pig.gz).

UniProt-GOA News Archive

Latest UniProt-GOA releases

UniProt-GOA News Feed

Date	UniProt-GOA Release
10 January, 2012	GOA UniProt 104 Released Version 104 UniProt GO annotation has been released. GOA Human 106 Released Version 106 of human GOA has been released. GOA Mouse 92 Released Version 92 of mouse GOA has been released. GOA Rat 92 Released Version 92 of rat GOA has been released. GOA Arabidopsis 79 Released Version 79 of arabidopsis GOA has been released. GOA Zebrafish 79 Released Version 79 of zebrafish GOA has been released. GOA Chicken 76 Released Version 76 of chicken GOA has been released. GOA Cow 69 Released Version 69 of cow GOA has been released. GOA Dicty 7 Released Version 7 of dicty GOA has been released. GOA Dog 7 Released Version 7 of dog GOA has been released. GOA Pig 7 Released Version 7 of pig GOA has been released. GOA Fly 7 Released Version 7 of fly GOA has been released. GOA Worm 7 Released Version 7 of worm GOA has been released. GOA Yeast 7 Released Version 7 of yeast GOA has been released. GOA PDB 93 Released GOA Proteome Sets 81 Released We are pleased to introduce GO annotation to 2884 proteome sets in this release. For information please follow this link.
13 December, 2011	GOA UniProt 103 Released Version 103 UniProt GO annotation has been released. GOA Human 105 Released Version 105 of human GOA has been released. GOA Mouse 91 Released Version 91 of mouse GOA has been released. GOA Rat 91 Released Version 91 of rat GOA has been released. GOA Arabidopsis 78 Released Version 78 of arabidopsis GOA has been released. GOA Zebrafish 78 Released Version 78 of zebrafish GOA has been released. GOA Chicken 75 Released Version 75 of chicken GOA has been released. GOA Cow 68 Released Version 68 of cow GOA has been released. GOA Dicty 6 Released Version 6 of dicty GOA has been released. GOA Dog 6 Released Version 6 of dog GOA has been released. GOA Pig 6 Released Version 6 of pig GOA has been released. GOA Fly 6 Released Version 6 of fly GOA has been released. GOA Worm 6 Released Version 6 of worm GOA has been released. GOA Yeast 6 Released Version 6 of yeast GOA has been released. GOA PDB 92 Released GOA Proteome Sets 80 Released We are pleased to introduce GO annotation to 1872 proteome sets in this release. For information please follow this link.
15 November, 2011	GOA UniProt 102 Released Version 102 UniProt GO annotation has been released. GOA Human 104 Released Version 104 of human GOA has been released. GOA Mouse 90 Released Version 90 of mouse GOA has been released. GOA Rat 90 Released Version 90 of rat GOA has been released. GOA Arabidopsis 77 Released Version 77 of arabidopsis GOA has been released. GOA Zebrafish 77 Released Version 77 of zebrafish GOA has been released. GOA Chicken 74 Released Version 74 of chicken GOA has been released. GOA Cow 67 Released Version 67 of cow GOA has been released. GOA Dicty 5 Released Version 5 of dicty GOA has been released. GOA Dog 5 Released Version 5 of dog GOA has been released. GOA Pig 5 Released Version 5 of pig GOA has been released. GOA Fly 5 Released Version 5 of fly GOA has been released. GOA Worm 5 Released Version 5 of worm GOA has been released. GOA Yeast 5 Released Version 5 of yeast GOA has been released. GOA PDB 91 Released GOA Proteome Sets 79 Released We are pleased to introduce GO annotation to 1873 proteome sets in this release. For information please follow this link.
18 October, 2011	GOA UniProt 101 Released Version 101 UniProt GO annotation has been released. GOA Human 103 Released Version 103 of human GOA has been released. GOA Mouse 89 Released Version 89 of mouse GOA has been released. GOA Rat 89 Released Version 89 of rat GOA has been released. GOA Arabidopsis 76 Released Version 76 of arabidopsis GOA has been released. GOA Zebrafish 76 Released Version 76 of zebrafish GOA has been released. GOA Chicken 73 Released Version 73 of chicken GOA has been released. GOA Cow 66 Released Version 66 of cow GOA has been released. GOA Dicty 4 Released Version 4 of dicty GOA has been released. GOA Dog 4 Released Version 4 of dog GOA has been released. GOA Pig 4 Released Version 4 of pig GOA has been released. GOA Fly 4 Released Version 4 of fly GOA has been released. GOA Worm 4 Released Version 4 of worm GOA has been released. GOA Yeast 4 Released Version 4 of yeast GOA has been released. GOA PDB 90 Released GOA Proteome Sets 78 Released We are pleased to introduce GO annotation to 1846 proteome sets in this release. For information please follow this link.
20 September, 2011	GOA UniProt 100 Released Version 100 UniProt GO annotation has been released. GOA Human 102 Released Version 102 of human GOA has been released. GOA Mouse 88 Released Version 88 of mouse GOA has been released. GOA Rat 88 Released Version 88 of rat GOA has been released. GOA Arabidopsis 75 Released Version 75 of arabidopsis GOA has been released. GOA Zebrafish 75 Released Version 75 of zebrafish GOA has been released. GOA Chicken 72 Released Version 72 of chicken GOA has been released. GOA Cow 65 Released Version 65 of cow GOA has been released. GOA Dicty 3 Released Version 3 of dicty GOA has been released. GOA Dog 3 Released Version 3 of dog GOA has been released. GOA Pig 3 Released Version 3 of pig GOA has been released. GOA Fly 3 Released Version 3 of fly GOA has been released. GOA Worm 3 Released Version 3 of worm GOA has been released. GOA Yeast 3 Released Version 3 of yeast GOA has been released. GOA PDB 89 Released GOA Proteome Sets 77 Released We are pleased to introduce GO annotation to 1764 proteome sets in this release. For information please follow this link.
24 August, 2011	GOA UniProt 99 Released Version 99 UniProt GO annotation has been released. GOA Human 101 Released Version 101 of human GOA has been released. GOA Mouse 87 Released Version 87 of mouse GOA has been released. GOA Rat 87 Released Version 87 of rat GOA has been released. GOA Arabidopsis 74 Released Version 74 of arabidopsis GOA has been released. GOA Zebrafish 74 Released Version 74 of zebrafish GOA has been released. GOA Chicken 71 Released Version 71 of chicken GOA has been released. GOA Cow 64 Released Version 64 of cow GOA has been released. GOA Dicty 2 Released Version 2 of dicty GOA has been released. GOA Dog 2 Released Version 2 of dog GOA has been released. GOA Pig 2 Released Version 2 of pig GOA has been released. GOA Fly 2 Released Version 2 of fly GOA has been released. GOA Worm 2 Released Version 2 of worm GOA has been released. GOA Yeast 2 Released Version 2 of yeast GOA has been released. GOA PDB 88 Released GOA Proteome Sets 76 Released We are pleased to introduce GO annotation to 1759 proteome sets in this release. For information please follow this link.
28 July, 2011	GOA UniProt 98 Released Version 98 UniProt GO annotation has been released. GOA Human 100 Released Version 100 of human GOA has been released. GOA Mouse 86 Released Version 86 of mouse GOA has been released. GOA Rat 86 Released Version 86 of rat GOA has been released. GOA Arabidopsis 73 Released Version 73 of arabidopsis GOA has been released. GOA Zebrafish 73 Released Version 73 of zebrafish GOA has been released. GOA Chicken 70 Released Version 70 of chicken GOA has been released. GOA Cow 63 Released Version 63 of cow GOA has been released. GOA Dicty 1 Released Version 1 of dicty GOA has been released. GOA Dog 1 Released Version 1 of dog GOA has been released. GOA Pig 1 Released Version 1 of pig GOA has been released. GOA Fly 1 Released Version 1 of fly GOA has been released. GOA Worm 1 Released Version 1 of worm GOA has been released. GOA Yeast 1 Released Version 1 of yeast GOA has been released. GOA PDB 87 Released GOA Proteome Sets 75 Released We are pleased to introduce GO annotation to 1707 proteome sets in this release. For information please follow this link.

UniProt-GOA Release Archive

Funding

Current Funding:

EMBL
NIH grant number R01HG02273-02: Gene Ontology Consortium
British Heart Foundation grant (SP:07/007/23671) 'The Integration of the knowledge if genes involved in heart development and cardiovascular processes from biomedical research, using standardised Gene Ontology'
Kidney Research UK Project Grant RP26/2008 - 'Integration of knowledge of genes involved in renal processes from biomedical research using the Gene Ontology'.
NIH grant number 2U01HG02712-04: UniProtKB Consortium

Previous Funding:

European Union grant number QLRI-CT-2001000015: TEMBLOR - The European Molecular Biology Linked Original Resources
European Union grant number QLRT-CT-2001-00981; BioBabel- Enhanced Interoperability of Biological Databases by Standardisation of Biochemical Terminology and Introduction of a Shared Ontology
BBSRC Tools and Resources Fund grant (BB/E023541/1) 'Further development of the QuickGO web interface for browsing and retrieving Gene Ontology Annotation Data'.

UniProt-GOA is also grateful to the developers and curators from the GO Consortium and GO associate member databases.