The GOA database: Gene Ontology annotation updates for 2015
By Rachael P. Huntley, T. Sawford, Prudence Mutowo-Meullenet, Aleksandra Shypitsyna, C. Bonilla, Maria Jesus Martin, C. O’Donovan. Nucleic Acids Res., 2014
585 citations recorded by the source corpus.
The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480 000 taxonomic groups. The resource now provides annotations to five times the number of proteins it did 4 years ago. As a member of the GO Consortium, we adhere to the most up-to-date Consortium-agreed annotation guidelines via the use of quality control checks that ensures that the GOA resource supplies high-quality functional information to proteins from a wide range of species. Annotations from GOA are freely available and are accessible through a powerful web browser as well as a variety of annotation file formats.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/18725f2d323a4d2cf30f504d9ae498135fe7679c
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Citations in the corpus
- GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank (2017, methodology): “all annotation without ’IEA’ or ’RCA’ evidence and some annotations with IEA evidence before 2016 from GOA [12]).”
- Bilingual language model for protein sequence and structure (2024, unknown): “Expanding ProstT5 from being bilingual into becoming truly polyglot by adding other, potentially more function-centric, conditioning tags such as Gene Ontology terms [70] might be the first step toward future advanced pLMs.”
- Pi-Pi contacts are an overlooked protein feature relevant to phase separation (2018, methodology): “Phase separation scores for analyzed proteins were considered with respect to known interactions, and functional annotations, using the gene ontology database (release Oct-04–2016), UniProt’s Swiss-Prot and TREMBL sequence databases, including the reference proteome annotations, vertebrate protein s”
- Systematic integration of biomedical knowledge prioritizes drugs for repurposing (2017, background): “Gene–participates–Biological Process , Gene–participates–Cellular Component , and Gene–participates–Molecular Function edges are from Gene Ontology annotations ( Huntley et al., 2015 ).”
- Gene Ontology: Pitfalls, Biases, and Remedies. (2016, background): “As a result, currently less than 1% of all experimental annotations are negative ones in UniProt-GOA (30).”
- CATH: increased structural coverage of functional space (2020, methodology): “For each FunFam, CATH provides sequence alignments (generated using MAFFT (9)), profile hidden Markov models (HMMs, generated using HMMER3 (10)), and a set of high-quality GO annotations from UniProt-GOA (11).”