The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

By Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, E. Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, Rolf Apweiler. Nucleic Acids Res., 2004

967 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6052a20665da1f23bf25bce2cbe8e41443a4fd24

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Citations in the corpus

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, methodology): “We based our classifications on the discrete COG functional categories and on the hierarchical, multifunctional terms of the Gene Ontology (GO) [73,74] and MultiFun classification schemas [25].”
A census of mammalian imprinting. (2005, methodology): “Although gene annotations are incomplete and often fail to embody the higher order functions of mammalian development and behaviour, we have examined gene ontologies in an attempt to obtain an objective assessment of the functions of imprinted genes [ 44 ].”
The UCSC Genome Browser Database: update 2006 (2005, background): “org/ (20), to which UCSC adds a table ‘goaPart’ containing gene associations for supported organisms.”
WEGO: a web tool for plotting GO annotations (2006, methodology): “Corresponding entries or GO ID will be given as output (Figure 2). Compared with the QuickGO (17, 18 ), which was developed by the GOA (Gene Ontology Annotation project), the External to GO Query is a simpler but handier tool.”
The Gene Ontology (GO) project in 2006 (2005, background): “Tel: +44 0 1223 494667; Fax: +44 0 1223 494468; Email: midori@ebi.ac.uk *The current members of the GO Consortium are: Midori A. Harris, Jennifer I. Clark, Amelia Ireland, Jane Lomax (GO-EBI, Hinxton, UK); Michael Ashburner, Russell Collins (FlyBase, Department of Genetics, University of Cambridge, ”
Bridging semantics and syntax with graph algorithms —state-of-the-art of extracting biomedical relations (2015, methodology): “To keep up with the exponential growth of the literature, automated methods have been applied to mining protein-protein interactions [15,16], gene-phenotype associations [17,18], gene ontology [19], and pathway information [20], which we collectively call biomolecular information extraction.”
Bridging semantics and syntax with graph algorithms - state-of-the-art of extracting biomedical relations (2017, methodology): “To keep up with the exponential growth of the literature, automated methods have been applied to mining protein–protein interactions (PPIs) [20, 21], gene–phenotype associations [22, 23], gene ontology [24] and pathway information [25], which we collectively call biomolecular information extraction.”
DEEPre: sequence-based enzyme EC number prediction by deep learning (2017, background): “A large number of protein function prediction problems are hierarchical classification problems, such as GO term (Camon et al. , 2004), transporter classification (Saier et al. , 2016) and G-protein-coupled receptors (GPCR) hierarchy (Davies et al. , 2007).”
Some remarks on protein attribute prediction and pseudo amino acid composition (2010, methodology): “The information extracted from the GO database (Ashburner et al., 2000; Camon et al., 2004; Harris et al., 2004) was used to formulate PseAAC for predicting protein subcellular localization (Cai and Chou, 2003; Chou and Cai, 2003b; Chou and Cai, 2004d; Chou and Shen, 2006a; Chou and Shen, 2006b; Cho”
High-throughput functional annotation and data mining with the Blast2GO suite (2008, background): “At present GOSlim mappings for plants, a generic one as well the GOA (Gene Ontology Annotation)(33)-specific one is available.”
The Universal Protein Resource (UniProt) (2004, methodology): “The UniProt curators also contribute to the work of the GOA project (27) by assigning GO terms from each of the GOs, i.”
Protein Molecular Function Prediction by Bayesian Phylogenomics (2005, methodology): “Each annotation in the GO annotation (GOA) database [44] includes an evidence code, which describes how the annotation was determined.”
ProFunc: a server for predicting protein function from 3D structure (2005, background): “entries from which the hits have come, but also from any available functional annotations from these databases and from the Gene Ontology (26,27).”
iLoc-Euk: A Multi-Label Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Eukaryotic Proteins (2011, methodology): “(1) Only the integer numbers 0 and 1 were used to reflect the GO (gene ontology) [46,47] information in formulating protein samples; this might cause some information lost and limit the prediction quality.”
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006, methodology): “cerevisiae [29] were obtained from the GOA database [50].”