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Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- Jiangyi Shao,
- Shutao Chen,
- Ziwen Wang,
- Zixu Chen,
- and Bin Liu
Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
...(Ashburner et al. 2000; Nei et al. 2010; Peng et al. 2020; Kulenkampff et al. 2021). 36 Specifically, Gene Ontology (GO) contains a standardized vocabulary (term) for 37 describing the biological roles, molecular functions, and cellular localizations of genes 38 and their products (proteins...
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Resource: Variation Ontology for annotation of variation effects and mechanisms
- Mauno Vihinen
Genome Res. February 2014 24: 356-364; Published in Advance October 25, 2013, doi:10.1101/gr.157495.113
.... Ontologies are central for implementation of the semantic web. Several ontologies and other standardized systems are available to describe genes, proteins, and diseases. The HUGO Gene Nomenclature Committee (HGNC) nomenclature (Seal at al. 2011) provides official gene names, abbreviations, and symbols. Many...
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RESOURCE: Creating the Gene Ontology Resource: Design and Implementation
- The Gene Ontology Consortium
Genome Res. August 1, 2001 11: 1425-1433; doi:10.1101/gr.180801
...and their products. The Gene Ontology (GO) project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism. This work includes building three extensive ontologies to describe molecular function, biological process, and cellular...
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LETTER: From Gene Networks to Gene Function
- Thomas Schlitt,
- Kimmo Palin,
- Johan Rung,
- Sabine Dietmann,
- Michael Lappe,
- Esko Ukkonen,
- and Alvis Brazma
Genome Res. December 2003 13: 2568-2576; doi:10.1101/gr.1111403
...Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 29 : 80 -81. ↵ Blake, J. and Harris, M. 2003 . The Gene Ontology (GO) Project: Structured vocabularies for molecular biology and their application to and expression analysis. In Current protocols...
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METHODS: Predicting Gene Function From Patterns of Annotation
- Oliver D. King,
- Rebecca E. Foulger,
- Selina S. Dwight,
- James V. White,
- and Frederick P. Roth
Genome Res. May 1, 2003 13: 896-904; Published in Advance April 14, 2003, doi:10.1101/gr.440803
...; 5Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA Abstract The Gene Ontology (GO) Consortium has produced a controlled vocabulary for annotation of gene function that is used in many organism-specific gene annotation databases. This allows...
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ENSEMBL Special: The Ensembl Automatic Gene Annotation System
- Val Curwen,
- Eduardo Eyras,
- T. Daniel Andrews,
- Laura Clarke,
- Emmanuel Mongin,
- Steven M.J. Searle,
- and Michele Clamp
Genome Res. May 2004 14: 942-950; doi:10.1101/gr.1858004
...a set of predicted gene structures to which we can link extra biological information such as gene family information, expression data, and gene ontologies. As with the Ensembl analysis pipeline ( Potter et al. 2004 ), the Ensembl gene build software is comprised of a set of Runnables and Runnable...
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METHODS: Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation
- Francis D. Gibbons and
- Frederick P. Roth
Genome Res. October 1, 2002 12: 1574-1581; doi:10.1101/gr.397002
...evaluated by examining the relationship between clusters produced and the known attributes of the genes in those clusters, as annotated with a controlled vocabulary for gene attributes. We used the Saccharomyces Genome Database (SGD) annotation of S. cerevisiae genes with the gene ontology developed...
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RESOURCE: eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
- Janet Kelso,
- Johann Visagie,
- Gregory Theiler,
- Alan Christoffels,
- Soraya Bardien,
- Damian Smedley,
- Darren Otgaar,
- Gary Greyling,
- C. Victor Jongeneel,
- Mark I. McCarthy,
- Tania Hide,
- and Winston Hide
Genome Res. June 2003 13: 1222-1230; doi:10.1101/gr.985203
...with transparent access to multiple heterogeneous bioinformatics resources. Other ontologies focusing on specific aspects of biology include the Gene Ontology Consortium ( Ashburner et al. 2000 ), which provides vocabularies that can be used to describe gene products in any organism, the EcoCyc ontology ( Karp et...
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METHODS: Using Text Analysis to Identify Functionally Coherent Gene Groups
- Soumya Raychaudhuri,
- Hinrich Schütze,
- and Russ B. Altman
Genome Res. October 1, 2002 12: 1582-1590; doi:10.1101/gr.116402
...from the literature or by manual annotation. Jenssen and colleagues used co-occurrence of gene names in abstracts to create networks of related genes automatically form literature ( Jenssen et al. 2001 ). They showed that those groups were useful in gene expression analysis. The Gene Ontology (GO...
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RESOURCE: Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications
- Pierre Hilson,
- Joke Allemeersch,
- Thomas Altmann,
- Sébastien Aubourg,
- Alexandra Avon,
- Jim Beynon,
- Rishikesh P. Bhalerao,
- Frédérique Bitton,
- Michel Caboche,
- Bernard Cannoot,
- Vasil Chardakov,
- Cécile Cognet-Holliger,
- Vincent Colot,
- Mark Crowe,
- Caroline Darimont,
- Steffen Durinck,
- Holger Eickhoff,
- Andéol Falcon de Longevialle,
- Edward E. Farmer,
- Murray Grant,
- Martin T.R. Kuiper,
- Hans Lehrach,
- Céline Léon,
- Antonio Leyva,
- Joakim Lundeberg,
- Claire Lurin,
- Yves Moreau,
- Wilfried Nietfeld,
- Javier Paz-Ares,
- Philippe Reymond,
- Pierre Rouzé,
- Goran Sandberg,
- Maria Dolores Segura,
- Carine Serizet,
- Alexandra Tabrett,
- Ludivine Taconnat,
- Vincent Thareau,
- Paul Van Hummelen,
- Steven Vercruysse,
- Marnik Vuylsteke,
- Magdalena Weingartner,
- Peter J. Weisbeek,
- Valtteri Wirta,
- Floyd R.A. Wittink,
- Marc Zabeau,
- and Ian Small
Genome Res. October 15, 2004 14: 2176-2189; doi:10.1101/gr.2544504
...relevant for model species characterized by a high level of genetic redundancy. As in many other land plants, the Arabidopsis has undergone multiple rounds of polyploidization and gene amplification events leading to extensive duplication of large regions and many small tandem duplications. Consequently...

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