{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T07:03:20Z","timestamp":1758265400764},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs.<\/jats:p>\n               <jats:p>Availability and implementation: A-DaGO-Fun is freely available to the research community at http:\/\/web.cbio.uct.ac.za\/ITGOM\/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence).<\/jats:p>\n               <jats:p>Contact: gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv590","type":"journal-article","created":{"date-parts":[[2015,10,18]],"date-time":"2015-10-18T01:38:30Z","timestamp":1445132310000},"page":"477-479","source":"Crossref","is-referenced-by-count":28,"title":["A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool"],"prefix":"10.1093","volume":"32","author":[{"given":"Gaston K.","family":"Mazandu","sequence":"first","affiliation":[{"name":"1 Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and"},{"name":"2 African Institute for Mathematical Sciences (AIMS), Cape Town, South Africa and Cape Coast, Ghana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emile R.","family":"Chimusa","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mamana","family":"Mbiyavanga","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicola J.","family":"Mulder","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,17]]},"reference":[{"key":"2023020110313296300_btv590-B1","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1093\/bioinformatics\/btu144","article-title":"GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the gene ontology","volume":"30","author":"Caniza","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020110313296300_btv590-B2","doi-asserted-by":"crossref","first-page":"D345","DOI":"10.1093\/nar\/gkp463","article-title":"G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery","volume":"37","author":"Du","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020110313296300_btv590-B3","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/1471-2105-8-166","article-title":"GOSim\u2013an R-package for computation of information theoretic GO similarities between terms and gene products","volume":"8","author":"Fr\u00f6hlich","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020110313296300_btv590-B4","doi-asserted-by":"crossref","first-page":"D559","DOI":"10.1093\/nar\/gkr1028","article-title":"The gene ontology: enhancements for 2011","volume":"40","author":"GO-Consortium","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020110313296300_btv590-B5","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1093\/bioinformatics\/btt581","article-title":"The Semantic Measures library and Toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies","volume":"30","author":"Harispe","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020110313296300_btv590-B6","doi-asserted-by":"crossref","first-page":"D1057","DOI":"10.1093\/nar\/gku1113","article-title":"The GOA database: gene ontology annotation updates for 2015","volume":"43","author":"Huntley","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020110313296300_btv590-B7","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1109\/TCBB.2014.2343963","article-title":"A new semantic functional similarity over gene ontology","volume":"12","author":"Jeong","year":"2014","journal-title":"IEEE\/ACM Trans. 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