{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T05:28:41Z","timestamp":1783142921898,"version":"3.54.6"},"reference-count":42,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,6,19]],"date-time":"2020-06-19T00:00:00Z","timestamp":1592524800000},"content-version":"vor","delay-in-days":170,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health\/National Human Genome Research Institute grant","award":["1U24HG010859-01"],"award-info":[{"award-number":["1U24HG010859-01"]}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council-UK","doi-asserted-by":"crossref","award":["MR\/L001020\/1 (WB)"],"award-info":[{"award-number":["MR\/L001020\/1 (WB)"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Institutes of Health\/National Heart, Lung and Blood Institute","award":["HL64541 to R.G.D."],"award-info":[{"award-number":["HL64541 to R.G.D."]}]},{"name":"National Institutes of Health\/National Human Genome Research Institute grants","award":["P41HG002659 (ZFIN), U24HG002223 (WB), U41HG000739 (FB), U41HG001315 (SGD), HG000330 (MGD), U41HG002273 (GOC)"],"award-info":[{"award-number":["P41HG002659 (ZFIN), U24HG002223 (WB), U41HG000739 (FB), U41HG001315 (SGD), HG000330 (MGD), U41HG002273 (GOC)"]}]},{"name":"National Institutes of Health\/National Human Genome Research Institute grant","award":["U24HG002223-19S1, 1U24HG010859"],"award-info":[{"award-number":["U24HG002223-19S1, 1U24HG010859"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages.<\/jats:p>","DOI":"10.1093\/database\/baaa037","type":"journal-article","created":{"date-parts":[[2020,4,30]],"date-time":"2020-04-30T19:09:49Z","timestamp":1588273789000},"source":"Crossref","is-referenced-by-count":53,"title":["Automated generation of gene summaries at the Alliance of Genome Resources"],"prefix":"10.1093","volume":"2020","author":[{"given":"Ranjana","family":"Kishore","sequence":"first","affiliation":[{"name":"WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerio","family":"Arnaboldi","sequence":"first","affiliation":[{"name":"WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ceri E","family":"Van Slyke","sequence":"first","affiliation":[{"name":"ZFIN, The Institute of Neuroscience, 222 Huestis Hall, University of Oregon, Eugene, OR 97403-1254, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juancarlos","family":"Chan","sequence":"first","affiliation":[{"name":"WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert S","family":"Nash","sequence":"first","affiliation":[{"name":"Saccharomyces Genome Database, Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose M","family":"Urbano","sequence":"first","affiliation":[{"name":"FlyBase, Department of Physiology, Development and Neuroscience, 7 Downing Pl, University of Cambridge, Cambridge CB2 3DY, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary E","family":"Dolan","sequence":"first","affiliation":[{"name":"MGI, The Jackson Laboratory, Bar Harbor, ME 04609, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacia R","family":"Engel","sequence":"first","affiliation":[{"name":"Saccharomyces Genome Database, Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary","family":"Shimoyama","sequence":"first","affiliation":[{"name":"Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul W","family":"Sternberg","sequence":"first","affiliation":[{"name":"WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"the Alliance of","family":"Genome Resources","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,6,19]]},"reference":[{"key":"2020061910233788500_ref1","doi-asserted-by":"publisher","first-page":"D762","DOI":"10.1093\/nar\/gkz920","article-title":"WormBase: a modern model organism information resource","volume":"48","author":"Harris","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref2","doi-asserted-by":"publisher","first-page":"D743","DOI":"10.1093\/nar\/gkz892","article-title":"Transcriptome visualization and data availability at the Saccharomyces Genome Database","volume":"48","author":"Ng","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref3","doi-asserted-by":"publisher","first-page":"D700","DOI":"10.1093\/nar\/gkr1029","article-title":"Saccharomyces Genome Database: the genomics resource of budding yeast","volume":"40","author":"Cherry","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref4","doi-asserted-by":"publisher","first-page":"D463","DOI":"10.1093\/nar\/gkp952","article-title":"WormBase: a comprehensive resource for nematode research","volume":"38","author":"Harris","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref5","doi-asserted-by":"publisher","first-page":"D759","DOI":"10.1093\/nar\/gky1003","article-title":"FlyBase 2.0: the next generation","volume":"47","author":"Thurmond","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref6","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baz152","article-title":"Building a pipeline to solicit expert knowledge from the community to aid gene summary curation","volume":"2020","author":"Antonazzo","year":"2020","journal-title":"Database"},{"key":"2020061910233788500_ref7","doi-asserted-by":"publisher","first-page":"D731","DOI":"10.1093\/nar\/gkz1041","article-title":"The year of the rat: the Rat Genome Database at 20: a multi-species knowledgebase and analysis platform","volume":"48","author":"Smith","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref8","doi-asserted-by":"publisher","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The Gene Ontology Resource: 20 years and still GOing strong","volume":"47","author":"Carbon","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref9","doi-asserted-by":"publisher","first-page":"D955","DOI":"10.1093\/nar\/gky1032","article-title":"Human Disease Ontology 2018 update: classification, content and workflow expansion","volume":"47","author":"Schriml","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref10","doi-asserted-by":"publisher","first-page":"44.","DOI":"10.1093\/nar\/gkv1217","article-title":"WormBase 2016: expanding to enable helminth genomic research","volume":"4","author":"Howe","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref11","doi-asserted-by":"publisher","first-page":"D1186","DOI":"10.1093\/nar\/gky1036","article-title":"ECO, the Evidence & Conclusion Ontology: community standard for evidence information","volume":"47","author":"Giglio","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref12","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gky1056","article-title":"Mouse Genome Database (MGD) 2019","volume":"47","author":"Bult","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref13","doi-asserted-by":"crossref","first-page":"D562","DOI":"10.1093\/nar\/gkj085","article-title":"The Mouse Genome Database (MGD): updates and enhancements","volume":"34","author":"Blake","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref14","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1016\/j.ipm.2007.01.018","article-title":"Generating gene summaries from biomedical literature: a study of semi-structured summarization","volume":"43","author":"Ling","year":"2007","journal-title":"Inf. Process. Manag."},{"key":"2020061910233788500_ref15","volume-title":"Proceedings of BioNLP","author":"Jin","year":"2009"},{"key":"2020061910233788500_ref16","doi-asserted-by":"publisher","first-page":"D650","DOI":"10.1093\/nar\/gkz813","article-title":"Alliance of Genome Resources Portal: unified model organism research platform","volume":"48","author":"Agapite","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref17","doi-asserted-by":"publisher","first-page":"47.","DOI":"10.1093\/nar\/gky1090","article-title":"The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources","volume":"8","author":"Ruzicka","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref18","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.jalgor.2005.08.001","article-title":"Lowest common ancestors in trees and directed acyclic graphs","volume":"57","author":"Bender","year":"2005","journal-title":"J. Algorithms"},{"key":"2020061910233788500_ref19","doi-asserted-by":"publisher","first-page":"D9","DOI":"10.1093\/nar\/gkz899","article-title":"Database resources of the National Center for Biotechnology Information","volume":"48","author":"Sayers","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref20","doi-asserted-by":"publisher","first-page":"D745","DOI":"10.1093\/nar\/gky1113","article-title":"Ensembl 2019","volume":"47","author":"Cunningham","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref21","doi-asserted-by":"publisher","first-page":"D1057","DOI":"10.1093\/nar\/gku1113","article-title":"The GOA database: Gene Ontology annotation updates for 2015","volume":"43","author":"Huntley","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref22","doi-asserted-by":"publisher","first-page":"D786","DOI":"10.1093\/nar\/gky930","article-title":"Genenames.org: the HGNC and VGNC resources in 2019","volume":"47","author":"Braschi","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref23","doi-asserted-by":"publisher","first-page":"D1038","DOI":"10.1093\/nar\/gky1151","article-title":"OMIM.org: leveraging knowledge across phenotype-gene relationships","volume":"47","author":"Amberger","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref24","doi-asserted-by":"publisher","DOI":"10.1186\/2041-1480-5-12","article-title":"The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio","volume":"5","author":"Van, Slyke","year":"2014","journal-title":"J. Biomed. Inform."},{"key":"2020061910233788500_ref25","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1002\/cfg.248","article-title":"Building a cell and anatomy ontology of Caenorhabditis elegans","volume":"4","author":"Lee","year":"2003","journal-title":"Int. J. Genomics"},{"key":"2020061910233788500_ref26","doi-asserted-by":"publisher","DOI":"10.1186\/2041-1480-4-32","article-title":"The Drosophila anatomy ontology","volume":"4","author":"Costa","year":"2013","journal-title":"J. Biomed. Semant."},{"key":"2020061910233788500_ref27","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1007\/s00335-015-9584-9","article-title":"Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data","volume":"26","author":"Hayamizu","year":"2015","journal-title":"Mamm. Genome"},{"key":"2020061910233788500_ref28","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1093\/bib\/bbr042","article-title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology Consortium","volume":"12","author":"Gaudet","year":"2011","journal-title":"Brief. Bioinform."},{"key":"2020061910233788500_ref29","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1186\/1471-2105-12-357","article-title":"An integrative approach to ortholog prediction for disease-focused and other functional studies","volume":"12","author":"Hu","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2020061910233788500_ref30","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bar068","article-title":"Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation","volume":"2012","author":"Burge","year":"2012","journal-title":"Database"},{"key":"2020061910233788500_ref31","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/978-1-4939-3743-1_17","article-title":"Annotation extensions","volume":"1446","author":"Huntley","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"2020061910233788500_ref32","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1287\/moor.4.3.233","article-title":"A greedy heuristic for the set-covering problem","volume":"4","author":"Chvatal","year":"1979","journal-title":"Math. Oper. Res."},{"key":"2020061910233788500_ref33","doi-asserted-by":"publisher","DOI":"10.7490\/f1000research.1113853.1","volume-title":"10th International Biocuration Conference","author":"Lee","year":"2017"},{"key":"2020061910233788500_ref34","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.knosys.2010.10.001","article-title":"Ontology-based information content computation","volume":"24","author":"S\u00e1nchez","year":"2011","journal-title":"Knowl.-Based Syst."},{"key":"2020061910233788500_ref35","first-page":"1089","volume-title":"Proc. of 16th European Conference on Artificial Intelligence, ECAI","author":"Seco","year":"2004"},{"key":"2020061910233788500_ref36","doi-asserted-by":"publisher","first-page":"15107","DOI":"10.1038\/s41598-018-33219-y","article-title":"GOGO: an improved algorithm to measure the semantic similarity between gene ontology terms","volume":"8","author":"Zhao","year":"2018","journal-title":"Sci. Rep."},{"key":"2020061910233788500_ref37","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/292063","article-title":"Information content-based gene ontology semantic similarity approaches: toward a unified framework theory","volume":"2013","author":"Mazandu","year":"2013","journal-title":"Biomed. Res. Int."},{"key":"2020061910233788500_ref38","doi-asserted-by":"publisher","DOI":"10.1186\/2041-1480-3-S1-S3","article-title":"Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL","volume":"3","author":"Jupp","year":"2012","journal-title":"J. Biomed. Semant."},{"key":"2020061910233788500_ref39","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1038\/s41684-018-0150-4","article-title":"Model organism data evolving in support of translational medicine","volume":"47","author":"Howe","year":"2018","journal-title":"Lab. Anim."},{"key":"2020061910233788500_ref40","doi-asserted-by":"publisher","first-page":"D322","DOI":"10.1093\/nar\/gkl799","article-title":"GO PaD: the Gene Ontology Partition Database","volume":"35","author":"Alterovitz","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref41","doi-asserted-by":"publisher","first-page":"D331","DOI":"10.1093\/nar\/gkp1018","article-title":"The Gene Ontology in 2010: extensions and refinements","volume":"38","author":"Gene Ontology Consortium","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2020061910233788500_ref42","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0500-1","article-title":"Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems","volume":"51","author":"Thomas","year":"(2019)","journal-title":"Nat. Genet."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa037\/33405542\/baaa037.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa037\/33405542\/baaa037.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,19]],"date-time":"2020-06-19T14:24:30Z","timestamp":1592576670000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa037\/5859735"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,1]]},"references-count":42,"URL":"https:\/\/doi.org\/10.1093\/database\/baaa037","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020]]},"published":{"date-parts":[[2020,1,1]]},"article-number":"baaa037"}}