{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T11:26:48Z","timestamp":1775302008306,"version":"3.50.1"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,10,14]],"date-time":"2020-10-14T00:00:00Z","timestamp":1602633600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Office of Sponsored Research","award":["URF\/1\/3454-01-01"],"award-info":[{"award-number":["URF\/1\/3454-01-01"]}]},{"name":"Office of Sponsored Research","award":["URF\/1\/3790-01-01"],"award-info":[{"award-number":["URF\/1\/3790-01-01"]}]},{"name":"Office of Sponsored Research","award":["FCC\/1\/1976-08-01"],"award-info":[{"award-number":["FCC\/1\/1976-08-01"]}]},{"name":"Office of Sponsored Research","award":["FCC\/1\/1976-08-08"],"award-info":[{"award-number":["FCC\/1\/1976-08-08"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Over the past years, many computational methods have been developed to incorporate information about phenotypes for disease\u2013gene prioritization task. These methods generally compute the similarity between a patient\u2019s phenotypes and a database of gene-phenotype to find the most phenotypically similar match. The main limitation in these methods is their reliance on knowledge about phenotypes associated with particular genes, which is not complete in humans as well as in many model organisms, such as the mouse and fish. Information about functions of gene products and anatomical site of gene expression is available for more genes and can also be related to phenotypes through ontologies and machine-learning models.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed a novel graph-based machine-learning method for biomedical ontologies, which is able to exploit axioms in ontologies and other graph-structured data. Using our machine-learning method, we embed genes based on their associated phenotypes, functions of the gene products and anatomical location of gene expression. We then develop a machine-learning model to predict gene\u2013disease associations based on the associations between genes and multiple biomedical ontologies, and this model significantly improves over state-of-the-art methods. Furthermore, we extend phenotype-based gene prioritization methods significantly to all genes, which are associated with phenotypes, functions or site of expression.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Software and data are available at https:\/\/github.com\/bio-ontology-research-group\/DL2Vec.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa879","type":"journal-article","created":{"date-parts":[[2020,9,28]],"date-time":"2020-09-28T07:26:19Z","timestamp":1601277979000},"page":"853-860","source":"Crossref","is-referenced-by-count":30,"title":["Predicting candidate genes from phenotypes, functions and anatomical site of expression"],"prefix":"10.1093","volume":"37","author":[{"given":"Jun","family":"Chen","sequence":"first","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical & Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955, Saudi Arabia"}]},{"given":"Azza","family":"Althagafi","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical & Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955, Saudi Arabia"},{"name":"Computer Science Department, College of Computers and Information Technology, Taif University , Taif 26571, Saudi Arabia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8149-5890","authenticated-orcid":false,"given":"Robert","family":"Hoehndorf","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical & Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955, Saudi Arabia"}]}],"member":"286","published-online":{"date-parts":[[2020,10,14]]},"reference":[{"key":"2023051704121402900_btaa879-B1","doi-asserted-by":"crossref","first-page":"D408","DOI":"10.1093\/nar\/gkw985","article-title":"HIPPIE v2.0: enhancing meaningfulness and reliability of protein\u2013protein interaction networks","volume":"45","author":"Alanis-Lobato","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023051704121402900_btaa879-B2","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s12920-020-00743-8","article-title":"What is the right sequencing approach? 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