{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T22:49:20Z","timestamp":1761518960465},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2313,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species.<\/jats:p>\n               <jats:p>Results: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee.<\/jats:p>\n               <jats:p>Availability: download section of the Bgee website http:\/\/bgee.unil.ch\/<\/jats:p>\n               <jats:p>Contact: \u00a0marc.robinson-rechavi@unil.ch<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq283","type":"journal-article","created":{"date-parts":[[2010,6,3]],"date-time":"2010-06-03T01:10:05Z","timestamp":1275527405000},"page":"1766-1771","source":"Crossref","is-referenced-by-count":17,"title":["Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy"],"prefix":"10.1093","volume":"26","author":[{"given":"Gilles","family":"Parmentier","sequence":"first","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland and 2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"},{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland and 2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederic B.","family":"Bastian","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland and 2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"},{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland and 2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Robinson-Rechavi","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland and 2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"},{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland and 2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,6,2]]},"reference":[{"key":"2023012507580485900_B1","doi-asserted-by":"crossref","first-page":"2773","DOI":"10.1093\/bioinformatics\/bti409","article-title":"Formalizing concepts of species, sex and developmental stage in anatomical ontologies","volume":"21","author":"Aitken","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012507580485900_B2","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1385\/NI:1:4:309","article-title":"EMAP and EMAGE: a framework for understanding spatially organized data","volume":"1","author":"Baldock","year":"2003","journal-title":"Neuroinformatics"},{"key":"2023012507580485900_B3","first-page":"124","volume-title":"Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species.","author":"Bastian","year":"2008"},{"key":"2023012507580485900_B4","doi-asserted-by":"crossref","first-page":"D761","DOI":"10.1093\/nar\/gkm826","article-title":"Xenbase: a Xenopus biology and genomics resource","volume":"36","author":"Bowes","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012507580485900_B5","doi-asserted-by":"crossref","first-page":"2198","DOI":"10.1093\/bioinformatics\/btm112","article-title":"OBO-Edit - 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