{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T04:10:26Z","timestamp":1790395826400,"version":"4.1.0"},"reference-count":23,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2012,9,14]],"date-time":"2012-09-14T00:00:00Z","timestamp":1347580800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Anatomy"],"published-print":{"date-parts":[[2012,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>This paper describes a new ontology of human developmental anatomy covering the first 49\u2005days [<jats:styled-content style=\"fixed-case\">C<\/jats:styled-content>arnegie stages (CS)1\u201320], primarily structured around the parts of organ systems and their development. The ontology includes more than 2000 anatomical entities (<jats:styled-content style=\"fixed-case\">AE<\/jats:styled-content>s) that range from the whole embryo, through organ systems and organ parts down to simple or leaf tissues (groups of cells with the same morphological phenotype), as well as features such as cavities. Each <jats:styled-content style=\"fixed-case\">AE<\/jats:styled-content> has assigned to it a set of facts of the form &lt;<jats:italic><jats:styled-content style=\"fixed-case\">AE<\/jats:styled-content><\/jats:italic>&gt;&lt;<jats:italic>relationship<\/jats:italic>&gt;&lt;<jats:italic>parent<\/jats:italic>&gt;, with the relationships including <jats:italic>starts_at<\/jats:italic> and <jats:italic>ends_at<\/jats:italic> (CSs), <jats:italic>part_of<\/jats:italic> (there can be several parents) and <jats:italic>is_a<\/jats:italic> (this gives the type of tissue, from an organ system down to one of ~ 80 simple tissues predominantly composed of a single cell kind, which is also specified). Leaf tissues also have a <jats:italic>develops_from<\/jats:italic> link to its parent tissue. The ontology includes ~14\u2005000 such facts, which are mainly from the literature and an earlier ontology of human developmental anatomy (<jats:styled-content style=\"fixed-case\">EHDAA<\/jats:styled-content>, now withdrawn). The relationships enable these facts to be integrated into a single, complex hierarchy (or mathematical graph) that was made and can be viewed in the <jats:styled-content style=\"fixed-case\">OBO<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">E<\/jats:styled-content>dit browser (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/oboedit.org\">oboedit.org<\/jats:ext-link>). Each <jats:styled-content style=\"fixed-case\">AE<\/jats:styled-content> has an <jats:styled-content style=\"fixed-case\">EHDAA<\/jats:styled-content>2 <jats:styled-content style=\"fixed-case\">ID<\/jats:styled-content> that may be useful in an informatics context, while the ontology as a whole can be used for organizing databases of human development. It is also a knowledge resource: a user can trace the lineage of any tissue back to the egg, study the changes in cell phenotype that occur as a tissue develops, and use the structure to add further (e.g. molecular) information. The ontology may be downloaded from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"www.obofoundry.org\">www.obofoundry.org<\/jats:ext-link>. Queries and corrections should be sent to <jats:email>j.bard@ed.ac.uk<\/jats:email>.<\/jats:p>","DOI":"10.1111\/j.1469-7580.2012.01566.x","type":"journal-article","created":{"date-parts":[[2012,9,15]],"date-time":"2012-09-15T03:23:42Z","timestamp":1347679422000},"page":"406-416","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["A new ontology (structured hierarchy) of human developmental anatomy for the first 7\u2005weeks (<scp>C<\/scp>arnegie <scp>s<\/scp>tages 1\u201320)"],"prefix":"10.1111","volume":"221","author":[{"given":"Jonathan","family":"Bard","sequence":"first","affiliation":[{"name":"Department of Physiology Anatomy and Genetics University of Oxford Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2012,9,14]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-7580.2011.01371.x"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2012.00018"},{"key":"e_1_2_7_4_1","article-title":"Driving developmental and evolutionary change, a systems biology view","author":"Bard J","year":"2012","journal-title":"Prog Biophys Mol Biol"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0925-4773(98)00069-0"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/dvdy.21652"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-84628-885-2"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrn2252"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm112"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1109\/IEMBS.2009.5333362"},{"key":"e_1_2_7_11_1","volume-title":"CARO \u2013 The Common Anatomy Reference Ontology. 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