{"id":"https://openalex.org/W2156343366","doi":"https://doi.org/10.1093/bioinformatics/bti409","title":"Formalizing concepts of species, sex and developmental stage in anatomical ontologies","display_name":"Formalizing concepts of species, sex and developmental stage in anatomical ontologies","publication_year":2005,"publication_date":"2005-03-29","ids":{"openalex":"https://openalex.org/W2156343366","doi":"https://doi.org/10.1093/bioinformatics/bti409","mag":"2156343366","pmid":"https://pubmed.ncbi.nlm.nih.gov/15797906"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2773/48971414/bioinformatics_21_11_2773.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2773/48971414/bioinformatics_21_11_2773.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033861256","display_name":"Stuart Aitken","orcid":"https://orcid.org/0000-0003-4867-4568"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"S. Aitken","raw_affiliation_strings":["School of Informatics, The University of Edinburgh, Edinburgh EH8 9LE, United Kingdom. stuart@aiai.ed.ac.uk","School of Informatics, The University of Edinburgh  Edinburgh EH8 9LE, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Informatics, The University of Edinburgh, Edinburgh EH8 9LE, United Kingdom. stuart@aiai.ed.ac.uk","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"School of Informatics, The University of Edinburgh  Edinburgh EH8 9LE, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033861256"],"corresponding_institution_ids":["https://openalex.org/I98677209"],"apc_list":null,"apc_paid":null,"fwci":0.886,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.72593037,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"11","first_page":"2773","last_page":"2779"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9939000010490417,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9939000010490417,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10895","display_name":"Species Distribution and Climate Change","score":0.9818999767303467,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13238","display_name":"Botanical Studies and Applications","score":0.9343000054359436,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6940724849700928},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6847856640815735},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.6257467865943909},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5232228636741638},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.513388991355896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.510270357131958},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.49398499727249146},{"id":"https://openalex.org/keywords/stage","display_name":"Stage (stratigraphy)","score":0.4550013542175293},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.436404824256897},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4197829067707062},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29958242177963257},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23288345336914062},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.1860801875591278},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1450563371181488},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.1071685254573822}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6940724849700928},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6847856640815735},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.6257467865943909},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5232228636741638},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.513388991355896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.510270357131958},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.49398499727249146},{"id":"https://openalex.org/C146357865","wikidata":"https://www.wikidata.org/wiki/Q1123245","display_name":"Stage (stratigraphy)","level":2,"score":0.4550013542175293},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.436404824256897},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4197829067707062},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29958242177963257},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23288345336914062},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.1860801875591278},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1450563371181488},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.1071685254573822},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000715","descriptor_name":"Anatomy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000715","descriptor_name":"Anatomy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000715","descriptor_name":"Anatomy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004626","descriptor_name":"Embryology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004626","descriptor_name":"Embryology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004626","descriptor_name":"Embryology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008953","descriptor_name":"Models, Anatomic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008953","descriptor_name":"Models, Anatomic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008953","descriptor_name":"Models, Anatomic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012727","descriptor_name":"Sex Characteristics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012727","descriptor_name":"Sex Characteristics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012727","descriptor_name":"Sex Characteristics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2773/48971414/bioinformatics_21_11_2773.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15797906","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15797906","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.97.1512","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.97.1512","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/21/11/2773.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2773/48971414/bioinformatics_21_11_2773.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320359","display_name":"University of Aberdeen","ror":"https://ror.org/016476m91"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2156343366.pdf","grobid_xml":"https://content.openalex.org/works/W2156343366.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W89025026","https://openalex.org/W113317323","https://openalex.org/W1492225798","https://openalex.org/W1564365643","https://openalex.org/W1576479172","https://openalex.org/W1804031886","https://openalex.org/W1836367264","https://openalex.org/W1971891056","https://openalex.org/W1976119155","https://openalex.org/W1996599952","https://openalex.org/W1998923621","https://openalex.org/W2002185882","https://openalex.org/W2048845779","https://openalex.org/W2078288474","https://openalex.org/W2098780184","https://openalex.org/W2100316327","https://openalex.org/W2103017472","https://openalex.org/W2125349610","https://openalex.org/W2133992441","https://openalex.org/W2138618671","https://openalex.org/W2158648246","https://openalex.org/W2163670493","https://openalex.org/W2172172820","https://openalex.org/W3150202998"],"related_works":["https://openalex.org/W1998735789","https://openalex.org/W4251503124","https://openalex.org/W37398608","https://openalex.org/W2337423123","https://openalex.org/W2054476758","https://openalex.org/W1989811317","https://openalex.org/W3202867831","https://openalex.org/W2399614206","https://openalex.org/W2361756669","https://openalex.org/W2576362586"],"abstract_inverted_index":{"The":[0,90],"framework":[1,91],"we":[2],"have":[3,26,57],"defined":[4],"for":[5,85],"anatomical":[6,68,105],"ontologies":[7],"allows":[8],"the":[9,36,83,102],"canonical":[10],"anatomy":[11,55],"structures":[12,106],"of":[13,35,40,104],"a":[14,46,53,62,111],"given":[15],"species":[16],"to":[17,21,25,56],"be":[18],"those":[19],"common":[20,63,109],"all":[22],"sexes,":[23],"and":[24,51,67,79,81,98],"either":[27],"male,":[28],"female":[29],"or":[30],"hermaphrodite":[31],"parts--but":[32],"not":[33],"combinations":[34],"latter.":[37],"Temporal":[38],"aspects":[39],"development":[41],"are":[42,70,108],"addressed":[43],"by":[44,72],"associating":[45],"stage":[47,69],"with":[48],"organism":[49],"parts":[50,58],"requiring":[52],"connected":[54],"that":[59,107],"exist":[60],"at":[61],"stage.":[64],"Both":[65],"sex":[66],"represented":[71],"attributes.":[73],"This":[74],"formalization":[75],"clarifies":[76],"ontological":[77],"structure":[78],"meaning":[80],"increases":[82],"capacity":[84],"formal":[86],"reasoning":[87],"about":[88],"anatomy.":[89],"also":[92],"supports":[93],"generalizations":[94],"such":[95],"as":[96],"vertebrate":[97],"invertebrate,":[99],"thereby":[100],"allowing":[101],"representation":[103],"across":[110],"sub-phylum.":[112]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
