{"id":"https://openalex.org/W11577617","doi":"https://doi.org/10.1007/978-3-540-92673-3_20","title":"Ontologies for Formal Representation of Biological Systems","display_name":"Ontologies for Formal Representation of Biological Systems","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W11577617","doi":"https://doi.org/10.1007/978-3-540-92673-3_20","mag":"11577617"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-540-92673-3_20","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-540-92673-3_20","pdf_url":null,"source":null,"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Handbook on Ontologies","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108071956","display_name":"Nigam Shah","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nigam Shah","raw_affiliation_strings":["Stanford Medical Informatics, Stanford, CA, USA, 94305"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Medical Informatics, Stanford, CA, USA, 94305","institution_ids":["https://openalex.org/I4210137306"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009128820","display_name":"Mark A. Musen","orcid":"https://orcid.org/0000-0003-3325-793X"},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Musen","raw_affiliation_strings":["Stanford Medical Informatics, Stanford, CA, USA, 94305"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Medical Informatics, Stanford, CA, USA, 94305","institution_ids":["https://openalex.org/I4210137306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210137306"],"apc_list":null,"apc_paid":null,"fwci":1.362,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.79025448,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"445","last_page":"461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9945999979972839,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.667691707611084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6602598428726196},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.5847139954566956},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.5747183561325073},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5491481423377991},{"id":"https://openalex.org/keywords/declaration","display_name":"Declaration","score":0.5129737257957458},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.47377800941467285},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.4668019115924835},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4568120241165161},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4468298852443695},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4437774419784546},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.43647658824920654},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.4222722053527832},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4163419008255005},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36172667145729065},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.2651902437210083},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2097330391407013},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19847697019577026},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.187829852104187},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12362286448478699},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11726531386375427},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.11198928952217102}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.667691707611084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6602598428726196},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.5847139954566956},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.5747183561325073},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5491481423377991},{"id":"https://openalex.org/C138147947","wikidata":"https://www.wikidata.org/wiki/Q1183659","display_name":"Declaration","level":2,"score":0.5129737257957458},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.47377800941467285},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.4668019115924835},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4568120241165161},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4468298852443695},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4437774419784546},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.43647658824920654},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.4222722053527832},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4163419008255005},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36172667145729065},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.2651902437210083},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2097330391407013},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19847697019577026},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.187829852104187},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12362286448478699},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11726531386375427},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.11198928952217102},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/978-3-540-92673-3_20","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-540-92673-3_20","pdf_url":null,"source":null,"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Handbook on Ontologies","raw_type":"book-chapter"},{"id":"pmh:oai:RePEc:spr:ihichp:978-3-540-92673-3_20","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"book"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W3814261","https://openalex.org/W157491709","https://openalex.org/W317210108","https://openalex.org/W1481919380","https://openalex.org/W1557491384","https://openalex.org/W1578484316","https://openalex.org/W1876343039","https://openalex.org/W1965610986","https://openalex.org/W1971739873","https://openalex.org/W1974833742","https://openalex.org/W1979736490","https://openalex.org/W1981021538","https://openalex.org/W2017079657","https://openalex.org/W2017220776","https://openalex.org/W2031810131","https://openalex.org/W2043710019","https://openalex.org/W2045089599","https://openalex.org/W2050533674","https://openalex.org/W2050604932","https://openalex.org/W2061280979","https://openalex.org/W2088519259","https://openalex.org/W2095134486","https://openalex.org/W2099007946","https://openalex.org/W2100603120","https://openalex.org/W2101011890","https://openalex.org/W2103260426","https://openalex.org/W2103734240","https://openalex.org/W2105941683","https://openalex.org/W2113024448","https://openalex.org/W2116137060","https://openalex.org/W2117041603","https://openalex.org/W2117123116","https://openalex.org/W2117632114","https://openalex.org/W2120337732","https://openalex.org/W2120702690","https://openalex.org/W2121588207","https://openalex.org/W2122174694","https://openalex.org/W2123767501","https://openalex.org/W2127480960","https://openalex.org/W2134788911","https://openalex.org/W2135230352","https://openalex.org/W2136539307","https://openalex.org/W2137881949","https://openalex.org/W2137999759","https://openalex.org/W2138107070","https://openalex.org/W2149665940","https://openalex.org/W2150908245","https://openalex.org/W2151337118","https://openalex.org/W2155331065","https://openalex.org/W2163670493","https://openalex.org/W2169804422","https://openalex.org/W2416168304","https://openalex.org/W2496848976","https://openalex.org/W2523935660","https://openalex.org/W2610714868","https://openalex.org/W2611370172","https://openalex.org/W3189912187","https://openalex.org/W4233575130","https://openalex.org/W4234803542","https://openalex.org/W4237251429","https://openalex.org/W4285719527","https://openalex.org/W6685124837","https://openalex.org/W6724997288","https://openalex.org/W6829814225","https://openalex.org/W7074035217"],"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/W2399614206","https://openalex.org/W1969271108","https://openalex.org/W11577617","https://openalex.org/W2080218387","https://openalex.org/W4234527451"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
