{"id":"https://openalex.org/W2082243333","doi":"https://doi.org/10.1109/iembs.2011.6090060","title":"TumorML: Concept and requirements of an in silico cancer modelling markup language","display_name":"TumorML: Concept and requirements of an in silico cancer modelling markup language","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W2082243333","doi":"https://doi.org/10.1109/iembs.2011.6090060","mag":"2082243333","pmid":"https://pubmed.ncbi.nlm.nih.gov/22254343"},"language":"en","primary_location":{"id":"doi:10.1109/iembs.2011.6090060","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iembs.2011.6090060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447151","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065955048","display_name":"David Johnson","orcid":"https://orcid.org/0000-0002-2323-6847"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David Johnson","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom. david.johnson@cs.ox.ac.uk","Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom. david.johnson@cs.ox.ac.uk","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027917052","display_name":"Jonathan Cooper","orcid":"https://orcid.org/0000-0001-6009-3542"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jonathan Cooper","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK","Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027129096","display_name":"Steve McKeever","orcid":"https://orcid.org/0000-0002-1970-2884"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Steve McKeever","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK","Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":null,"apc_paid":null,"fwci":3.3471,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.91188811,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"5","issue":null,"first_page":"441","last_page":"444"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9882000088691711,"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/markup-language","display_name":"Markup language","score":0.9593381881713867},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7793382406234741},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5611180663108826},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.554797887802124},{"id":"https://openalex.org/keywords/modeling-language","display_name":"Modeling language","score":0.5520414113998413},{"id":"https://openalex.org/keywords/european-commission","display_name":"European commission","score":0.525198757648468},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5038411021232605},{"id":"https://openalex.org/keywords/domain-specific-language","display_name":"Domain-specific language","score":0.4994065761566162},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.454720675945282},{"id":"https://openalex.org/keywords/xhtml","display_name":"XHTML","score":0.4410630464553833},{"id":"https://openalex.org/keywords/ruleml","display_name":"RuleML","score":0.4337802529335022},{"id":"https://openalex.org/keywords/conceptual-model","display_name":"Conceptual model","score":0.43114301562309265},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.39894556999206543},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.32730621099472046},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.21994176506996155},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.14261838793754578},{"id":"https://openalex.org/keywords/european-union","display_name":"European union","score":0.1373133659362793}],"concepts":[{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.9593381881713867},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7793382406234741},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5611180663108826},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.554797887802124},{"id":"https://openalex.org/C179603123","wikidata":"https://www.wikidata.org/wiki/Q1941921","display_name":"Modeling language","level":3,"score":0.5520414113998413},{"id":"https://openalex.org/C3020782553","wikidata":"https://www.wikidata.org/wiki/Q8880","display_name":"European commission","level":3,"score":0.525198757648468},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5038411021232605},{"id":"https://openalex.org/C135257023","wikidata":"https://www.wikidata.org/wiki/Q691358","display_name":"Domain-specific language","level":2,"score":0.4994065761566162},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.454720675945282},{"id":"https://openalex.org/C189139006","wikidata":"https://www.wikidata.org/wiki/Q166074","display_name":"XHTML","level":4,"score":0.4410630464553833},{"id":"https://openalex.org/C196388810","wikidata":"https://www.wikidata.org/wiki/Q631877","display_name":"RuleML","level":5,"score":0.4337802529335022},{"id":"https://openalex.org/C13606891","wikidata":"https://www.wikidata.org/wiki/Q2623243","display_name":"Conceptual model","level":2,"score":0.43114301562309265},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39894556999206543},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.32730621099472046},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.21994176506996155},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.14261838793754578},{"id":"https://openalex.org/C2910001868","wikidata":"https://www.wikidata.org/wiki/Q458","display_name":"European union","level":2,"score":0.1373133659362793},{"id":"https://openalex.org/C105639569","wikidata":"https://www.wikidata.org/wiki/Q582577","display_name":"Economic policy","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/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000503","qualifier_name":"physiopathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000503","qualifier_name":"physiopathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000503","qualifier_name":"physiopathology","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1109/iembs.2011.6090060","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iembs.2011.6090060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society","raw_type":"proceedings-article"},{"id":"pmid:22254343","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22254343","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null},{"id":"pmh:oai:DiVA.org:uu-447151","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447151","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1530406","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/1530406/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"In: (pp. pp. 441-444). (2011)","raw_type":"Proceedings paper"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:eb294d79-1a0d-4829-83a2-777c167f37d4","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:eb294d79-1a0d-4829-83a2-777c167f37d4","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Department of Computer Science","raw_type":"Conference item"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/11583","is_oa":false,"landing_page_url":"http://hdl.handle.net/10044/1/11583","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society","raw_type":"Conference Paper"}],"best_oa_location":{"id":"pmh:oai:DiVA.org:uu-447151","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447151","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1532857487","https://openalex.org/W1725463170","https://openalex.org/W1982174804","https://openalex.org/W2009494530","https://openalex.org/W2042880070","https://openalex.org/W2047475087","https://openalex.org/W2087779040","https://openalex.org/W2100525485","https://openalex.org/W2123663722","https://openalex.org/W2131645519","https://openalex.org/W2143292574","https://openalex.org/W2153241479","https://openalex.org/W2168103533","https://openalex.org/W2170419021","https://openalex.org/W4245543188","https://openalex.org/W4252427272","https://openalex.org/W6903572773"],"related_works":["https://openalex.org/W2768131452","https://openalex.org/W1831550526","https://openalex.org/W10129681","https://openalex.org/W2187952378","https://openalex.org/W4205261768","https://openalex.org/W2383389726","https://openalex.org/W2211309320","https://openalex.org/W2043722775","https://openalex.org/W1957705281","https://openalex.org/W2358918344"],"abstract_inverted_index":{"This":[0],"paper":[1,33],"describes":[2],"the":[3,11,36,52,61,71,87],"initial":[4],"groundwork":[5],"carried":[6],"out":[7],"as":[8],"part":[9],"of":[10,77],"European":[12],"Commission":[13],"funded":[14],"Transatlantic":[15],"Tumor":[16],"Model":[17],"Repositories":[18],"project,":[19],"to":[20,51,59,65,68,85],"develop":[21,69],"a":[22,40,75],"new":[23],"markup":[24,80],"language":[25,88],"for":[26,38],"computational":[27],"cancer":[28,53],"modelling,":[29],"TumorML.":[30],"In":[31],"this":[32],"we":[34],"describe":[35,60],"motivations":[37],"such":[39],"language,":[41],"arguing":[42],"that":[43,63],"current":[44],"state-of-the-art":[45],"biomodelling":[46],"languages":[47,81],"are":[48],"not":[49],"suited":[50],"modelling":[54],"domain.":[55],"We":[56],"go":[57],"on":[58],"work":[62],"needs":[64],"be":[66,83],"done":[67],"TumorML,":[70],"conceptual":[72],"design,":[73],"and":[74],"description":[76],"what":[78],"existing":[79],"will":[82],"used":[84],"compose":[86],"specification.":[89]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
