{"id":"https://openalex.org/W2762472790","doi":"https://doi.org/10.1186/s13326-017-0152-y","title":"Towards refactoring the Molecular Function Ontology with a UML profile for function modeling","display_name":"Towards refactoring the Molecular Function Ontology with a UML profile for function modeling","publication_year":2017,"publication_date":"2017-10-04","ids":{"openalex":"https://openalex.org/W2762472790","doi":"https://doi.org/10.1186/s13326-017-0152-y","mag":"2762472790","pmid":"https://pubmed.ncbi.nlm.nih.gov/28978337"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-017-0152-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-017-0152-y","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-017-0152-y","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-017-0152-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087160134","display_name":"Patryk Burek","orcid":"https://orcid.org/0000-0001-8165-0272"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Patryk Burek","raw_affiliation_strings":["Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020824094","display_name":"Frank Loebe","orcid":"https://orcid.org/0000-0003-4537-5212"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frank Loebe","raw_affiliation_strings":["Computer Science Institute, University of Leipzig, Augustusplatz 10, Leipzig, 04109, Germany. frank.loebe@informatik.uni-leipzig.de","Computer Science Institute, University of Leipzig, Augustusplatz 10, Leipzig, 04109, Germany"],"affiliations":[{"raw_affiliation_string":"Computer Science Institute, University of Leipzig, Augustusplatz 10, Leipzig, 04109, Germany. frank.loebe@informatik.uni-leipzig.de","institution_ids":[]},{"raw_affiliation_string":"Computer Science Institute, University of Leipzig, Augustusplatz 10, Leipzig, 04109, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020087024","display_name":"Heinrich Herre","orcid":"https://orcid.org/0000-0001-5343-9218"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Heinrich Herre","raw_affiliation_strings":["Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5087160134"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1661,"currency":"EUR","value_usd":1791},"fwci":0.5595,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.6695088,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"1","first_page":"48","last_page":"48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9973000288009644,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/code-refactoring","display_name":"Code refactoring","score":0.8561141490936279},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8319324254989624},{"id":"https://openalex.org/keywords/unified-modeling-language","display_name":"Unified Modeling Language","score":0.7705074548721313},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7282876968383789},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5310469269752502},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5266956090927124},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.41760891675949097},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3243553638458252},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.12607243657112122}],"concepts":[{"id":"https://openalex.org/C152752567","wikidata":"https://www.wikidata.org/wiki/Q116877","display_name":"Code refactoring","level":3,"score":0.8561141490936279},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8319324254989624},{"id":"https://openalex.org/C145644426","wikidata":"https://www.wikidata.org/wiki/Q169411","display_name":"Unified Modeling Language","level":3,"score":0.7705074548721313},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7282876968383789},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5310469269752502},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5266956090927124},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.41760891675949097},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3243553638458252},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.12607243657112122},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","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":[{"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":"D007255","descriptor_name":"Information Services","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007255","descriptor_name":"Information Services","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007255","descriptor_name":"Information Services","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s13326-017-0152-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-017-0152-y","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-017-0152-y","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:28978337","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28978337","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":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:doaj.org/article:f2ca8c250d55435496b58c75316fbaea","is_oa":true,"landing_page_url":"https://doaj.org/article/f2ca8c250d55435496b58c75316fbaea","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Biomedical Semantics, Vol 8, Iss 1, Pp 1-11 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4559910","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5628467","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13326-017-0152-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-017-0152-y","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-017-0152-y","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.46000000834465027,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8330397625","display_name":null,"funder_award_id":"Funding","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2762472790.pdf","grobid_xml":"https://content.openalex.org/works/W2762472790.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W59128197","https://openalex.org/W156592512","https://openalex.org/W174691002","https://openalex.org/W175551733","https://openalex.org/W1504705153","https://openalex.org/W1523715833","https://openalex.org/W1527927437","https://openalex.org/W1582487692","https://openalex.org/W1918604556","https://openalex.org/W1963354518","https://openalex.org/W1970846593","https://openalex.org/W1995862677","https://openalex.org/W1996457327","https://openalex.org/W1998017916","https://openalex.org/W2007786863","https://openalex.org/W2020389323","https://openalex.org/W2033377040","https://openalex.org/W2089631246","https://openalex.org/W2097688921","https://openalex.org/W2103260426","https://openalex.org/W2103573767","https://openalex.org/W2105941683","https://openalex.org/W2107038434","https://openalex.org/W2121939662","https://openalex.org/W2122924260","https://openalex.org/W2137665890","https://openalex.org/W2150432840","https://openalex.org/W2166752908","https://openalex.org/W2282090784","https://openalex.org/W2404350942","https://openalex.org/W2460787798","https://openalex.org/W2746990315","https://openalex.org/W2916147039","https://openalex.org/W4234895322"],"related_works":["https://openalex.org/W4313549863","https://openalex.org/W4231266416","https://openalex.org/W2395465245","https://openalex.org/W2072205733","https://openalex.org/W3176957927","https://openalex.org/W4296534969","https://openalex.org/W3194667890","https://openalex.org/W4312761314","https://openalex.org/W2476494490","https://openalex.org/W2096877983"],"abstract_inverted_index":{"FueL":[0],"enables":[1],"the":[2,30,37,53,57,60],"systematic,":[3],"graphical":[4],"representation":[5],"of":[6,40,59,62],"functions":[7],"and":[8,66,74],"their":[9],"interrelations,":[10],"including":[11],"making":[12],"information":[13],"explicit":[14],"that":[15,52],"is":[16,23],"currently":[17],"either":[18],"implicit":[19],"in":[20,26],"MFO":[21,63],"or":[22],"mainly":[24],"captured":[25],"textual":[27],"descriptions.":[28],"Moreover,":[29],"considered":[31],"subsumption":[32],"patterns":[33],"lend":[34],"themselves":[35],"to":[36,45],"methodical":[38],"analysis":[39],"refactoring":[41],"options":[42],"with":[43],"respect":[44],"MFO.":[46],"On":[47],"this":[48],"basis":[49],"we":[50],"argue":[51],"approach":[54],"can":[55,67],"increase":[56],"comprehensibility":[58],"structure":[61],"for":[64,70],"humans":[65],"support":[68],"communication,":[69],"example,":[71],"during":[72],"revision":[73],"further":[75],"development.":[76]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
