{"id":"https://openalex.org/W2695731692","doi":"https://doi.org/10.1186/s13326-017-0127-z","title":"Ontological interpretation of biomedical database content","display_name":"Ontological interpretation of biomedical database content","publication_year":2017,"publication_date":"2017-06-26","ids":{"openalex":"https://openalex.org/W2695731692","doi":"https://doi.org/10.1186/s13326-017-0127-z","mag":"2695731692","pmid":"https://pubmed.ncbi.nlm.nih.gov/28651575"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-017-0127-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-017-0127-z","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-017-0127-z","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/s13326-017-0127-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077056982","display_name":"Filipe Santana da Silva","orcid":"https://orcid.org/0000-0002-6803-1407"},"institutions":[{"id":"https://openalex.org/I25112270","display_name":"Universidade Federal de Pernambuco","ror":"https://ror.org/047908t24","country_code":"BR","type":"education","lineage":["https://openalex.org/I25112270"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Filipe Santana da Silva","raw_affiliation_strings":["Centro de Inform\u00e1tica, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, 50.740-560, Recife, Brazil","N\u00facleo de Telessa\u00fade, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 50670-420, Recife, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-6803-1407","affiliations":[{"raw_affiliation_string":"Centro de Inform\u00e1tica, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, 50.740-560, Recife, Brazil","institution_ids":["https://openalex.org/I25112270"]},{"raw_affiliation_string":"N\u00facleo de Telessa\u00fade, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 50670-420, Recife, Brazil","institution_ids":["https://openalex.org/I25112270"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044902964","display_name":"Ludger Jansen","orcid":"https://orcid.org/0000-0002-0097-6359"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ludger Jansen","raw_affiliation_strings":["Institut f\u00fcr Philosophie, Universit\u00e4t Rostock, D-18051, Rostock, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0097-6359","affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Philosophie, Universit\u00e4t Rostock, D-18051, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103176344","display_name":"Fred Freitas","orcid":"https://orcid.org/0000-0003-0425-6786"},"institutions":[{"id":"https://openalex.org/I25112270","display_name":"Universidade Federal de Pernambuco","ror":"https://ror.org/047908t24","country_code":"BR","type":"education","lineage":["https://openalex.org/I25112270"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Fred Freitas","raw_affiliation_strings":["Centro de Inform\u00e1tica, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, 50.740-560, Recife, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Inform\u00e1tica, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, 50.740-560, Recife, Brazil","institution_ids":["https://openalex.org/I25112270"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101773732","display_name":"Stefan Schulz","orcid":"https://orcid.org/0000-0001-7222-3287"},"institutions":[{"id":"https://openalex.org/I202276237","display_name":"Medical University of Graz","ror":"https://ror.org/02n0bts35","country_code":"AT","type":"education","lineage":["https://openalex.org/I202276237"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Stefan Schulz","raw_affiliation_strings":["Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Auenbruggerplatz 2/V, Graz, 8036, Austria. stefan.schulz@medunigraz.at","Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Auenbruggerplatz 2/V, Graz, 8036, Austria"],"raw_orcid":"https://orcid.org/0000-0001-7222-3287","affiliations":[{"raw_affiliation_string":"Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Auenbruggerplatz 2/V, Graz, 8036, Austria. stefan.schulz@medunigraz.at","institution_ids":["https://openalex.org/I202276237"]},{"raw_affiliation_string":"Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Auenbruggerplatz 2/V, Graz, 8036, Austria","institution_ids":["https://openalex.org/I202276237"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101773732"],"corresponding_institution_ids":["https://openalex.org/I202276237"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":0.8108,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.70586273,"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":"24","last_page":"24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9624000191688538,"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":0.9624000191688538,"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":0.020400000736117363,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0071000000461936,"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/computer-science","display_name":"Computer science","score":0.8393193483352661},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.6316171288490295},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5784481763839722},{"id":"https://openalex.org/keywords/content","display_name":"Content (measure theory)","score":0.47962602972984314},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42317235469818115},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3390601873397827},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12836039066314697}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8393193483352661},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.6316171288490295},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5784481763839722},{"id":"https://openalex.org/C2778152352","wikidata":"https://www.wikidata.org/wiki/Q5165061","display_name":"Content (measure theory)","level":2,"score":0.47962602972984314},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42317235469818115},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3390601873397827},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12836039066314697},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","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":"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":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s13326-017-0127-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-017-0127-z","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-017-0127-z","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:28651575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28651575","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:aef8f717136f4274aa3d443b3fd3b5c8","is_oa":false,"landing_page_url":"https://doaj.org/article/aef8f717136f4274aa3d443b3fd3b5c8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Biomedical Semantics, Vol 8, Iss 1, Pp 1-14 (2017)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5485580","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5485580","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13326-017-0127-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-017-0127-z","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-017-0127-z","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/10","score":0.6899999976158142,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G3779362384","display_name":null,"funder_award_id":"140698/2012-4","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G581965161","display_name":null,"funder_award_id":"2012-4","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G5924823403","display_name":null,"funder_award_id":"3914/2014-03","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2695731692.pdf","grobid_xml":"https://content.openalex.org/works/W2695731692.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W60583076","https://openalex.org/W820713278","https://openalex.org/W1461258677","https://openalex.org/W1482134990","https://openalex.org/W1490161904","https://openalex.org/W1492864441","https://openalex.org/W1551938995","https://openalex.org/W1555563750","https://openalex.org/W1595227046","https://openalex.org/W1654805921","https://openalex.org/W1678959094","https://openalex.org/W1802346448","https://openalex.org/W1884111252","https://openalex.org/W1981732549","https://openalex.org/W1998028266","https://openalex.org/W2001341831","https://openalex.org/W2012881519","https://openalex.org/W2049161578","https://openalex.org/W2103260426","https://openalex.org/W2106830745","https://openalex.org/W2113142309","https://openalex.org/W2113449293","https://openalex.org/W2136317480","https://openalex.org/W2138162238","https://openalex.org/W2140080033","https://openalex.org/W2144573571","https://openalex.org/W2145003065","https://openalex.org/W2152901032","https://openalex.org/W2161056277","https://openalex.org/W2164010954","https://openalex.org/W2165084432","https://openalex.org/W2165428180","https://openalex.org/W2168120333","https://openalex.org/W2408202220","https://openalex.org/W2531563875","https://openalex.org/W2572885380","https://openalex.org/W2739999456","https://openalex.org/W2912565176","https://openalex.org/W2963658122","https://openalex.org/W3144889436","https://openalex.org/W3192048314","https://openalex.org/W4211007335","https://openalex.org/W4212986840","https://openalex.org/W4230266413"],"related_works":["https://openalex.org/W4313320911","https://openalex.org/W4327743144","https://openalex.org/W4245077728","https://openalex.org/W2607424049","https://openalex.org/W4390922876","https://openalex.org/W3183204001","https://openalex.org/W4206302830","https://openalex.org/W2185941092","https://openalex.org/W4386782890","https://openalex.org/W3210948575"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biological":[1],"databases":[2,59,308],"store":[3],"data":[4,16],"about":[5],"laboratory":[6],"experiments,":[7],"together":[8],"with":[9,64,106,262,278],"semantic":[10,304],"annotations,":[11],"in":[12,26,47,266,282,306,312],"order":[13],"to":[14,182,203,209,259],"support":[15],"aggregation":[17],"and":[18,43,61,70,104,119,146,175,229,231,237,264,268,309,327],"retrieval.":[19],"The":[20,91,148,317],"exact":[21],"meaning":[22],"of":[23,29,117,124,172,188,221,227,243,290,323],"such":[24],"annotations":[25,305,328],"the":[27,58,86,110,122,170,200,205,215,219,244,247,257,276],"context":[28],"a":[30,48,54,115,225,297,320],"database":[31,45,96,131,216,292,324],"record":[32],"is":[33,114,192,224,232,294,319],"often":[34],"ambiguous.":[35],"We":[36],"address":[37],"this":[38],"problem":[39],"by":[40,204,296],"grounding":[41],"implicit":[42,301],"explicit":[44],"content":[46,65,132,293,326],"formal-ontological":[49],"framework.":[50],"METHODS:":[51],"By":[52],"using":[53,134],"typical":[55],"extract":[56,210],"from":[57,66,214],"UniProt":[60],"Ensembl,":[62],"annotated":[63],"GO,":[67],"PR,":[68],"ChEBI":[69],"NCBI":[71],"Taxonomy,":[72],"we":[73,128],"created":[74,184],"four":[75,126,156,245,248],"ontological":[76,166,212],"models":[77,94,149],"(in":[78],"OWL),":[79],"which":[80],"generate":[81],"explicit,":[82],"distinct":[83],"interpretations":[84],"under":[85,152,199],"BioTopLite2":[87],"(BTL2)":[88],"upper-level":[89,315],"ontology.":[90,316],"first":[92],"three":[93],"interpret":[95],"entries":[97],"as":[98,136,252,329],"individuals":[99,174,261],"(IND),":[100],"defined":[101,197],"classes":[102,105,201,265],"(SUBC),":[103],"dispositions":[107],"(DISP),":[108],"respectively;":[109],"fourth":[111],"model":[112],"(HYBR)":[113],"combination":[116],"SUBC":[118,191,228,267],"DISP.":[120],"For":[121,241],"evaluation":[123],"these":[125,153],"models,":[127,246],"consider":[129],"(i)":[130],"retrieval,":[133],"ontologies":[135],"query":[137,238],"vocabulary;":[138],"(ii)":[139],"information":[140],"completeness;":[141],"and,":[142],"(iii)":[143],"DL":[144,253],"complexity":[145],"decidability.":[147],"were":[150,250],"tested":[151],"criteria":[154],"against":[155],"competency":[157],"questions":[158],"(CQs).":[159],"RESULTS:":[160],"IND":[161],"does":[162,271],"not":[163,272],"raise":[164],"any":[165],"claim,":[167],"besides":[168],"asserting":[169],"existence":[171,220],"sample":[173],"relations":[176],"among":[177],"them.":[178],"Modelling":[179],"patterns":[180],"have":[181],"be":[183],"for":[185],"each":[186,242],"type":[187],"annotation":[189],"referent.":[190],"interpreted":[193],"regarding":[194,235],"maximally":[195],"fine-grained":[196],"subclasses":[198],"referred":[202],"data.":[206],"DISP":[207,230,270],"attempts":[208],"truly":[211],"statements":[213],"records,":[217],"claiming":[218],"dispositions.":[222],"HYBR":[223],"hybrid":[226],"more":[233],"parsimonious":[234],"expressiveness":[236],"answering":[239],"complexity.":[240],"CQs":[249],"submitted":[251],"queries.":[254],"This":[255],"shows":[256],"ability":[258],"retrieve":[260,273],"IND,":[263],"HYBR.":[269],"anything":[274],"because":[275],"axioms":[277],"disposition":[279],"are":[280],"embedded":[281],"General":[283],"Class":[284],"Inclusion":[285],"(GCI)":[286],"statements.":[287],"CONCLUSION:":[288],"Ambiguity":[289],"biological":[291,307],"addressed":[295],"method":[298],"that":[299],"identifies":[300],"knowledge":[302],"behind":[303],"grounds":[310],"it":[311],"an":[313],"expressive":[314],"result":[318],"seamless":[321],"representation":[322],"structure,":[325],"OWL":[330],"models.":[331]},"counts_by_year":[{"year":2026,"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":2},{"year":2018,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2017-06-30T00:00:00"}
