{"id":"https://openalex.org/W4413409257","doi":"https://doi.org/10.1186/s13326-025-00337-2","title":"Mapping between clinical and preclinical terminologies: eTRANSAFE\u2019s Rosetta stone approach","display_name":"Mapping between clinical and preclinical terminologies: eTRANSAFE\u2019s Rosetta stone approach","publication_year":2025,"publication_date":"2025-08-21","ids":{"openalex":"https://openalex.org/W4413409257","doi":"https://doi.org/10.1186/s13326-025-00337-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/40841963"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-025-00337-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00337-2","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00337-2","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/counter/pdf/10.1186/s13326-025-00337-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053857782","display_name":"Erik M. van Mulligen","orcid":"https://orcid.org/0000-0003-1377-9386"},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Erik M. van Mulligen","raw_affiliation_strings":["Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands. e.vanmulligen@erasmusmc.nl","Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands. e.vanmulligen@erasmusmc.nl","institution_ids":["https://openalex.org/I2801952686"]},{"raw_affiliation_string":"Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089905971","display_name":"Rowan Parry","orcid":null},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Rowan Parry","raw_affiliation_strings":["Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023215576","display_name":"Johan van der Lei","orcid":"https://orcid.org/0000-0002-9203-3410"},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Johan van der Lei","raw_affiliation_strings":["Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005077862","display_name":"Jan A. Kors","orcid":"https://orcid.org/0000-0002-4929-026X"},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jan A. Kors","raw_affiliation_strings":["Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053857782"],"corresponding_institution_ids":["https://openalex.org/I2801952686"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1306913,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"16","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9884999990463257,"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":0.9884999990463257,"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/T12881","display_name":"linguistics and terminology studies","score":0.003000000026077032,"subfield":{"id":"https://openalex.org/subfields/1203","display_name":"Language and Linguistics"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.001500000013038516,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/snomed-ct","display_name":"SNOMED CT","score":0.9475409984588623},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.8377680778503418},{"id":"https://openalex.org/keywords/systematized-nomenclature-of-medicine","display_name":"Systematized Nomenclature of Medicine","score":0.8019708395004272},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7378104329109192},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4613296091556549},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.4199843108654022},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4071351885795593},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3976553678512573},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09658482670783997}],"concepts":[{"id":"https://openalex.org/C206497026","wikidata":"https://www.wikidata.org/wiki/Q1753883","display_name":"SNOMED CT","level":3,"score":0.9475409984588623},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.8377680778503418},{"id":"https://openalex.org/C44681071","wikidata":"https://www.wikidata.org/wiki/Q4048820","display_name":"Systematized Nomenclature of Medicine","level":4,"score":0.8019708395004272},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7378104329109192},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4613296091556549},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.4199843108654022},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4071351885795593},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3976553678512573},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09658482670783997},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"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":"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":"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":"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":"D039061","descriptor_name":"Systematized Nomenclature of Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039061","descriptor_name":"Systematized Nomenclature of Medicine","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":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s13326-025-00337-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00337-2","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00337-2","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:40841963","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40841963","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:pure.eur.nl:openaire_cris_publications/d30595c1-e2ad-48f9-88ae-0d8e42f2699b","is_oa":false,"landing_page_url":"https://pure.eur.nl/en/publications/d30595c1-e2ad-48f9-88ae-0d8e42f2699b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401266","display_name":"EUR Research Repository (Erasmus University Rotterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I913958620","host_organization_name":"Erasmus University Rotterdam","host_organization_lineage":["https://openalex.org/I913958620"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"van Mulligen, E M, Parry, R, van der Lei, J & Kors, J A 2025, 'Mapping between clinical and preclinical\u00a0terminologies : eTRANSAFE\u2019s Rosetta stone approach', Journal of Biomedical Semantics, vol. 16, no. 1, 15. https://doi.org/10.1186/s13326-025-00337-2","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:d44798d8d4324baabb62296c3556f58c","is_oa":true,"landing_page_url":"https://doaj.org/article/d44798d8d4324baabb62296c3556f58c","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":"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 16, Iss 1, Pp 1-11 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11182173","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12372267","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13326-025-00337-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00337-2","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00337-2","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7626668788","display_name":null,"funder_award_id":"777365","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"},{"id":"https://openalex.org/G7951625825","display_name":"Enhacing TRANslational SAFEty Assessment through Integrative Knowledge Management","funder_award_id":"777365","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320314178","display_name":"European Federation of Pharmaceutical Industries and Associations","ror":"https://ror.org/00g1x4v36"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413409257.pdf","grobid_xml":"https://content.openalex.org/works/W4413409257.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1537617436","https://openalex.org/W2042631179","https://openalex.org/W2101747459","https://openalex.org/W2110362051","https://openalex.org/W2113097201","https://openalex.org/W2156005162","https://openalex.org/W2159583324","https://openalex.org/W2163685645","https://openalex.org/W2621329358","https://openalex.org/W2883024595","https://openalex.org/W2980292307","https://openalex.org/W3135202150","https://openalex.org/W3214803164","https://openalex.org/W4380610193","https://openalex.org/W4390578581"],"related_works":["https://openalex.org/W2581432157","https://openalex.org/W983237315","https://openalex.org/W4386159309","https://openalex.org/W4295077997","https://openalex.org/W4384914659","https://openalex.org/W2419080317","https://openalex.org/W1708042184","https://openalex.org/W1511848092","https://openalex.org/W2405923535","https://openalex.org/W4407837198"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,126,288,315],"eTRANSAFE":[2,85],"project":[3,16],"developed":[4,249],"tools":[5],"that":[6,106,158,170,250],"support":[7],"translational":[8,341],"research.":[9],"One":[10],"of":[11,43,61,72,74,93,118,124,174,179,207,218,269,307,313,331],"the":[12,54,90,108,142,155,172,175,187,240,253,264,267,270,273],"challenges":[13],"in":[14,84,340],"this":[15],"was":[17,183,276],"to":[18,64,89,110,131,145,236,298,317,327],"combine":[19],"preclinical":[20,44,62,79,119,143,211,259,308,332],"and":[21,30,32,40,52,80,116,165,192,229,255,260,304,333],"clinical":[22,38,81,114,129,231,261,302,334],"data,":[23,335],"which":[24,58,336],"are":[25,33],"coded":[26],"with":[27,121,186,193,310],"different":[28,47,70,122,311],"terminologies":[29,82,130,144,212],"granularities,":[31],"expressed":[34],"as":[35,41,102,239],"single":[36],"pre-coordinated,":[37],"concepts":[39,45,63,115,120,182,209,303,309],"combinations":[42,60,117],"from":[46,78,128,136,141,210,272],"terminologies.":[48],"This":[49],"study":[50],"develops":[51],"evaluates":[53],"Rosetta":[55,188,289],"Stone":[56,189,290],"approach,":[57],"maps":[59],"clinical,":[65],"pre-coordinated":[66,113,181,301],"concepts,":[67],"allowing":[68],"for":[69,162,216,282],"levels":[71,123,312],"exactness":[73],"mappings.":[75],"METHODS:":[76],"Concepts":[77],"used":[83],"have":[86],"been":[87,248],"mapped":[88,184,235],"Systematized":[91],"Nomenclature":[92],"Medicine":[94],"Clinical":[95],"Terms":[96],"(SNOMED":[97],"CT).":[98],"SNOMED":[99,132,146,237],"CT":[100,133,147,238],"acts":[101],"an":[103],"intermediary":[104,241],"terminology":[105,232,245,274,297],"provides":[107],"semantics":[109],"bridge":[111],"between":[112,258,300],"granularity.":[125],"mappings":[127,140,257,271,325],"were":[134,148,201,234],"taken":[135],"existing":[137],"resources,":[138],"while":[139],"manually":[149,202],"created.":[150],"A":[151,177,205,244],"coordination":[152],"template":[153],"defines":[154],"relation":[156],"types":[157],"can":[159,337],"be":[160,338],"explored":[161],"a":[163,167,194,230,293,305],"mapping":[164],"assigns":[166],"penalty":[168],"score":[169],"reflects":[171],"inexactness":[173],"mapping.":[176],"subset":[178],"60":[180],"both":[185],"semantic":[190],"approach":[191,291],"lexical":[195,283],"term":[196,284],"matching":[197,285],"approach.":[198],"Both":[199],"results":[200],"evaluated.":[203],"RESULTS:":[204],"total":[206],"34,308":[208],"(Histopathology":[213],"terminology,":[214],"Standard":[215],"Exchange":[217],"Nonclinical":[219],"Data":[220],"(SEND)":[221],"code":[222],"lists,":[223],"Mouse":[224],"Adult":[225],"Gross":[226],"Anatomy":[227],"Ontology)":[228],"(MedDRA)":[233],"bridging":[242],"terminology.":[243],"service":[246,275],"has":[247],"returns":[251],"dynamically":[252],"exact":[254,321],"inexact":[256,324],"concepts.":[262],"On":[263],"evaluation":[265],"set,":[266],"precision":[268],"high":[277],"(95%),":[278],"much":[279],"higher":[280],"than":[281],"(22%).":[286],"CONCLUSION:":[287],"uses":[292],"semantically":[294],"rich":[295],"intermediate":[296],"map":[299],"combination":[306],"exactness.":[314],"possibility":[316],"generate":[318],"not":[319],"only":[320],"but":[322],"also":[323],"allows":[326],"relate":[328],"larger":[329],"amounts":[330],"helpful":[339],"use":[342],"cases.":[343]},"counts_by_year":[],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
