{"id":"https://openalex.org/W4295690887","doi":"https://doi.org/10.48550/arxiv.2209.04732","title":"Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality","display_name":"Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality","publication_year":2022,"publication_date":"2022-09-10","ids":{"openalex":"https://openalex.org/W4295690887","doi":"https://doi.org/10.48550/arxiv.2209.04732"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2209.04732","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2209.04732","pdf_url":"https://arxiv.org/pdf/2209.04732","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2209.04732","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031147343","display_name":"Tiffany J. Callahan","orcid":"https://orcid.org/0000-0002-8169-9049"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Callahan, Tiffany J.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034793798","display_name":"Adrianne L. Stefanski","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stefanski, Adrianne L.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035907836","display_name":"Jordan M Wyrwa","orcid":"https://orcid.org/0000-0002-5455-5859"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wyrwa, Jordan M.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042491541","display_name":"Chenjie Zeng","orcid":"https://orcid.org/0000-0002-0149-5661"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zeng, Chenjie","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015201397","display_name":"Anna Ostropolets","orcid":"https://orcid.org/0000-0002-0847-6682"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ostropolets, Anna","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011590035","display_name":"Juan M. Banda","orcid":"https://orcid.org/0000-0001-8499-824X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Banda, Juan M.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030261399","display_name":"William A. Baumgartner","orcid":"https://orcid.org/0000-0001-6717-5313"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Baumgartner, William A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102921689","display_name":"Richard D. Boyce","orcid":"https://orcid.org/0000-0002-2993-2085"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Boyce, Richard D.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079939753","display_name":"Elena Casiraghi","orcid":"https://orcid.org/0000-0003-2024-7572"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Casiraghi, Elena","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011730721","display_name":"Ben D. Coleman","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Coleman, Ben D.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087174417","display_name":"Janine Collins","orcid":"https://orcid.org/0000-0002-8716-3261"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Collins, Janine H.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028496552","display_name":"Sara J. Deakyne-Davies","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Deakyne-Davies, Sara J.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039864309","display_name":"James A. Feinstein","orcid":"https://orcid.org/0000-0003-3074-8805"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Feinstein, James A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064320417","display_name":"Melissa Haendel","orcid":"https://orcid.org/0000-0001-9114-8737"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Haendel, Melissa A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054021116","display_name":"Asiyah Y. Lin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lin, Asiyah Y.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102447064","display_name":"Blake Martin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Martin, Blake","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040603724","display_name":"Nicolas Matentzoglu","orcid":"https://orcid.org/0000-0002-7356-1779"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matentzoglu, Nicolas A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089705492","display_name":"Daniella Meeker","orcid":"https://orcid.org/0000-0002-1034-7628"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Meeker, Daniella","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073533486","display_name":"Justin Reese","orcid":"https://orcid.org/0000-0002-2170-2250"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Reese, Justin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074960306","display_name":"Jessica Sinclair","orcid":"https://orcid.org/0000-0003-2391-6305"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sinclair, Jessica","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020941065","display_name":"Sanya B. Taneja","orcid":"https://orcid.org/0000-0003-1707-1617"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Taneja, Sanya B.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077029401","display_name":"Katy E. Trinkley","orcid":"https://orcid.org/0000-0003-2041-7404"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Trinkley, Katy E.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041814853","display_name":"Nicole Vasilevsky","orcid":"https://orcid.org/0000-0001-5208-3432"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vasilevsky, Nicole A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101881308","display_name":"Andrew E. Williams","orcid":"https://orcid.org/0000-0002-0692-412X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Williams, Andrew","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020875876","display_name":"Xingman A. Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Xingman A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033225381","display_name":"Peter N. Robinson","orcid":"https://orcid.org/0000-0002-0736-9199"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Denny, Joshua C.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065153070","display_name":"Patrick Ryan","orcid":"https://orcid.org/0000-0002-9727-2138"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robinson, Peter N.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053670656","display_name":"George Hripcsak","orcid":"https://orcid.org/0000-0003-2664-7614"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ryan, Patrick","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075439357","display_name":"Tellen D. Bennett","orcid":"https://orcid.org/0000-0003-1483-4236"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hripcsak, George","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041860080","display_name":"Lawrence Hunter","orcid":"https://orcid.org/0000-0003-1455-3370"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bennett, Tellen D.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060507817","display_name":"Michael G. Kahn","orcid":"https://orcid.org/0000-0003-4786-6875"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hunter, Lawrence E.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Kahn, Michael G.","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kahn, Michael G.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":32,"corresponding_author_ids":["https://openalex.org/A5031147343"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9987000226974487,"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":0.9987000226974487,"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":0.9914000034332275,"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":0.9581000208854675,"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":0.7316669225692749},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.7275406718254089},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6774454116821289},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5489826202392578},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.518398106098175},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4346843957901001},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.42121607065200806},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.41650205850601196},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3517400026321411},{"id":"https://openalex.org/keywords/knowledge-management","display_name":"Knowledge management","score":0.2820611894130707},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2769773006439209},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.27327942848205566},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.26021796464920044},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.2250240445137024}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7316669225692749},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.7275406718254089},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6774454116821289},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5489826202392578},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.518398106098175},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4346843957901001},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.42121607065200806},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.41650205850601196},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3517400026321411},{"id":"https://openalex.org/C56739046","wikidata":"https://www.wikidata.org/wiki/Q192060","display_name":"Knowledge management","level":1,"score":0.2820611894130707},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2769773006439209},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27327942848205566},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.26021796464920044},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.2250240445137024},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2209.04732","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2209.04732","pdf_url":"https://arxiv.org/pdf/2209.04732","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2209.04732","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2209.04732","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2209.04732","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2209.04732","pdf_url":"https://arxiv.org/pdf/2209.04732","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.5699999928474426,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2127299687","https://openalex.org/W2357854711","https://openalex.org/W1506177826","https://openalex.org/W372138008","https://openalex.org/W2532736362","https://openalex.org/W2726617685","https://openalex.org/W4243448361","https://openalex.org/W2051700896","https://openalex.org/W1552255772","https://openalex.org/W2111524952"],"abstract_inverted_index":{"Background:":[0],"Common":[1],"data":[2,51],"models":[3],"solve":[4],"many":[5],"challenges":[6],"of":[7,38,45,98],"standardizing":[8],"electronic":[9],"health":[10],"record":[11],"(EHR)":[12],"data,":[13],"but":[14],"are":[15],"unable":[16],"to":[17,52,76,111,134,142],"semantically":[18],"integrate":[19],"all":[20],"the":[21,43,116],"resources":[22],"needed":[23],"for":[24,68,85],"deep":[25,145],"phenotyping.":[26,146],"Open":[27],"Biological":[28],"and":[29,41,59,91],"Biomedical":[30],"Ontology":[31],"(OBO)":[32],"Foundry":[33],"ontologies":[34,54,136],"provide":[35],"computable":[36],"representations":[37],"biological":[39],"knowledge":[40],"enable":[42],"integration":[44],"heterogeneous":[46],"data.":[47],"However,":[48],"mapping":[49,69],"EHR":[50],"OBO":[53,77,135],"requires":[55],"significant":[56],"manual":[57],"curation":[58],"domain":[60],"expertise.":[61],"Objective:":[62],"We":[63],"introduce":[64],"OMOP2OBO,":[65,81],"an":[66],"algorithm":[67,138],"Observational":[70],"Medical":[71],"Outcomes":[72],"Partnership":[73],"(OMOP)":[74],"vocabularies":[75,133],"ontologies.":[78],"Results:":[79],"Using":[80],"we":[82],"produced":[83],"mappings":[84,117],"92,367":[86],"conditions,":[87],"8611":[88],"drug":[89],"ingredients,":[90],"10,673":[92],"measurement":[93],"results,":[94],"which":[95],"covered":[96],"68-99%":[97],"concepts":[99],"used":[100,110],"in":[101],"clinical":[102],"practice":[103],"when":[104],"examined":[105],"across":[106],"24":[107],"hospitals.":[108],"When":[109],"phenotype":[112],"rare":[113],"disease":[114],"patients,":[115],"helped":[118],"systematically":[119],"identify":[120],"undiagnosed":[121],"patients":[122],"who":[123],"might":[124],"benefit":[125],"from":[126],"genetic":[127],"testing.":[128],"Conclusions:":[129],"By":[130],"aligning":[131],"OMOP":[132],"our":[137],"presents":[139],"new":[140],"opportunities":[141],"advance":[143],"EHR-based":[144]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
