{"id":"https://openalex.org/W4413864914","doi":"https://doi.org/10.1186/s13326-025-00335-4","title":"A prototype ETL pipeline that uses HL7 FHIR RDF resources when deploying pure functions to enrich knowledge graph patient data","display_name":"A prototype ETL pipeline that uses HL7 FHIR RDF resources when deploying pure functions to enrich knowledge graph patient data","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4413864914","doi":"https://doi.org/10.1186/s13326-025-00335-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/40887611"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-025-00335-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00335-4","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00335-4","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/s13326-025-00335-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086136168","display_name":"Anusha Ansari","orcid":"https://orcid.org/0000-0001-6173-9384"},"institutions":[{"id":"https://openalex.org/I1338135719","display_name":"Centre for Addiction and Mental Health","ror":"https://ror.org/03e71c577","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1338135719"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Adeel Ansari","raw_affiliation_strings":["Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, 250 College St., Toronto, ON, M5T 1R8, Canada. adeel.ansari@camh.ca"],"raw_orcid":"https://orcid.org/0000-0001-6173-9384","affiliations":[{"raw_affiliation_string":"Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, 250 College St., Toronto, ON, M5T 1R8, Canada. adeel.ansari@camh.ca","institution_ids":["https://openalex.org/I1338135719"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034640849","display_name":"Marisa Conte","orcid":"https://orcid.org/0000-0001-7377-163X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marisa Conte","raw_affiliation_strings":["Department of Learning Health Sciences, Knowledge Systems Laboratory, University of Michigan Medical School, Victor Vaughan Building, Room 209, 1111 Catherine St., Ann Arbor, MI, 48109, USA"],"raw_orcid":"https://orcid.org/0000-0001-7377-163X","affiliations":[{"raw_affiliation_string":"Department of Learning Health Sciences, Knowledge Systems Laboratory, University of Michigan Medical School, Victor Vaughan Building, Room 209, 1111 Catherine St., Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052432646","display_name":"Allen Flynn","orcid":"https://orcid.org/0000-0002-3471-3063"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Allen Flynn","raw_affiliation_strings":["Department of Learning Health Sciences, Knowledge Systems Laboratory, University of Michigan Medical School, Victor Vaughan Building, Room 209, 1111 Catherine St., Ann Arbor, MI, 48109, USA"],"raw_orcid":"https://orcid.org/0000-0002-3471-3063","affiliations":[{"raw_affiliation_string":"Department of Learning Health Sciences, Knowledge Systems Laboratory, University of Michigan Medical School, Victor Vaughan Building, Room 209, 1111 Catherine St., Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":null,"display_name":"Avanti Paturkar","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Avanti Paturkar","raw_affiliation_strings":["Department of Learning Health Sciences, Knowledge Systems Laboratory, University of Michigan Medical School, Victor Vaughan Building, Room 209, 1111 Catherine St., Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Learning Health Sciences, Knowledge Systems Laboratory, University of Michigan Medical School, Victor Vaughan Building, Room 209, 1111 Catherine St., Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10629207,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"16","issue":"1","first_page":"16","last_page":"16"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.27309998869895935,"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"}},"topics":[{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.27309998869895935,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.25,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.09960000216960907,"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/computer-science","display_name":"Computer science","score":0.8957515358924866},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.8073163628578186},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5520161986351013},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5472594499588013},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.526833713054657},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4951459467411041},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.48590412735939026},{"id":"https://openalex.org/keywords/linked-data","display_name":"Linked data","score":0.444546639919281},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41784366965293884},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37567582726478577},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2794099450111389},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2678130269050598},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.2088628113269806}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8957515358924866},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.8073163628578186},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5520161986351013},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5472594499588013},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.526833713054657},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4951459467411041},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.48590412735939026},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.444546639919281},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41784366965293884},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37567582726478577},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2794099450111389},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2678130269050598},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2088628113269806}],"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":"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":"D057208","descriptor_name":"Health Level Seven","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057208","descriptor_name":"Health Level Seven","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","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":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s13326-025-00335-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00335-4","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00335-4","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:40887611","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40887611","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:7748add295204ca8a4bbb5875dc96376","is_oa":true,"landing_page_url":"https://doaj.org/article/7748add295204ca8a4bbb5875dc96376","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 1-12 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11211334","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12400713","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:12400713","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12400713/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13326-025-00335-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00335-4","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00335-4","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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413864914.pdf","grobid_xml":"https://content.openalex.org/works/W4413864914.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W203440368","https://openalex.org/W1555486317","https://openalex.org/W1808652302","https://openalex.org/W1971938965","https://openalex.org/W2043705607","https://openalex.org/W2132322340","https://openalex.org/W2302501749","https://openalex.org/W2404901863","https://openalex.org/W2589119372","https://openalex.org/W2900083938","https://openalex.org/W3034674374","https://openalex.org/W3143661006","https://openalex.org/W3163194020","https://openalex.org/W4211077092","https://openalex.org/W4220730040","https://openalex.org/W4285021577","https://openalex.org/W4289711564","https://openalex.org/W4304808564","https://openalex.org/W4306173528","https://openalex.org/W4307829815","https://openalex.org/W4384694918","https://openalex.org/W4388213822","https://openalex.org/W4394693910","https://openalex.org/W4399577811","https://openalex.org/W4401834045","https://openalex.org/W4408083674"],"related_works":["https://openalex.org/W2283287182","https://openalex.org/W2776293731","https://openalex.org/W82112649","https://openalex.org/W1485690712","https://openalex.org/W2058923328","https://openalex.org/W2897957211","https://openalex.org/W2945730294","https://openalex.org/W199330785","https://openalex.org/W2054214855","https://openalex.org/W2400121884"],"abstract_inverted_index":{"BACKGROUND:":[0],"For":[1],"clinical":[2],"care":[3],"and":[4,21,36,63,76,86,101,125,155,192],"research,":[5],"knowledge":[6,19,41,57,94],"graphs":[7,42,58],"with":[8,32,43,97,147,185],"patient":[9,30,46,54,102],"data":[10,55,65,80,109,131,150,171],"can":[11,68,121,144],"be":[12,122,145],"enriched":[13],"by":[14,114,128],"extracting":[15],"parameters":[16],"from":[17,167],"a":[18,78,92],"graph":[20,95,142],"then":[22,126],"using":[23],"them":[24],"as":[25],"inputs":[26],"to":[27,91,134,162,177],"compute":[28],"new":[29,79,130,164,180,196],"features":[31,47,166],"pure":[33,160],"functions.":[34],"Systematic":[35],"transparent":[37],"methods":[38],"for":[39,83,153],"enriching":[40,52],"newly":[44,88,136],"computed":[45,89],"are":[48],"of":[49,159,183,194],"interest.":[50],"When":[51],"the":[53,157,190],"in":[56],"this":[59,129],"way,":[60],"existing":[61,168],"ontologies":[62],"well-known":[64],"resource":[66,110],"standards":[67],"help":[69],"promote":[70],"semantic":[71,149],"interoperability.":[72],"RESULTS:":[73],"We":[74,105],"developed":[75],"tested":[77],"processing":[81,132,151,172],"pipeline":[82,133],"extracting,":[84],"computing,":[85],"returning":[87],"results":[90],"large":[93],"populated":[96],"electronic":[98],"health":[99],"record":[100],"survey":[103],"data.":[104,169],"show":[106],"that":[107,188],"RDF":[108,119],"types":[111],"already":[112],"specified":[113],"Health":[115],"Level":[116],"7's":[117],"FHIR":[118],"effort":[120],"programmatically":[123],"validated":[124],"used":[127],"represent":[135],"derived":[137],"patient-level":[138,165,181],"features.":[139],"CONCLUSIONS:":[140],"Knowledge":[141],"technology":[143],"augmented":[146],"standards-based":[148],"pipelines":[152,173],"deploying":[154],"tracing":[156],"use":[158],"functions":[161],"derive":[163],"Semantic":[170],"enable":[174],"research":[175],"enterprises":[176],"report":[178],"on":[179],"computations":[182],"interest":[184],"linked":[186],"metadata":[187],"details":[189],"origin":[191],"background":[193],"every":[195],"computation.":[197]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
