{"id":"https://openalex.org/W2537773440","doi":"https://doi.org/10.1007/978-3-319-48472-3_43","title":"An Ontology-Enabled Natural Language Processing Pipeline for Provenance Metadata Extraction from Biomedical Text (Short Paper)","display_name":"An Ontology-Enabled Natural Language Processing Pipeline for Provenance Metadata Extraction from Biomedical Text (Short Paper)","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2537773440","doi":"https://doi.org/10.1007/978-3-319-48472-3_43","mag":"2537773440","pmid":"https://pubmed.ncbi.nlm.nih.gov/28664200"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-319-48472-3_43","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-319-48472-3_43","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110400510","display_name":"Joshua Valdez","orcid":null},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Valdez","raw_affiliation_strings":["Division of Medical Informatics and Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Medical Informatics and Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018392233","display_name":"Michael Rueschman","orcid":"https://orcid.org/0000-0002-0506-8368"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I1316535847","display_name":"Beth Israel Deaconess Medical Center","ror":"https://ror.org/04drvxt59","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1316535847"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Rueschman","raw_affiliation_strings":["Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","Departments of Medicine, Brigham and Women\u2019s Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","institution_ids":["https://openalex.org/I1316535847"]},{"raw_affiliation_string":"Departments of Medicine, Brigham and Women\u2019s Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I1316535847"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100680285","display_name":"Matthew Kim","orcid":"https://orcid.org/0000-0001-5316-5181"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I1316535847","display_name":"Beth Israel Deaconess Medical Center","ror":"https://ror.org/04drvxt59","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1316535847"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Kim","raw_affiliation_strings":["Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","Departments of Medicine, Brigham and Women\u2019s Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","institution_ids":["https://openalex.org/I1316535847"]},{"raw_affiliation_string":"Departments of Medicine, Brigham and Women\u2019s Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I1316535847"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050330450","display_name":"Susan Redline","orcid":"https://orcid.org/0000-0002-6585-1610"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I1316535847","display_name":"Beth Israel Deaconess Medical Center","ror":"https://ror.org/04drvxt59","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1316535847"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan Redline","raw_affiliation_strings":["Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","Departments of Medicine, Brigham and Women\u2019s Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","institution_ids":["https://openalex.org/I1316535847"]},{"raw_affiliation_string":"Departments of Medicine, Brigham and Women\u2019s Hospital and Beth Israel Deaconess Medical Center, Harvard University, Boston, MA, USA","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I1316535847"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050196876","display_name":"Satya S. Sahoo","orcid":"https://orcid.org/0000-0001-9190-4256"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Satya S. Sahoo","raw_affiliation_strings":["Division of Medical Informatics and Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Medical Informatics and Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050196876"],"corresponding_institution_ids":["https://openalex.org/I58956616"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":4.2554,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.95583152,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"10033","issue":null,"first_page":"699","last_page":"708"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9865000247955322,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9861000180244446,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.8297652006149292},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8125935792922974},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5923776030540466},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5833519101142883},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5768110752105713},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5746283531188965},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5518282055854797},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.44879215955734253},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.44644901156425476},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4447647035121918},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3776848018169403},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33056700229644775},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22156015038490295},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.14856025576591492}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8297652006149292},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8125935792922974},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5923776030540466},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5833519101142883},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5768110752105713},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5746283531188965},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5518282055854797},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.44879215955734253},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.44644901156425476},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4447647035121918},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3776848018169403},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33056700229644775},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22156015038490295},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.14856025576591492},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":[],"locations_count":3,"locations":[{"id":"doi:10.1007/978-3-319-48472-3_43","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-319-48472-3_43","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmid:28664200","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28664200","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":"On the move to meaningful Internet systems ... : CoopIS, DOA, and ODBASE : Confederated International Conferences, CoopIS, DOA, and ODBASE ... proceedings. OTM Confederated International Conferences","raw_type":null},{"id":"pmh:oai:europepmc.org:4331092","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5486409","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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6600000262260437,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2862297731","display_name":null,"funder_award_id":"R24 HL114473","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G3596492883","display_name":null,"funder_award_id":"U01 EB020955","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W102787101","https://openalex.org/W300523251","https://openalex.org/W1550258693","https://openalex.org/W1637593105","https://openalex.org/W1814060816","https://openalex.org/W1971290995","https://openalex.org/W2048060485","https://openalex.org/W2096797897","https://openalex.org/W2104655020","https://openalex.org/W2114388055","https://openalex.org/W2122402213","https://openalex.org/W2132646664","https://openalex.org/W2137516955","https://openalex.org/W2146089916","https://openalex.org/W2159583324","https://openalex.org/W2344257056","https://openalex.org/W2620914285"],"related_works":["https://openalex.org/W3004288456","https://openalex.org/W4362496998","https://openalex.org/W2184397297","https://openalex.org/W1663435917","https://openalex.org/W2004087619","https://openalex.org/W2539274330","https://openalex.org/W2810079151","https://openalex.org/W4321472216","https://openalex.org/W2557094866","https://openalex.org/W2469016277"],"abstract_inverted_index":null,"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":2}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
