{"id":"https://openalex.org/W4282920482","doi":"https://doi.org/10.1186/s13326-022-00272-6","title":"PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature","display_name":"PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature","publication_year":2022,"publication_date":"2022-06-11","ids":{"openalex":"https://openalex.org/W4282920482","doi":"https://doi.org/10.1186/s13326-022-00272-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/35690873"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-022-00272-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-022-00272-6","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-022-00272-6","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/counter/pdf/10.1186/s13326-022-00272-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013073771","display_name":"Samar Binkheder","orcid":"https://orcid.org/0000-0003-0400-823X"},"institutions":[{"id":"https://openalex.org/I2801066305","display_name":"King Saud Medical City","ror":"https://ror.org/03aj9rj02","country_code":"SA","type":"healthcare","lineage":["https://openalex.org/I2801066305"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["SA","US"],"is_corresponding":false,"raw_author_name":"Samar Binkheder","raw_affiliation_strings":["Department of Biohealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA","Medical Informatics Unit, Department of Medical Education, College of Medicine, King Saud University, Riyadh, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0003-0400-823X","affiliations":[{"raw_affiliation_string":"Department of Biohealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Medical Informatics Unit, Department of Medical Education, College of Medicine, King Saud University, Riyadh, Saudi Arabia","institution_ids":["https://openalex.org/I2801066305"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100552223","display_name":"Heng\u2010Yi Wu","orcid":"https://orcid.org/0009-0000-5415-8186"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Heng-Yi Wu","raw_affiliation_strings":["Development Science Informatics, Genentech, South San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Development Science Informatics, Genentech, South San Francisco, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061341188","display_name":"Sara K. Quinney","orcid":"https://orcid.org/0000-0002-6554-0695"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sara K. Quinney","raw_affiliation_strings":["Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA","institution_ids":["https://openalex.org/I55769427","https://openalex.org/I4394709130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040863807","display_name":"Shijun Zhang","orcid":"https://orcid.org/0000-0001-9732-5925"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shijun Zhang","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034627844","display_name":"Md Muntasir Zitu","orcid":"https://orcid.org/0000-0001-9103-1467"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Md. Muntasir Zitu","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102101965","display_name":"Chien\u2010Wei Chiang","orcid":"https://orcid.org/0000-0002-0988-8478"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chien\u2010Wei Chiang","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100736263","display_name":"Lei Wang","orcid":"https://orcid.org/0000-0002-8420-6860"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lei Wang","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050362156","display_name":"Josette Jones","orcid":"https://orcid.org/0000-0002-4996-8595"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Josette Jones","raw_affiliation_strings":["Department of Biohealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biohealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100383618","display_name":"Lang Li","orcid":"https://orcid.org/0000-0002-5334-8719"},"institutions":[{"id":"https://openalex.org/I4210122295","display_name":"Columbus Center","ror":"https://ror.org/02qxd8910","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210122295"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lang Li","raw_affiliation_strings":[", 250 Lincoln Tower, 1800 Cannon Drive, Columbus, OH, 43210, USA. lang.li@osumc.edu","Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA. lang.li@osumc.edu","Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":", 250 Lincoln Tower, 1800 Cannon Drive, Columbus, OH, 43210, USA. lang.li@osumc.edu","institution_ids":["https://openalex.org/I4210122295"]},{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA. lang.li@osumc.edu","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100383618"],"corresponding_institution_ids":["https://openalex.org/I4210122295","https://openalex.org/I52357470"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.7555,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.67736783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":"1","first_page":"17","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.45590001344680786,"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":0.45590001344680786,"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/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.4081999957561493,"subfield":{"id":"https://openalex.org/subfields/3005","display_name":"Toxicology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10350","display_name":"Electronic Health Records Systems","score":0.03759999945759773,"subfield":{"id":"https://openalex.org/subfields/3605","display_name":"Health Information Management"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7152583003044128},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6267582178115845},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.6266676187515259},{"id":"https://openalex.org/keywords/inclusion","display_name":"Inclusion (mineral)","score":0.56568843126297},{"id":"https://openalex.org/keywords/dimension","display_name":"Dimension (graph theory)","score":0.5203472971916199},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.48235076665878296},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.45463863015174866},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4546036124229431},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36028197407722473},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33564406633377075},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.23067596554756165},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07415425777435303}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7152583003044128},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6267582178115845},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.6266676187515259},{"id":"https://openalex.org/C109359841","wikidata":"https://www.wikidata.org/wiki/Q728944","display_name":"Inclusion (mineral)","level":2,"score":0.56568843126297},{"id":"https://openalex.org/C33676613","wikidata":"https://www.wikidata.org/wiki/Q13415176","display_name":"Dimension (graph theory)","level":2,"score":0.5203472971916199},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.48235076665878296},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.45463863015174866},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4546036124229431},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36028197407722473},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33564406633377075},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.23067596554756165},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07415425777435303},{"id":"https://openalex.org/C199289684","wikidata":"https://www.wikidata.org/wiki/Q83353","display_name":"Mineralogy","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s13326-022-00272-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-022-00272-6","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-022-00272-6","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:35690873","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35690873","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:pubmedcentral.nih.gov:9188713","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9188713","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Biomed Semantics","raw_type":"Text"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/30926","is_oa":true,"landing_page_url":"https://hdl.handle.net/1805/30926","pdf_url":"https://scholarworks.indianapolis.iu.edu/bitstreams/41a41bbf-ea9a-4a31-a443-e58227619cde/download","source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"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":"Publisher","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:27997d7d695640b7988d6d73e3318b51","is_oa":true,"landing_page_url":"https://doaj.org/article/27997d7d695640b7988d6d73e3318b51","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 13, Iss 1, Pp 1-17 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13326-022-00272-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-022-00272-6","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-022-00272-6","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":[{"display_name":"Reduced inequalities","score":0.5400000214576721,"id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G1898671489","display_name":null,"funder_award_id":"NSF1622526","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2094698340","display_name":null,"funder_award_id":"R01 GM117206","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G352873457","display_name":null,"funder_award_id":"R01 GM124104","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7485123540","display_name":null,"funder_award_id":"R01 AG025152","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G8260017461","display_name":null,"funder_award_id":"R01 LM011945","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309374","display_name":"Ohio State University","ror":"https://ror.org/00rs6vg23"},{"id":"https://openalex.org/F4320310263","display_name":"Indiana University-Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4282920482.pdf","grobid_xml":"https://content.openalex.org/works/W4282920482.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W165823196","https://openalex.org/W1135673779","https://openalex.org/W1444168786","https://openalex.org/W1480287196","https://openalex.org/W1483357098","https://openalex.org/W1489237918","https://openalex.org/W1578843544","https://openalex.org/W1678732033","https://openalex.org/W1759667598","https://openalex.org/W1808652302","https://openalex.org/W1974660612","https://openalex.org/W1978116440","https://openalex.org/W1983745852","https://openalex.org/W1998557820","https://openalex.org/W2019453867","https://openalex.org/W2027867013","https://openalex.org/W2029592334","https://openalex.org/W2034460449","https://openalex.org/W2051689038","https://openalex.org/W2054429952","https://openalex.org/W2057443209","https://openalex.org/W2060341629","https://openalex.org/W2071478164","https://openalex.org/W2085752173","https://openalex.org/W2087432624","https://openalex.org/W2105637130","https://openalex.org/W2113952938","https://openalex.org/W2119110156","https://openalex.org/W2121382432","https://openalex.org/W2126130217","https://openalex.org/W2129767020","https://openalex.org/W2131668595","https://openalex.org/W2132724073","https://openalex.org/W2136127280","https://openalex.org/W2138162199","https://openalex.org/W2145578524","https://openalex.org/W2149369282","https://openalex.org/W2151068025","https://openalex.org/W2156782747","https://openalex.org/W2159583324","https://openalex.org/W2159985898","https://openalex.org/W2162442688","https://openalex.org/W2163107094","https://openalex.org/W2164146524","https://openalex.org/W2169099542","https://openalex.org/W2172767501","https://openalex.org/W2192926868","https://openalex.org/W2204691302","https://openalex.org/W2205496875","https://openalex.org/W2317648909","https://openalex.org/W2326662926","https://openalex.org/W2421476601","https://openalex.org/W2467651252","https://openalex.org/W2585785990","https://openalex.org/W2589364158","https://openalex.org/W2594685110","https://openalex.org/W2623271764","https://openalex.org/W2626407095","https://openalex.org/W2762181533","https://openalex.org/W2765492483","https://openalex.org/W2768114048","https://openalex.org/W2803290558","https://openalex.org/W2806568653","https://openalex.org/W2996552889","https://openalex.org/W4205404495","https://openalex.org/W4236912465","https://openalex.org/W4250001050","https://openalex.org/W4294214983"],"related_works":["https://openalex.org/W1892467659","https://openalex.org/W1529400504","https://openalex.org/W2035950535","https://openalex.org/W2357241418","https://openalex.org/W2793539281","https://openalex.org/W3108142956","https://openalex.org/W2971623275","https://openalex.org/W159132833","https://openalex.org/W4252011628","https://openalex.org/W2476287482"],"abstract_inverted_index":{"BACKGROUND:":[0],"Adverse":[1],"events":[2,30],"induced":[3],"by":[4],"drug-drug":[5],"interactions":[6],"are":[7,54,117],"a":[8,43,47,74,85,140,158,282],"major":[9,151,166],"concern":[10],"in":[11,37,100,119,175,292],"the":[12,34,63,101,109,120,137,143,186,198,207,232],"United":[13],"States.":[14],"Current":[15],"research":[16],"is":[17,40,72,106],"moving":[18],"toward":[19],"using":[20],"electronic":[21],"health":[22],"record":[23],"(EHR)":[24],"data,":[25],"including":[26],"for":[27,45,58,95,127,142,147,171,197,206,216,231,249,286,299],"adverse":[28],"drug":[29],"discovery.":[31],"One":[32,61],"of":[33,49,62,66,111,145,160,194,203,213,222,228,240,246,252],"first":[35,64],"steps":[36,65],"EHR-based":[38],"studies":[39],"to":[41,80,89,107,184],"define":[42],"phenotype":[44,52,97,115,148,173,290],"establishing":[46],"cohort":[48],"patients.":[50],"However,":[51],"definitions":[53,98,116,174,291],"not":[55],"readily":[56],"available":[57],"all":[59,271],"phenotypes.":[60],"developing":[67],"automated":[68,93],"text":[69,129,300],"mining":[70,96,130,289,301],"tools":[71],"building":[73,91],"corpus.":[75],"Therefore,":[76],"this":[77],"study":[78],"aimed":[79],"develop":[81],"annotation":[82,180,277],"guidelines":[83,181,278],"and":[84,122,155,169,210,262,276,288,294],"gold":[86],"standard":[87],"corpus":[88,138,187,275],"facilitate":[90],"future":[92,128],"approaches":[94],"contained":[99,189],"literature.":[102,177],"Furthermore,":[103],"our":[104],"aim":[105],"improve":[108],"understanding":[110],"how":[112,123],"these":[113],"published":[114,176],"presented":[118],"literature":[121],"we":[124],"annotate":[125,185],"them":[126],"tasks.":[131],"RESULTS:":[132],"Two":[133],"annotators":[134],"manually":[135],"annotated":[136,223,241],"on":[139],"sentence-level":[141],"presence":[144],"evidence":[146],"definitions.":[149],"Three":[150],"categories":[152],"(inclusion,":[153],"intermediate,":[154],"exclusion)":[156],"with":[157],"total":[159],"ten":[161],"dimensions":[162],"were":[163,182],"proposed":[164],"characterizing":[165],"contextual":[167],"patterns":[168],"cues":[170],"presenting":[172],"The":[178,219,237,254,274],"developed":[179],"used":[183,297],"that":[188],"3971":[190,195,204,214,229,247],"sentences:":[191],"1923":[192],"out":[193,202,212,227,245],"(48.4%)":[196],"inclusion":[199],"category,":[200,209],"1851":[201],"(46.6%)":[205],"intermediate":[208],"2273":[211],"(57.2%)":[215],"exclusion":[217],"category.":[218],"highest":[220],"number":[221,239],"sentences":[224,242],"was":[225,243,259],"1449":[226],"(36.5%)":[230],"\"Biomedical":[233],"&":[234],"Procedure\"":[235],"dimension.":[236],"lowest":[238],"49":[244],"(1.2%)":[248],"\"The":[250],"use":[251],"NLP\".":[253],"overall":[255],"percent":[256],"inter-annotator":[257,268],"agreement":[258,269],"97.8%.":[260],"Percent":[261],"Kappa":[263],"statistics":[264],"also":[265],"showed":[266],"high":[267],"across":[270],"dimensions.":[272],"CONCLUSIONS:":[273],"can":[279,295],"serve":[280],"as":[281],"foundational":[283],"informatics":[284],"approach":[285],"annotating":[287],"literature,":[293],"be":[296],"later":[298],"applications.":[302]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
