{"id":"https://openalex.org/W2921645231","doi":"https://doi.org/10.1109/tcbb.2019.2904231","title":"Extracting Inter-Sentence Relations for Associating Biological Context with Events in Biomedical Texts","display_name":"Extracting Inter-Sentence Relations for Associating Biological Context with Events in Biomedical Texts","publication_year":2019,"publication_date":"2019-03-11","ids":{"openalex":"https://openalex.org/W2921645231","doi":"https://doi.org/10.1109/tcbb.2019.2904231","mag":"2921645231","pmid":"https://pubmed.ncbi.nlm.nih.gov/30869629"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2904231","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2904231","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","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/A5042363520","display_name":"Enrique Noriega-Atala","orcid":"https://orcid.org/0000-0001-7150-2989"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enrique Noriega-Atala","raw_affiliation_strings":["School of Information, University of Arizona, Tucson, AZ, USA"],"raw_orcid":"https://orcid.org/0000-0001-7150-2989","affiliations":[{"raw_affiliation_string":"School of Information, University of Arizona, Tucson, AZ, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088093912","display_name":"Paul D. Hein","orcid":null},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul D. Hein","raw_affiliation_strings":["Department of Computer Science, University of Arizona, Tucson, AZ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Arizona, Tucson, AZ, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023973306","display_name":"Shraddha S. Thumsi","orcid":"https://orcid.org/0000-0002-5392-8166"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shraddha S. Thumsi","raw_affiliation_strings":["School of Information, University of Arizona, Tucson, AZ, USA"],"raw_orcid":"https://orcid.org/0000-0002-5392-8166","affiliations":[{"raw_affiliation_string":"School of Information, University of Arizona, Tucson, AZ, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032595407","display_name":"Zechy Wong","orcid":"https://orcid.org/0000-0002-9410-0605"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zechy Wong","raw_affiliation_strings":["Department of Linguistics, University of Arizona, Tucson, AZ, USA"],"raw_orcid":"https://orcid.org/0000-0002-9410-0605","affiliations":[{"raw_affiliation_string":"Department of Linguistics, University of Arizona, Tucson, AZ, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100397933","display_name":"Xia Wang","orcid":"https://orcid.org/0000-0003-1960-4157"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xia Wang","raw_affiliation_strings":["Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087375436","display_name":"Sean M. Hendryx","orcid":"https://orcid.org/0000-0003-4456-6455"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean M. Hendryx","raw_affiliation_strings":["School of Information, University of Arizona, Tucson, AZ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information, University of Arizona, Tucson, AZ, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017273810","display_name":"Clayton T. Morrison","orcid":"https://orcid.org/0000-0002-3606-0078"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Clayton T. Morrison","raw_affiliation_strings":["School of Information, University of Arizona, Tucson, AZ, USA"],"raw_orcid":"https://orcid.org/0000-0002-3606-0078","affiliations":[{"raw_affiliation_string":"School of Information, University of Arizona, Tucson, AZ, USA","institution_ids":["https://openalex.org/I138006243"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I138006243"],"apc_list":null,"apc_paid":null,"fwci":0.3795,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.56608725,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"17","issue":"6","first_page":"1895","last_page":"1906"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10028","display_name":"Topic Modeling","score":0.9986000061035156,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9955999851226807,"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":0.6590936183929443},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.628994882106781},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6069155335426331},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5983669757843018},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5918266773223877},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5709341764450073},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5434236526489258},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.5000503063201904},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.46062225103378296},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4199652671813965},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.4157508313655853},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.24670115113258362},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20298850536346436},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.1441877782344818}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6590936183929443},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.628994882106781},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6069155335426331},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5983669757843018},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5918266773223877},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5709341764450073},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5434236526489258},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.5000503063201904},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.46062225103378296},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4199652671813965},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.4157508313655853},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.24670115113258362},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20298850536346436},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.1441877782344818},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","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":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2019.2904231","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2904231","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30869629","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30869629","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:repository.arizona.edu:10150/650754","is_oa":false,"landing_page_url":"http://hdl.handle.net/10150/650754","pdf_url":null,"source":{"id":"https://openalex.org/S4306400271","display_name":"UA Campus Repository (The University of Arizona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138006243","host_organization_name":"University of Arizona","host_organization_lineage":["https://openalex.org/I138006243"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"United States","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8100000023841858,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G451797860","display_name":null,"funder_award_id":"ARO W911NF-14-1-0395","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"}],"funders":[{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W143623734","https://openalex.org/W1480376833","https://openalex.org/W1493490255","https://openalex.org/W1532325895","https://openalex.org/W1678356000","https://openalex.org/W1786456657","https://openalex.org/W1970714600","https://openalex.org/W1988790447","https://openalex.org/W2010604520","https://openalex.org/W2017209271","https://openalex.org/W2038721957","https://openalex.org/W2060515712","https://openalex.org/W2085575316","https://openalex.org/W2097352005","https://openalex.org/W2097960255","https://openalex.org/W2100627415","https://openalex.org/W2101234009","https://openalex.org/W2116261113","https://openalex.org/W2123442489","https://openalex.org/W2127978399","https://openalex.org/W2133012565","https://openalex.org/W2153579005","https://openalex.org/W2153919256","https://openalex.org/W2171549925","https://openalex.org/W2251392452","https://openalex.org/W2252154718","https://openalex.org/W2295598076","https://openalex.org/W2738031524","https://openalex.org/W2894374770","https://openalex.org/W3102476541","https://openalex.org/W4213009331","https://openalex.org/W4235505822","https://openalex.org/W4248437541","https://openalex.org/W4294170691","https://openalex.org/W6605904769","https://openalex.org/W6629638141","https://openalex.org/W6638185459","https://openalex.org/W6653109512","https://openalex.org/W6675354045","https://openalex.org/W6682691769","https://openalex.org/W6692120018"],"related_works":["https://openalex.org/W159132833","https://openalex.org/W2962911543","https://openalex.org/W3108723547","https://openalex.org/W4312619320","https://openalex.org/W3104059174","https://openalex.org/W3171566221","https://openalex.org/W2347790038","https://openalex.org/W2770843237","https://openalex.org/W150863218","https://openalex.org/W4200223488"],"abstract_inverted_index":{"We":[0,29,50,100],"present":[1,51],"an":[2,112],"analysis":[3,87],"of":[4,7,36,55,88,91,94,114],"the":[5,37,89,109],"problem":[6],"identifying":[8],"biological":[9,32],"context":[10,33],"and":[11,41],"associating":[12],"it":[13],"with":[14,47,84],"biochemical":[15,48],"events":[16],"described":[17],"in":[18,116],"biomedical":[19,58],"texts.":[20],"This":[21],"constitutes":[22],"a":[23,52,85,92,117],"non-trivial,":[24],"inter-sentential":[25],"relation":[26],"extraction":[27],"task.":[28],"focus":[30],"on":[31,97],"as":[34],"descriptions":[35],"species,":[38],"tissue":[39],"type,":[40],"cell":[42],"type":[43],"that":[44,60,102],"are":[45],"associated":[46],"events.":[49],"new":[53],"corpus":[54],"open":[56],"access":[57],"texts":[59],"have":[61],"been":[62],"annotated":[63],"by":[64,107],"biology":[65],"subject":[66],"matter":[67],"experts":[68],"to":[69],"highlight":[70],"context-event":[71,81],"relations.":[72],"Using":[73],"this":[74],"corpus,":[75],"we":[76],"evaluate":[77],"several":[78],"classifiers":[79],"for":[80],"association":[82],"along":[83],"detailed":[86],"impact":[90],"variety":[93],"linguistic":[95],"features":[96],"classifier":[98],"performance.":[99],"find":[101],"gradient":[103],"tree":[104],"boosting":[105],"performs":[106],"far":[108],"best,":[110],"achieving":[111],"F1":[113],"0.865":[115],"cross-validation":[118],"study.":[119]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}