{"id":"https://openalex.org/W3165832785","doi":"https://doi.org/10.1016/j.jbi.2021.103820","title":"Causal relationship extraction from biomedical text using deep neural models: A comprehensive survey","display_name":"Causal relationship extraction from biomedical text using deep neural models: A comprehensive survey","publication_year":2021,"publication_date":"2021-05-24","ids":{"openalex":"https://openalex.org/W3165832785","doi":"https://doi.org/10.1016/j.jbi.2021.103820","mag":"3165832785","pmid":"https://pubmed.ncbi.nlm.nih.gov/34044157"},"language":"en","primary_location":{"id":"doi:10.1016/j.jbi.2021.103820","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jbi.2021.103820","pdf_url":null,"source":{"id":"https://openalex.org/S11622463","display_name":"Journal of Biomedical Informatics","issn_l":"1532-0464","issn":["1532-0464","1532-0480"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Informatics","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/A5001084471","display_name":"Abbas Akkasi","orcid":"https://orcid.org/0000-0003-4700-4896"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Abbas Akkasi","raw_affiliation_strings":["Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium; Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium. Electronic address: abbas.akkasi@gmail.com","Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium","Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium; Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium. Electronic address: abbas.akkasi@gmail.com","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110771988","display_name":"Mari-Francine Moens","orcid":null},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Mari-Francine Moens","raw_affiliation_strings":["Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium; Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium. Electronic address: sien.moens@kuleuven.be","Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium","Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium; Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium. Electronic address: sien.moens@kuleuven.be","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"Language Intelligence and Information Retrieval Lab, KU Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"Department of Computer Science, Celestijnenlaan 200 A, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5001084471"],"corresponding_institution_ids":["https://openalex.org/I99464096"],"apc_list":{"value":2980,"currency":"USD","value_usd":2980},"apc_paid":null,"fwci":4.0565,"has_fulltext":false,"cited_by_count":53,"citation_normalized_percentile":{"value":0.95303257,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"119","issue":null,"first_page":"103820","last_page":"103820"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9977999925613403,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9787999987602234,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8299458026885986},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7197616100311279},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5731537342071533},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5643109083175659},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5171493887901306},{"id":"https://openalex.org/keywords/word-embedding","display_name":"Word embedding","score":0.4802848994731903},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.47723865509033203},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.46282511949539185},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.45113641023635864},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.44231465458869934},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.44126901030540466},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3814731538295746},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.3717273473739624},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.3434056043624878}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8299458026885986},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7197616100311279},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5731537342071533},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5643109083175659},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5171493887901306},{"id":"https://openalex.org/C2777462759","wikidata":"https://www.wikidata.org/wiki/Q18395344","display_name":"Word embedding","level":3,"score":0.4802848994731903},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.47723865509033203},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.46282511949539185},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.45113641023635864},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.44231465458869934},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.44126901030540466},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3814731538295746},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.3717273473739624},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.3434056043624878},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1016/j.jbi.2021.103820","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jbi.2021.103820","pdf_url":null,"source":{"id":"https://openalex.org/S11622463","display_name":"Journal of Biomedical Informatics","issn_l":"1532-0464","issn":["1532-0464","1532-0480"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Informatics","raw_type":"journal-article"},{"id":"pmid:34044157","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34044157","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 informatics","raw_type":null},{"id":"pmh:oai:lirias2repo.kuleuven.be:123456789/677908","is_oa":false,"landing_page_url":"https://lirias.kuleuven.be/bitstream/123456789/677908/2/1-s2.0-S1532046421001490-main.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal Of Biomedical Informatics, vol. 119, Art.No. 103820","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.8199999928474426}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322308","display_name":"KU Leuven","ror":"https://ror.org/05f950310"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":95,"referenced_works":["https://openalex.org/W1489949474","https://openalex.org/W1493490255","https://openalex.org/W1568390176","https://openalex.org/W1601564520","https://openalex.org/W1604608156","https://openalex.org/W1623006543","https://openalex.org/W1636081627","https://openalex.org/W1832693441","https://openalex.org/W1971048089","https://openalex.org/W1978108654","https://openalex.org/W1987811240","https://openalex.org/W1991145427","https://openalex.org/W2049053063","https://openalex.org/W2054070929","https://openalex.org/W2063748751","https://openalex.org/W2064030835","https://openalex.org/W2076581021","https://openalex.org/W2097352005","https://openalex.org/W2099779943","https://openalex.org/W2103397879","https://openalex.org/W2106560678","https://openalex.org/W2107598941","https://openalex.org/W2114117930","https://openalex.org/W2116261113","https://openalex.org/W2119858020","https://openalex.org/W2120580278","https://openalex.org/W2131571251","https://openalex.org/W2138627627","https://openalex.org/W2145870355","https://openalex.org/W2152228269","https://openalex.org/W2152398020","https://openalex.org/W2158139315","https://openalex.org/W2163362093","https://openalex.org/W2165935464","https://openalex.org/W2168693035","https://openalex.org/W2174117436","https://openalex.org/W2217185886","https://openalex.org/W2250539671","https://openalex.org/W2251622960","https://openalex.org/W2397123654","https://openalex.org/W2485563723","https://openalex.org/W2495101885","https://openalex.org/W2559013665","https://openalex.org/W2587019100","https://openalex.org/W2608829447","https://openalex.org/W2768488789","https://openalex.org/W2782360413","https://openalex.org/W2798865369","https://openalex.org/W2801154470","https://openalex.org/W2802532163","https://openalex.org/W2803230074","https://openalex.org/W2882319491","https://openalex.org/W2888296742","https://openalex.org/W2889224519","https://openalex.org/W2892202918","https://openalex.org/W2911489562","https://openalex.org/W2912376836","https://openalex.org/W2917136881","https://openalex.org/W2918995630","https://openalex.org/W2930957955","https://openalex.org/W2952174148","https://openalex.org/W2952789225","https://openalex.org/W2962739339","https://openalex.org/W2962939608","https://openalex.org/W2963020213","https://openalex.org/W2963063408","https://openalex.org/W2963322543","https://openalex.org/W2964317478","https://openalex.org/W3014987848","https://openalex.org/W3043457491","https://openalex.org/W4237040408","https://openalex.org/W4247456275","https://openalex.org/W4301409532","https://openalex.org/W6600131322","https://openalex.org/W6600258949","https://openalex.org/W6636749155","https://openalex.org/W6637108133","https://openalex.org/W6647075091","https://openalex.org/W6675985199","https://openalex.org/W6681465903","https://openalex.org/W6683557909","https://openalex.org/W6684009808","https://openalex.org/W6688787801","https://openalex.org/W6691431627","https://openalex.org/W6691546939","https://openalex.org/W6704017408","https://openalex.org/W6722478005","https://openalex.org/W6733971936","https://openalex.org/W6736575147","https://openalex.org/W6747857200","https://openalex.org/W6750460212","https://openalex.org/W6751119307","https://openalex.org/W6754476267","https://openalex.org/W6754926606","https://openalex.org/W6780382358"],"related_works":["https://openalex.org/W842810586","https://openalex.org/W4319940250","https://openalex.org/W2352298027","https://openalex.org/W2092919065","https://openalex.org/W3138801416","https://openalex.org/W4236762297","https://openalex.org/W4286432911","https://openalex.org/W2369351710","https://openalex.org/W2594363579","https://openalex.org/W2169232658"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-10T14:07:55.174380","created_date":"2025-10-10T00:00:00"}
