{"id":"https://openalex.org/W4417302787","doi":"https://doi.org/10.1093/bioinformatics/btaf661","title":"Causal knowledge graph analysis identifies adverse drug effects","display_name":"Causal knowledge graph analysis identifies adverse drug effects","publication_year":2025,"publication_date":"2025-12-09","ids":{"openalex":"https://openalex.org/W4417302787","doi":"https://doi.org/10.1093/bioinformatics/btaf661","pmid":"https://pubmed.ncbi.nlm.nih.gov/41385310"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf661","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf661/65857148/btaf661.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf661/65857148/btaf661.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057787498","display_name":"Sumyyah Toonsi","orcid":"https://orcid.org/0000-0003-4746-4649"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Sumyyah Toonsi","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955,","King Abdullah University of Science and Technology Computer, Electrical and Mathematical Sciences & Engineering Division, , Thuwal 23955,"],"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955,","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology Computer, Electrical and Mathematical Sciences & Engineering Division, , Thuwal 23955,","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059588755","display_name":"Paul N. Schofield","orcid":"https://orcid.org/0000-0002-5111-7263"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210096386","display_name":"Bridge University","ror":"https://ror.org/00cbm0437","country_code":"SS","type":"education","lineage":["https://openalex.org/I4210096386"]}],"countries":["GB","SS"],"is_corresponding":false,"raw_author_name":"Paul N Schofield","raw_affiliation_strings":["University of Cambridge Department of Physiology, Development & Neuroscience, , Cambridge, CB2 3EG,","University of Cambridge Department of Physiology, Development & Neuroscience, , CB2 3EG,"],"affiliations":[{"raw_affiliation_string":"University of Cambridge Department of Physiology, Development & Neuroscience, , Cambridge, CB2 3EG,","institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210096386"]},{"raw_affiliation_string":"University of Cambridge Department of Physiology, Development & Neuroscience, , CB2 3EG,","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043808311","display_name":"Robert Hoehndorf","orcid":"https://orcid.org/0000-0001-8149-5890"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Robert Hoehndorf","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955,","King Abdullah University of Science and Technology KAUST Center of Excellence for Generative AI, , 4700 King Abdullah University of Science and Technology , Thuwal, Makkah, 23955,","King Abdullah University of Science and Technology KAUST Center of Excellence for Smart Health (KCSH), , 4700 King Abdullah University of Science and Technology , Thuwal, Makkah, 23955,","King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology KAUST Center of Excellence for Smart Health (KCSH), , Thuwal,"],"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955,","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology KAUST Center of Excellence for Generative AI, , 4700 King Abdullah University of Science and Technology , Thuwal, Makkah, 23955,","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology KAUST Center of Excellence for Smart Health (KCSH), , 4700 King Abdullah University of Science and Technology , Thuwal, Makkah, 23955,","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology KAUST Center of Excellence for Smart Health (KCSH), , Thuwal,","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5057787498"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.40390425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.45399999618530273,"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"}},"topics":[{"id":"https://openalex.org/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.45399999618530273,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.09629999846220016,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.06480000168085098,"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/graph","display_name":"Graph","score":0.4593999981880188},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.41130000352859497},{"id":"https://openalex.org/keywords/causal-analysis","display_name":"Causal analysis","score":0.398499995470047},{"id":"https://openalex.org/keywords/causal-model","display_name":"Causal model","score":0.34549999237060547},{"id":"https://openalex.org/keywords/causality","display_name":"Causality (physics)","score":0.33550000190734863},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.30390000343322754}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6717000007629395},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4593999981880188},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.41130000352859497},{"id":"https://openalex.org/C2987525970","wikidata":"https://www.wikidata.org/wiki/Q96374569","display_name":"Causal analysis","level":2,"score":0.398499995470047},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38350000977516174},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3490000069141388},{"id":"https://openalex.org/C11671645","wikidata":"https://www.wikidata.org/wiki/Q5054567","display_name":"Causal model","level":2,"score":0.34549999237060547},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33730000257492065},{"id":"https://openalex.org/C64357122","wikidata":"https://www.wikidata.org/wiki/Q1149766","display_name":"Causality (physics)","level":2,"score":0.33550000190734863},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.30979999899864197},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.30390000343322754},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.289900004863739},{"id":"https://openalex.org/C2993432071","wikidata":"https://www.wikidata.org/wiki/Q45959","display_name":"Drug reaction","level":3,"score":0.2831999957561493},{"id":"https://openalex.org/C158600405","wikidata":"https://www.wikidata.org/wiki/Q5054566","display_name":"Causal inference","level":2,"score":0.2809999883174896},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C197934379","wikidata":"https://www.wikidata.org/wiki/Q2047938","display_name":"Adverse effect","level":2,"score":0.26899999380111694},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.260699987411499}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf661","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf661/65857148/btaf661.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41385310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41385310","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12790815","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12790815/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/395221","is_oa":false,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/395221","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf661","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf661/65857148/btaf661.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5380366079","display_name":null,"funder_award_id":"URF/1/5041-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5645385827","display_name":null,"funder_award_id":"REI/1/5659-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417302787.pdf","grobid_xml":"https://content.openalex.org/works/W4417302787.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1507651605","https://openalex.org/W1715619412","https://openalex.org/W1824516519","https://openalex.org/W1908991493","https://openalex.org/W1934602670","https://openalex.org/W1976043651","https://openalex.org/W2000445173","https://openalex.org/W2010143351","https://openalex.org/W2025309870","https://openalex.org/W2035756448","https://openalex.org/W2082704080","https://openalex.org/W2087467131","https://openalex.org/W2113832063","https://openalex.org/W2119002393","https://openalex.org/W2123412102","https://openalex.org/W2128288763","https://openalex.org/W2134027168","https://openalex.org/W2143891888","https://openalex.org/W2152415104","https://openalex.org/W2232325453","https://openalex.org/W2285865907","https://openalex.org/W2319116535","https://openalex.org/W2550831966","https://openalex.org/W2789947373","https://openalex.org/W2902781503","https://openalex.org/W2937068696","https://openalex.org/W2964635562","https://openalex.org/W2982588758","https://openalex.org/W2987940998","https://openalex.org/W3010336026","https://openalex.org/W3011049567","https://openalex.org/W3011532367","https://openalex.org/W3047936160","https://openalex.org/W3096932862","https://openalex.org/W3114319529","https://openalex.org/W3121505931","https://openalex.org/W3137061630","https://openalex.org/W3153362321","https://openalex.org/W3201485036","https://openalex.org/W4200080698","https://openalex.org/W4214506943","https://openalex.org/W4284898547","https://openalex.org/W4308054131","https://openalex.org/W4378232223","https://openalex.org/W4382721724","https://openalex.org/W4383859609","https://openalex.org/W4396242640","https://openalex.org/W4401919708","https://openalex.org/W4403785188","https://openalex.org/W4403964783","https://openalex.org/W4404782447","https://openalex.org/W4405529168","https://openalex.org/W4409150806"],"related_works":[],"abstract_inverted_index":{"The":[0],"data":[1],"is":[2],"available":[3],"through":[4],"https://github.com/bio-ontology-research-group/Mediation-Analysis-using-Causal-Knowledge-Graph.":[5]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-12-13T00:00:00"}