{"id":"https://openalex.org/W4411750214","doi":"https://doi.org/10.1093/bioinformatics/btaf381","title":"AOP-helpFinder 3.0: from text mining to network visualization of key event relationships, and knowledge integration from multiple sources","display_name":"AOP-helpFinder 3.0: from text mining to network visualization of key event relationships, and knowledge integration from multiple sources","publication_year":2025,"publication_date":"2025-06-28","ids":{"openalex":"https://openalex.org/W4411750214","doi":"https://doi.org/10.1093/bioinformatics/btaf381","pmid":"https://pubmed.ncbi.nlm.nih.gov/40580447"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf381","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf381","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf381/63616051/btaf381.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/btaf381/63616051/btaf381.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060903119","display_name":"Thomas Jaylet","orcid":"https://orcid.org/0000-0002-4990-6634"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Thomas Jaylet","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,"],"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014304382","display_name":"Florence Jornod","orcid":"https://orcid.org/0000-0001-7586-6819"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Florence Jornod","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,"],"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117271495","display_name":"Quentin Capdet","orcid":null},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Quentin Capdet","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,"],"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056691363","display_name":"Olivier Armant","orcid":"https://orcid.org/0000-0001-7101-9209"},"institutions":[{"id":"https://openalex.org/I1293448361","display_name":"Institut de Radioprotection et de S\u00fbret\u00e9 Nucl\u00e9aire","ror":"https://ror.org/01ha22c77","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I1293448361"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Armant","raw_affiliation_strings":["PSE-ENV/SERPEN/LECO, Institut de Radioprotection et de S\u00fbret\u00e9 Nucl\u00e9aire (IRSN) , Saint-Paul-Lez-Durance,"],"affiliations":[{"raw_affiliation_string":"PSE-ENV/SERPEN/LECO, Institut de Radioprotection et de S\u00fbret\u00e9 Nucl\u00e9aire (IRSN) , Saint-Paul-Lez-Durance,","institution_ids":["https://openalex.org/I1293448361"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068822653","display_name":"Karine Audouze","orcid":"https://orcid.org/0000-0001-7525-4089"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Karine Audouze","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,"],"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, Inserm, HealthFex , Paris F-75006,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091437"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5060903119"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091437"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.5496,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.97673152,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"41","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9879000186920166,"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":0.9879000186920166,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9739999771118164,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9675999879837036,"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/key","display_name":"Key (lock)","score":0.7702977657318115},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7482301592826843},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6741242408752441},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.5783746838569641},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5401545763015747},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5091046690940857},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.43811625242233276},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08465114235877991}],"concepts":[{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.7702977657318115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7482301592826843},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6741242408752441},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.5783746838569641},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5401545763015747},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5091046690940857},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.43811625242233276},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08465114235877991},{"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}],"mesh":[{"descriptor_ui":"D000073931","descriptor_name":"Adverse Outcome Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000073931","descriptor_name":"Adverse Outcome Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000073931","descriptor_name":"Adverse Outcome Pathways","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf381","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf381","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf381/63616051/btaf381.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:40580447","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40580447","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:12263105","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12263105","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:hal-05266669v1","is_oa":false,"landing_page_url":"https://asnr.hal.science/hal-05266669","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2025, 41 (7), pp.btaf381. &#x27E8;10.1093/bioinformatics/btaf381&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf381","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf381","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf381/63616051/btaf381.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":[{"score":0.7599999904632568,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G4003490208","display_name":null,"funder_award_id":"900009","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6595194422","display_name":null,"funder_award_id":"825712","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8256239485","display_name":null,"funder_award_id":"101057014","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411750214.pdf","grobid_xml":"https://content.openalex.org/works/W4411750214.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W2000089305","https://openalex.org/W2041473955","https://openalex.org/W2092338995","https://openalex.org/W2095523033","https://openalex.org/W2138649409","https://openalex.org/W2313757172","https://openalex.org/W2586811253","https://openalex.org/W2730385059","https://openalex.org/W2935802524","https://openalex.org/W2995593899","https://openalex.org/W3033540123","https://openalex.org/W3209621873","https://openalex.org/W4212938668","https://openalex.org/W4248995092","https://openalex.org/W4379193888","https://openalex.org/W4406692101","https://openalex.org/W6779127440"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2081517010","https://openalex.org/W2121496884","https://openalex.org/W2387910809","https://openalex.org/W2294221496"],"abstract_inverted_index":{"AOP-helpFinder":[0],"is":[1],"available":[2],"at":[3],"https://aop-helpfinder-v3.u-paris-sciences.fr.":[4]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
