{"id":"https://openalex.org/W4313455051","doi":"https://doi.org/10.1021/acs.jcim.2c00824","title":"embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules","display_name":"embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules","publication_year":2023,"publication_date":"2023-01-03","ids":{"openalex":"https://openalex.org/W4313455051","doi":"https://doi.org/10.1021/acs.jcim.2c00824","pmid":"https://pubmed.ncbi.nlm.nih.gov/36595441"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00824","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00824","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5047688272","display_name":"Raghad Al\u2010Jarf","orcid":null},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Raghad Aljarf","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049261721","display_name":"Simon Tang","orcid":"https://orcid.org/0000-0002-4149-9990"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Simon Tang","raw_affiliation_strings":["Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0002-4149-9990","affiliations":[{"raw_affiliation_string":"Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071950872","display_name":"Douglas E. V. Pires","orcid":"https://orcid.org/0000-0002-3004-2119"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Douglas E. V. Pires","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","School of Computing and Information Systems, University of Melbourne, Parkville 3052, Victoria, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0002-3004-2119","affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Computing and Information Systems, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091903225","display_name":"David B. Ascher","orcid":"https://orcid.org/0000-0003-2948-2413"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"David B. Ascher","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia","Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0003-2948-2413","affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071950872","https://openalex.org/A5091903225"],"corresponding_institution_ids":["https://openalex.org/I142471025","https://openalex.org/I165143802","https://openalex.org/I165779595"],"apc_list":null,"apc_paid":null,"fwci":6.1979,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.96842462,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"63","issue":"2","first_page":"432","last_page":"441"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11964","display_name":"Pregnancy and Medication Impact","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11964","display_name":"Pregnancy and Medication Impact","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12229","display_name":"Pharmacological Effects and Toxicity Studies","score":0.986299991607666,"subfield":{"id":"https://openalex.org/subfields/2735","display_name":"Pediatrics, Perinatology and Child Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10290","display_name":"Pregnancy and preeclampsia studies","score":0.9708999991416931,"subfield":{"id":"https://openalex.org/subfields/2729","display_name":"Obstetrics and Gynecology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5931053161621094},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.5828697085380554},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4891844093799591},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4718194901943207},{"id":"https://openalex.org/keywords/pregnancy","display_name":"Pregnancy","score":0.4239479899406433},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37038326263427734},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35779649019241333},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22663918137550354},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.16471648216247559},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13759061694145203}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5931053161621094},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.5828697085380554},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4891844093799591},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4718194901943207},{"id":"https://openalex.org/C2779234561","wikidata":"https://www.wikidata.org/wiki/Q11995","display_name":"Pregnancy","level":2,"score":0.4239479899406433},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37038326263427734},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35779649019241333},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22663918137550354},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.16471648216247559},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13759061694145203},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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}],"mesh":[{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D011247","descriptor_name":"Pregnancy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011247","descriptor_name":"Pregnancy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011247","descriptor_name":"Pregnancy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c00824","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00824","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36595441","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36595441","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.699999988079071}],"awards":[{"id":"https://openalex.org/G6454673195","display_name":null,"funder_award_id":"GNT1174405","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W7778337","https://openalex.org/W1971903990","https://openalex.org/W1975763583","https://openalex.org/W1980990959","https://openalex.org/W1997994032","https://openalex.org/W2007372567","https://openalex.org/W2009867031","https://openalex.org/W2011647635","https://openalex.org/W2023884867","https://openalex.org/W2056744287","https://openalex.org/W2086718320","https://openalex.org/W2095404170","https://openalex.org/W2108475414","https://openalex.org/W2116089716","https://openalex.org/W2118633304","https://openalex.org/W2120324887","https://openalex.org/W2123400824","https://openalex.org/W2127432713","https://openalex.org/W2135732933","https://openalex.org/W2201735116","https://openalex.org/W2308716531","https://openalex.org/W2346940354","https://openalex.org/W2400041270","https://openalex.org/W2475308546","https://openalex.org/W2587361467","https://openalex.org/W2605361745","https://openalex.org/W2608362739","https://openalex.org/W2763327376","https://openalex.org/W2767891136","https://openalex.org/W2887961823","https://openalex.org/W2895757710","https://openalex.org/W2912219210","https://openalex.org/W2922359247","https://openalex.org/W2945403072","https://openalex.org/W2969676387","https://openalex.org/W2980372463","https://openalex.org/W2980583144","https://openalex.org/W2988031345","https://openalex.org/W2999615587","https://openalex.org/W3017740089","https://openalex.org/W3024429450","https://openalex.org/W3038264863","https://openalex.org/W3083008290","https://openalex.org/W3120179932","https://openalex.org/W3123397518","https://openalex.org/W3135324979","https://openalex.org/W3177133504","https://openalex.org/W3213514782","https://openalex.org/W3213837169","https://openalex.org/W4220744352","https://openalex.org/W4226105062","https://openalex.org/W4233213541"],"related_works":["https://openalex.org/W3114540110","https://openalex.org/W2793008352","https://openalex.org/W2024008300","https://openalex.org/W2109994796","https://openalex.org/W2798199048","https://openalex.org/W2132204699","https://openalex.org/W2352507830","https://openalex.org/W3046001131","https://openalex.org/W2277986189","https://openalex.org/W2071820258"],"abstract_inverted_index":{"Teratogenic":[0],"drugs":[1,23],"can":[2],"lead":[3],"to":[4,48,54,93,122,128,139],"extreme":[5],"fetal":[6],"malformation":[7],"and":[8,50,62,98,125,136,146],"consequently":[9],"critically":[10],"influence":[11],"the":[12,16,41,85],"fetus\u2019s":[13],"health,":[14],"yet":[15],"teratogenic":[17],"risks":[18],"associated":[19],"with":[20,74],"most":[21],"approved":[22],"are":[24],"unknown.":[25],"Here,":[26],"we":[27,150],"propose":[28],"a":[29,36,45,115,134],"novel":[30],"predictive":[31,111],"tool,":[32],"embryoTox,":[33],"which":[34],"utilizes":[35],"graph-based":[37],"signature":[38],"representation":[39],"of":[40,44,69,91],"chemical":[42],"structure":[43],"small":[46,72],"molecule":[47],"predict":[49],"classify":[51],"molecules":[52,73,127,145],"likely":[53],"be":[55],"safe":[56,126,144],"during":[57,130],"pregnancy.":[58,131],"embryoTox":[59,152],"was":[60],"trained":[61],"validated":[63],"using":[64],"in":[65],"vitro":[66],"bioactivity":[67],"data":[68],"over":[70],"700":[71],"characterized":[75],"teratogenicity":[76],"effects.":[77],"Our":[78],"final":[79],"model":[80],"achieved":[81],"an":[82],"area":[83],"under":[84],"receiver":[86],"operating":[87],"characteristic":[88],"curve":[89],"(AUC)":[90],"up":[92],"0.96":[94],"on":[95,100],"10-fold":[96],"cross-validation":[97],"0.82":[99],"nonredundant":[101],"blind":[102],"tests,":[103],"outperforming":[104],"alternative":[105],"approaches.":[106],"We":[107],"believe":[108],"that":[109],"our":[110],"tool":[112],"will":[113],"provide":[114,133],"practical":[116],"resource":[117],"for":[118,142],"optimizing":[119],"screening":[120],"libraries":[121],"determine":[123],"effective":[124],"use":[129],"To":[132],"simple":[135],"integrated":[137],"platform":[138],"rapidly":[140],"screen":[141],"potential":[143],"their":[147],"risk":[148],"factors,":[149],"made":[151],"freely":[153],"available":[154],"online":[155],"at":[156],"https://biosig.lab.uq.edu.au/embryotox/":[157],".":[158]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4}],"updated_date":"2026-06-14T06:11:07.267592","created_date":"2025-10-10T00:00:00"}
