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AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development
Abstract Motivation Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation...
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Published in: | Bioinformatics 2022-01, Vol.38 (4), p.1173-1175 |
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creator | Jornod, Florence Jaylet, Thomas Blaha, Ludek Sarigiannis, Denis Tamisier, Luc Audouze, Karine |
description | Abstract
Motivation
Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome.
Results
Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment.
Availability and implementation
AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php
Supplementary information
Supplementary data are available at Bioinformatics online. |
doi_str_mv | 10.1093/bioinformatics/btab750 |
format | article |
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Motivation
Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome.
Results
Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment.
Availability and implementation
AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php
Supplementary information
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btab750</identifier><identifier>PMID: 34718414</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Adverse Outcome Pathways ; Applications Notes ; Artificial Intelligence ; Bioinformatics ; Computer Science ; Data Management ; Databases, Factual ; Life Sciences ; Risk Assessment - methods ; Toxicology</subject><ispartof>Bioinformatics, 2022-01, Vol.38 (4), p.1173-1175</ispartof><rights>The Author(s) 2021. Published by Oxford University Press. 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c543t-43439beb1dfced505994c4b4cce7447cdf9442e230eab11d2d3f2d57e818f1fd3</citedby><cites>FETCH-LOGICAL-c543t-43439beb1dfced505994c4b4cce7447cdf9442e230eab11d2d3f2d57e818f1fd3</cites><orcidid>0000-0001-7525-4089</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8796376/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8796376/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34718414$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-04678124$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Wren, Jonathan</contributor><creatorcontrib>Jornod, Florence</creatorcontrib><creatorcontrib>Jaylet, Thomas</creatorcontrib><creatorcontrib>Blaha, Ludek</creatorcontrib><creatorcontrib>Sarigiannis, Denis</creatorcontrib><creatorcontrib>Tamisier, Luc</creatorcontrib><creatorcontrib>Audouze, Karine</creatorcontrib><title>AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome.
Results
Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment.
Availability and implementation
AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php
Supplementary information
Supplementary data are available at Bioinformatics online.</description><subject>Adverse Outcome Pathways</subject><subject>Applications Notes</subject><subject>Artificial Intelligence</subject><subject>Bioinformatics</subject><subject>Computer Science</subject><subject>Data Management</subject><subject>Databases, Factual</subject><subject>Life Sciences</subject><subject>Risk Assessment - methods</subject><subject>Toxicology</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNqNkctu1TAURSMEog_4hcpTBqF2fPJigHRVUYp0pTKAseXHCTFKYst2Ut1B_x1Xt60oI0a27L3WsbWL4oLRj4z2_FJZZ5fBhVkmq-OlSlK1NX1VnDJoaFnRun-d97xpS-goPynOYvxNac0A4G1xwqFlHTA4Le53t9_LESd_bReDgdyhihg2DJ-IJMm5ieQhRLvZBxxxiXZDIhc5HaKNxA0kjUgmmzDItAbMBImr9y4kIk22RCRuTRlH4mUa7-QhEoMbTs7PuKR3xZtBThHfP67nxc_rLz-ubsr97ddvV7t9qWvgqQQOvFeomBk0mjp_rgcNCrTGFqDVZugBKqw4RakYM5XhQ2XqFjvWDWww_Lz4fPT6Vc1odB4d5CR8sLMMB-GkFS9vFjuKX24TXds3vG2y4MNRMP6D3ez24uGMQtN2rIKN5WxzzOrgYgw4PAOMiofyxMvyxGN5Gbz4-5XP2FNbOcCOAbf6_5X-Adxhslw</recordid><startdate>20220127</startdate><enddate>20220127</enddate><creator>Jornod, Florence</creator><creator>Jaylet, Thomas</creator><creator>Blaha, Ludek</creator><creator>Sarigiannis, Denis</creator><creator>Tamisier, Luc</creator><creator>Audouze, Karine</creator><general>Oxford University Press</general><general>Oxford University Press (OUP)</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>1XC</scope><scope>VOOES</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-7525-4089</orcidid></search><sort><creationdate>20220127</creationdate><title>AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development</title><author>Jornod, Florence ; Jaylet, Thomas ; Blaha, Ludek ; Sarigiannis, Denis ; Tamisier, Luc ; Audouze, Karine</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c543t-43439beb1dfced505994c4b4cce7447cdf9442e230eab11d2d3f2d57e818f1fd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Adverse Outcome Pathways</topic><topic>Applications Notes</topic><topic>Artificial Intelligence</topic><topic>Bioinformatics</topic><topic>Computer Science</topic><topic>Data Management</topic><topic>Databases, Factual</topic><topic>Life Sciences</topic><topic>Risk Assessment - methods</topic><topic>Toxicology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jornod, Florence</creatorcontrib><creatorcontrib>Jaylet, Thomas</creatorcontrib><creatorcontrib>Blaha, Ludek</creatorcontrib><creatorcontrib>Sarigiannis, Denis</creatorcontrib><creatorcontrib>Tamisier, Luc</creatorcontrib><creatorcontrib>Audouze, Karine</creatorcontrib><collection>Open Access: Oxford University Press Open Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jornod, Florence</au><au>Jaylet, Thomas</au><au>Blaha, Ludek</au><au>Sarigiannis, Denis</au><au>Tamisier, Luc</au><au>Audouze, Karine</au><au>Wren, Jonathan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2022-01-27</date><risdate>2022</risdate><volume>38</volume><issue>4</issue><spage>1173</spage><epage>1175</epage><pages>1173-1175</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome.
Results
Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment.
Availability and implementation
AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php
Supplementary information
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>34718414</pmid><doi>10.1093/bioinformatics/btab750</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0001-7525-4089</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Adverse Outcome Pathways Applications Notes Artificial Intelligence Bioinformatics Computer Science Data Management Databases, Factual Life Sciences Risk Assessment - methods Toxicology |
title | AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development |
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