{"id":"https://openalex.org/W2289693310","doi":"https://doi.org/10.1186/s13321-016-0125-7","title":"Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets","display_name":"Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets","publication_year":2016,"publication_date":"2016-03-04","ids":{"openalex":"https://openalex.org/W2289693310","doi":"https://doi.org/10.1186/s13321-016-0125-7","mag":"2289693310","pmid":"https://pubmed.ncbi.nlm.nih.gov/26949417"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-016-0125-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0125-7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0125-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0125-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091416834","display_name":"Isidro Cort\u00e9s\u2010Ciriano","orcid":"https://orcid.org/0000-0002-2036-494X"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Isidro Cortes-Ciriano","raw_affiliation_strings":["Unit\u00e9 de Bioinformatique Structurale, CNRS UMR 3825, D\u00e9partement de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75015 Paris, France","Unit\u00e9 de Bioinformatique Structurale, CNRS UMR 3825, D\u00e9partement de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75015, Paris, France"],"affiliations":[{"raw_affiliation_string":"Unit\u00e9 de Bioinformatique Structurale, CNRS UMR 3825, D\u00e9partement de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75015 Paris, France","institution_ids":[]},{"raw_affiliation_string":"Unit\u00e9 de Bioinformatique Structurale, CNRS UMR 3825, D\u00e9partement de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75015, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091416834"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.8949,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.91152251,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"8","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.98089998960495,"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/T10274","display_name":"Synthesis and biological activity","score":0.9714999794960022,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8336425423622131},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7411902546882629},{"id":"https://openalex.org/keywords/categorical-variable","display_name":"Categorical variable","score":0.6604859232902527},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5499812364578247},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.5040437579154968},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4876197874546051},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36350393295288086},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33484387397766113},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3270198702812195},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2946379482746124},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2732797861099243},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17997807264328003},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09167173504829407}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8336425423622131},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7411902546882629},{"id":"https://openalex.org/C5274069","wikidata":"https://www.wikidata.org/wiki/Q2285707","display_name":"Categorical variable","level":2,"score":0.6604859232902527},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5499812364578247},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.5040437579154968},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4876197874546051},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36350393295288086},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33484387397766113},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3270198702812195},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2946379482746124},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2732797861099243},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17997807264328003},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09167173504829407}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13321-016-0125-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0125-7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0125-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:26949417","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26949417","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 cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4779235","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4779235","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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-016-0125-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0125-7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0125-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6299999952316284,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G5678582494","display_name":null,"funder_award_id":"Pasteur-Paris International PhD Programme","funder_id":"https://openalex.org/F4320322141","funder_display_name":"Institut Pasteur"}],"funders":[{"id":"https://openalex.org/F4320322141","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2289693310.pdf","grobid_xml":"https://content.openalex.org/works/W2289693310.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1965769390","https://openalex.org/W1967405986","https://openalex.org/W1988037271","https://openalex.org/W1988909822","https://openalex.org/W2012536183","https://openalex.org/W2021289165","https://openalex.org/W2039292327","https://openalex.org/W2041005506","https://openalex.org/W2046940765","https://openalex.org/W2058915131","https://openalex.org/W2059556517","https://openalex.org/W2071234745","https://openalex.org/W2076448934","https://openalex.org/W2107081909","https://openalex.org/W2117856769","https://openalex.org/W2129434099","https://openalex.org/W2129683878","https://openalex.org/W2142325821","https://openalex.org/W2143586989","https://openalex.org/W2146292423","https://openalex.org/W2158219301","https://openalex.org/W2161104773","https://openalex.org/W2161723275","https://openalex.org/W2168209541","https://openalex.org/W2168990503","https://openalex.org/W2213539420","https://openalex.org/W2213735563","https://openalex.org/W2328014372","https://openalex.org/W2330838234","https://openalex.org/W2342249984","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2973074952","https://openalex.org/W2594328795","https://openalex.org/W4283395020","https://openalex.org/W3183930479","https://openalex.org/W4320732452","https://openalex.org/W135095951","https://openalex.org/W4385588199","https://openalex.org/W3199987505","https://openalex.org/W4385760073","https://openalex.org/W4286980196"],"abstract_inverted_index":{"Here,":[0],"the":[1,11,41,45,69,78,94,104,112,116],"python":[2],"library":[3,37],"bioalerts":[4,38,74,108],"is":[5],"presented,":[6],"which":[7,54,85],"comprises":[8],"functionalities":[9,76,110],"for":[10,77,98,111],"automatic":[12],"derivation":[13,70],"of":[14,44,62,71,80,96,103,115],"structural":[15,72,118],"alerts":[16],"from":[17],"categorical":[18],"(dichotomous),":[19],"e.g.":[20,27],"toxic/non-toxic,":[21],"and":[22],"continuous":[23],"bioactivity":[24,91],"data":[25],"sets,":[26],"[Formula:":[28,32],"see":[29,33],"text]":[30,34],"or":[31],"values.":[35],"The":[36],"relies":[39],"on":[40],"RDKit":[42],"implementation":[43],"circular":[46],"Morgan":[47,83],"fingerprint":[48],"algorithm":[49],"to":[50,68],"compute":[51],"chemical":[52,105],"substructures,":[53],"are":[55],"derived":[56,117],"by":[57],"considering":[58],"radial":[59],"atom":[60],"neighbourhoods":[61],"increasing":[63],"bond":[64],"radius.":[65],"In":[66],"addition":[67],"alerts,":[73],"provides":[75,109],"calculation":[79],"unhashed":[81],"(keyed)":[82],"fingerprints,":[84],"can":[86],"be":[87],"used":[88],"in":[89],"predictive":[90],"modelling":[92],"with":[93],"advantage":[95],"allowing":[97],"a":[99],"chemically":[100],"meaningful":[101],"deconvolution":[102],"space.":[106],"Finally,":[107],"easy":[113],"visualization":[114],"alerts.":[119]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
