{"id":"https://openalex.org/W2096589119","doi":"https://doi.org/10.1093/bioinformatics/btt452","title":"The BioPAX Validator","display_name":"The BioPAX Validator","publication_year":2013,"publication_date":"2013-08-05","ids":{"openalex":"https://openalex.org/W2096589119","doi":"https://doi.org/10.1093/bioinformatics/btt452","mag":"2096589119","pmid":"https://pubmed.ncbi.nlm.nih.gov/23918249"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt452","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt452","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btt452","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086939772","display_name":"Igor Rodchenkov","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"Igor Rodchenkov","raw_affiliation_strings":["1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037803004","display_name":"Emek Demir","orcid":"https://orcid.org/0000-0002-3663-7113"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Emek Demir","raw_affiliation_strings":["1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008166270","display_name":"Chris Sander","orcid":"https://orcid.org/0000-0001-6059-6270"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Chris Sander","raw_affiliation_strings":["1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010789029","display_name":"Gary D. Bader","orcid":"https://orcid.org/0000-0003-0185-8861"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Gary D. Bader","raw_affiliation_strings":["1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5086939772"],"corresponding_institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I185261750"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5989,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.69379158,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"29","issue":"20","first_page":"2659","last_page":"2660"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9965999722480774,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9905999898910522,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/validator","display_name":"Validator","score":0.9967435598373413},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8206617832183838},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.49826788902282715},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.46707987785339355},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.44573238492012024},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.42458558082580566},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.37506115436553955},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3494700789451599},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.34388142824172974},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33949628472328186}],"concepts":[{"id":"https://openalex.org/C35292069","wikidata":"https://www.wikidata.org/wiki/Q1575458","display_name":"Validator","level":2,"score":0.9967435598373413},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8206617832183838},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.49826788902282715},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.46707987785339355},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.44573238492012024},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.42458558082580566},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.37506115436553955},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3494700789451599},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.34388142824172974},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33949628472328186},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt452","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt452","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:23918249","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23918249","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:3789551","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3789551","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:CiteSeerX.psu:10.1.1.853.3097","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.853.3097","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2013/08/05/bioinformatics.btt452.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt452","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt452","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":0.46000000834465027,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G1312109728","display_name":null,"funder_award_id":"U41HG006623","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3951133689","display_name":null,"funder_award_id":"1U41HG006623","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1969709265","https://openalex.org/W1986365650","https://openalex.org/W2127894639","https://openalex.org/W2134221731","https://openalex.org/W2143969914","https://openalex.org/W2163993275"],"related_works":["https://openalex.org/W1825982205","https://openalex.org/W2528467228","https://openalex.org/W1493446239","https://openalex.org/W2162118494","https://openalex.org/W1979547103","https://openalex.org/W2068737373","https://openalex.org/W4254917997","https://openalex.org/W2000780397","https://openalex.org/W2137409926","https://openalex.org/W4240242535"],"abstract_inverted_index":{"The":[0,59],"validator":[1,33],"recognizes":[2],"common":[3],"syntactic":[4],"errors":[5,24,47],"and":[6,9,25,48,54,65,74,81],"semantic":[7],"inconsistencies":[8],"reports":[10],"them":[11],"in":[12],"a":[13,36],"customizable":[14],"human":[15],"readable":[16],"format.":[17],"It":[18],"can":[19,76],"also":[20],"automatically":[21],"fix":[22],"some":[23],"normalize":[26],"BioPAX":[27,60],"data.":[28,58],"Since":[29],"its":[30],"release,":[31],"the":[32,40,52,82,87],"has":[34],"become":[35],"critical":[37],"tool":[38],"for":[39],"pathway":[41],"informatics":[42],"community,":[43],"detecting":[44],"thousands":[45],"of":[46,56,86],"helping":[49],"substantially":[50],"increase":[51],"conformity":[53],"uniformity":[55],"BioPAX-formatted":[57],"Validator":[61],"is":[62,90],"open":[63],"source":[64],"released":[66],"under":[67],"LGPL":[68],"v3":[69],"license.":[70],"All":[71],"sources,":[72],"binaries":[73],"documentation":[75],"be":[77],"found":[78],"at":[79,92],"sf.net/p/biopax,":[80],"latest":[83],"stable":[84],"version":[85],"web":[88],"application":[89],"available":[91],"biopax.org/validator.":[93]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
