{"id":"https://openalex.org/W1986365650","doi":"https://doi.org/10.1371/journal.pcbi.1003194","title":"Using Biological Pathway Data with Paxtools","display_name":"Using Biological Pathway Data with Paxtools","publication_year":2013,"publication_date":"2013-09-19","ids":{"openalex":"https://openalex.org/W1986365650","doi":"https://doi.org/10.1371/journal.pcbi.1003194","mag":"1986365650","pmid":"https://pubmed.ncbi.nlm.nih.gov/24068901"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003194","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003194","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003194&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003194&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emek Demir","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006448195","display_name":"\u00d6zg\u00fcn Babur","orcid":"https://orcid.org/0000-0002-0239-5259"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"\u00d6zg\u00fcn Babur","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Igor Rodchenkov","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020220136","display_name":"B\u00fclent Arman Aksoy","orcid":"https://orcid.org/0000-0002-0135-2505"},"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/I4210100942","display_name":"Tri-Institutional PhD Program in Chemical Biology","ror":"https://ror.org/016twdg30","country_code":"US","type":"education","lineage":["https://openalex.org/I4210100942"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B\u00fclent Arman Aksoy","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America","Tri-Institutional Training Program, Computational Biology and Medicine New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Tri-Institutional Training Program, Computational Biology and Medicine New York, New York, United States of America","institution_ids":["https://openalex.org/I4210100942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044584230","display_name":"Ken Fukuda","orcid":"https://orcid.org/0000-0001-7366-1094"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ken I. Fukuda","raw_affiliation_strings":["Intelligent Information Infrastructure Division, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan"],"affiliations":[{"raw_affiliation_string":"Intelligent Information Infrastructure Division, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026873890","display_name":"Benjamin Gro\u00df","orcid":"https://orcid.org/0000-0003-4976-8304"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Gross","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084799057","display_name":"Onur Sumer","orcid":null},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Onur Sel\u00e7uk S\u00fcmer","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010789029","display_name":"Gary D. Bader","orcid":"https://orcid.org/0000-0003-0185-8861"},"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Gary D. Bader","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Sander","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America","institution_ids":["https://openalex.org/I1334819555"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5037803004"],"corresponding_institution_ids":["https://openalex.org/I1334819555"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.7431,"has_fulltext":true,"cited_by_count":67,"citation_normalized_percentile":{"value":0.93758146,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"9","issue":"9","first_page":"e1003194","last_page":"e1003194"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9997000098228455,"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":0.996999979019165,"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":0.9896000027656555,"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/computer-science","display_name":"Computer science","score":0.7808257341384888},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.7032659649848938},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6420512199401855},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6368389129638672},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5085262060165405},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.4776657521724701},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4725888669490814},{"id":"https://openalex.org/keywords/software-system","display_name":"Software system","score":0.45397356152534485},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4375690817832947},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23073282837867737},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.12902316451072693}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7808257341384888},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7032659649848938},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6420512199401855},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6368389129638672},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5085262060165405},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4776657521724701},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4725888669490814},{"id":"https://openalex.org/C149091818","wikidata":"https://www.wikidata.org/wiki/Q2429814","display_name":"Software system","level":3,"score":0.45397356152534485},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4375690817832947},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23073282837867737},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.12902316451072693}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1003194","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003194","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003194&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:24068901","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24068901","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.781.2932","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.781.2932","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/5a/cb/pcbi.1003194.PMC3777916.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003194","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003194","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:5a8bc679ce1c4af4ba7b7b2b03bd20d6","is_oa":true,"landing_page_url":"https://doaj.org/article/5a8bc679ce1c4af4ba7b7b2b03bd20d6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 9, Iss 9, p e1003194 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2771997","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3777916","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/803477","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Using_Biological_Pathway_Data_with_Paxtools_/803477","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003194","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003194","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003194&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G3989842470","display_name":null,"funder_award_id":"U41 HG006623","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6227541006","display_name":null,"funder_award_id":"#5U41 HG006623-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8870980817","display_name":null,"funder_award_id":"5U41 HG006623-02","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1986365650.pdf","grobid_xml":"https://content.openalex.org/works/W1986365650.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1597403892","https://openalex.org/W1969709265","https://openalex.org/W1973661008","https://openalex.org/W2011726658","https://openalex.org/W2022619825","https://openalex.org/W2023292217","https://openalex.org/W2025183726","https://openalex.org/W2028133290","https://openalex.org/W2036407878","https://openalex.org/W2036904266","https://openalex.org/W2052688256","https://openalex.org/W2095556056","https://openalex.org/W2096766502","https://openalex.org/W2100714130","https://openalex.org/W2108366237","https://openalex.org/W2109555487","https://openalex.org/W2112580417","https://openalex.org/W2114124738","https://openalex.org/W2114904907","https://openalex.org/W2124649657","https://openalex.org/W2128601422","https://openalex.org/W2130410032","https://openalex.org/W2134185611","https://openalex.org/W2137531873","https://openalex.org/W2138155367","https://openalex.org/W2139550340","https://openalex.org/W2143969914","https://openalex.org/W2144940507","https://openalex.org/W2149441684","https://openalex.org/W2154947819","https://openalex.org/W2157658519","https://openalex.org/W2158439765","https://openalex.org/W2163993275","https://openalex.org/W2164298117","https://openalex.org/W2164750538","https://openalex.org/W4233060585"],"related_works":["https://openalex.org/W2606446052","https://openalex.org/W2036021480","https://openalex.org/W3195777957","https://openalex.org/W2382668227","https://openalex.org/W2348482143","https://openalex.org/W2024584030","https://openalex.org/W3104168426","https://openalex.org/W1603675680","https://openalex.org/W2343406053","https://openalex.org/W3081644756"],"abstract_inverted_index":{"A":[0,167],"rapidly":[1],"growing":[2],"corpus":[3],"of":[4,28],"formal,":[5],"computable":[6],"pathway":[7,57,101],"information":[8],"can":[9,41,104,161,175,187],"be":[10,42,162,176,188],"used":[11,43],"to":[12,48,87,97,140],"answer":[13],"important":[14],"biological":[15,76],"questions":[16],"including":[17],"finding":[18],"non-trivial":[19],"connections":[20],"between":[21],"cellular":[22,30],"processes,":[23],"identifying":[24],"significantly":[25],"altered":[26],"portions":[27],"the":[29,80,131,143,157],"network":[31],"in":[32,79,145,164,178],"a":[33,65,111,150],"disease":[34],"state":[35],"and":[36,51,73,99,115,127,172,184],"building":[37],"predictive":[38],"models":[39],"that":[40,68,109],"for":[44,75,152,156,170],"precision":[45],"medicine.":[46],"Due":[47],"its":[49],"complexity":[50],"fragmented":[52],"nature,":[53],"however,":[54],"working":[55],"with":[56,149],"data":[58],"is":[59,124,128],"still":[60],"difficult.":[61],"We":[62],"present":[63],"Paxtools,":[64],"Java":[66,112],"library":[67],"contains":[69],"algorithms,":[70],"software":[71,147],"components":[72],"converters":[74],"pathways":[77],"represented":[78],"standard":[81],"BioPAX":[82],"language.":[83],"Paxtools":[84,103,123,174],"allows":[85,138],"scientists":[86],"focus":[88],"on":[89,106,118],"their":[90,146],"scientific":[91],"problem":[92],"by":[93],"removing":[94],"technical":[95],"barriers":[96],"access":[98],"analyse":[100],"information.":[102],"run":[105],"any":[107],"platform":[108],"has":[110],"Runtime":[113],"Environment":[114],"was":[116],"tested":[117],"most":[119],"modern":[120],"operating":[121],"systems.":[122],"open":[125],"source":[126],"available":[129],"under":[130],"Lesser":[132],"GNU":[133],"public":[134],"license":[135],"(LGPL),":[136],"which":[137],"users":[139],"freely":[141],"use":[142],"code":[144,155],"systems":[148],"requirement":[151],"attribution.":[153],"Source":[154],"current":[158],"release":[159,185],"(4.2.0)":[160],"found":[163,177],"Software":[165],"S1.":[166,180],"detailed":[168],"manual":[169],"obtaining":[171],"using":[173],"Protocol":[179],"The":[181],"latest":[182],"sources":[183],"bundles":[186],"obtained":[189],"from":[190],"biopax.org/paxtools.":[191]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
