{"id":"https://openalex.org/W2234559012","doi":"https://doi.org/10.1093/bioinformatics/btv733","title":"PaxtoolsR: pathway analysis in R using Pathway Commons","display_name":"PaxtoolsR: pathway analysis in R using Pathway Commons","publication_year":2015,"publication_date":"2015-12-18","ids":{"openalex":"https://openalex.org/W2234559012","doi":"https://doi.org/10.1093/bioinformatics/btv733","mag":"2234559012","pmid":"https://pubmed.ncbi.nlm.nih.gov/26685306"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1262/6690699/btv733.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bioinformatics/article-pdf/32/8/1262/6690699/btv733.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026945351","display_name":"Augustin Luna","orcid":"https://orcid.org/0000-0001-5709-371X"},"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":"Augustin Luna","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","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, NY 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"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"]}],"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, NY 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emek Demir","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"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, NY 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","institution_ids":["https://openalex.org/I1334819555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5026945351"],"corresponding_institution_ids":["https://openalex.org/I1334819555"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7531,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.72751414,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"8","first_page":"1262","last_page":"1264"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9954000115394592,"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":0.9854999780654907,"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/bioconductor","display_name":"Bioconductor","score":0.9361783266067505},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.7995036244392395},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7644596695899963},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.5942829251289368},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5907939672470093},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5413479804992676},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.5048754811286926},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4555753767490387},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.44797390699386597},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4189557433128357},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.41095849871635437},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4023870825767517},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.37017470598220825},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3524986505508423},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3491625189781189},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3418189287185669},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.29332679510116577},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11386197805404663},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08825099468231201}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9361783266067505},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.7995036244392395},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7644596695899963},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.5942829251289368},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5907939672470093},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5413479804992676},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.5048754811286926},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4555753767490387},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.44797390699386597},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4189557433128357},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.41095849871635437},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4023870825767517},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.37017470598220825},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3524986505508423},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3491625189781189},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3418189287185669},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29332679510116577},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11386197805404663},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08825099468231201},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1262/6690699/btv733.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26685306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26685306","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:4824129","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4824129","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/8/1262","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/8/1262","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1262/6690699/btv733.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2234559012.pdf","grobid_xml":"https://content.openalex.org/works/W2234559012.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1969709265","https://openalex.org/W1986365650","https://openalex.org/W2023237744","https://openalex.org/W2096589119","https://openalex.org/W2126399647","https://openalex.org/W2127449417","https://openalex.org/W2130410032","https://openalex.org/W2144087930","https://openalex.org/W2164298117","https://openalex.org/W6608852248"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2524035291","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2098339479"],"abstract_inverted_index":{"paxtools@cbio.mskcc.org":[0],"or":[1],"lunaa@cbio.mskcc.org.":[2]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
