{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:55Z","timestamp":1740185155406,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,6,15]],"date-time":"2021-06-15T00:00:00Z","timestamp":1623715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>PAX2GRAPHML is an open-source Python library that allows to easily manipulate BioPAX source files as regulated reaction graphs described in.graphml format. The concept of regulated reactions, which allows connecting regulatory, signaling and metabolic levels, has been used. Biochemical reactions and regulatory interactions are homogeneously described by regulated reactions involving substrates, products, activators and inhibitors as elements. PAX2GRAPHML is highly flexible and allows generating graphs of regulated reactions from a single BioPAX source or by combining and filtering BioPAX sources. Supported by the graph exchange format .graphml, the large-scale graphs produced from one or more data sources can be further analyzed with PAX2GRAPHML or standard Python and R graph libraries.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/pax2graphml.genouest.org.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab441","type":"journal-article","created":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T11:09:03Z","timestamp":1623668943000},"page":"4889-4891","source":"Crossref","is-referenced-by-count":1,"title":["PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6740-1632","authenticated-orcid":false,"given":"Fran\u00e7ois","family":"Moreews","sequence":"first","affiliation":[{"name":"Univ Rennes, Inria, CNRS, IRISA , Rennes, France"},{"name":"Pegase, Inrae, Institut Agro , 35590 Saint-Gilles, France"}]},{"given":"Hugo","family":"Simon","sequence":"additional","affiliation":[{"name":"Univ Rennes, Inria, CNRS, IRISA , Rennes, France"}]},{"given":"Anne","family":"Siegel","sequence":"additional","affiliation":[{"name":"Univ Rennes, Inria, CNRS, IRISA , Rennes, France"}]},{"given":"Florence","family":"Gondret","sequence":"additional","affiliation":[{"name":"Pegase, Inrae, Institut Agro , 35590 Saint-Gilles, France"}]},{"given":"Emmanuelle","family":"Becker","sequence":"additional","affiliation":[{"name":"Univ Rennes, Inria, CNRS, IRISA , Rennes, France"}]}],"member":"286","published-online":{"date-parts":[[2021,6,15]]},"reference":[{"key":"2023051607125583000_btab441-B1","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1093\/bioinformatics\/btp665","article-title":"ChiBE: interactive visualization and manipulation of BioPAX pathway models","volume":"26","author":"Babur","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051607125583000_btab441-B2","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btt539","article-title":"Pattern search in BioPAXmodels","volume":"30","author":"Babur","year":"2014","journal-title":"Bioinformatics"},{"key":"2023051607125583000_btab441-B3","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/1752-0509-8-32","article-title":"Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism","volume":"8","author":"Blavy","year":"2014","journal-title":"BMC Syst. 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Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab441\/39300702\/btab441.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/24\/4889\/50334666\/btab441.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/24\/4889\/50334666\/btab441.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T07:38:26Z","timestamp":1684222706000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/24\/4889\/6299382"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,6,15]]},"references-count":8,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2021,12,11]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab441","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,12,15]]},"published":{"date-parts":[[2021,6,15]]}}}