{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T05:46:23Z","timestamp":1779083183977,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,11,9]],"date-time":"2019-11-09T00:00:00Z","timestamp":1573257600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NTNU's Horizon 2020 Incentive programme"},{"DOI":"10.13039\/501100005416","name":"Norwegian Research Council","doi-asserted-by":"publisher","award":["247727\/O70"],"award-info":[{"award-number":["247727\/O70"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The BioGateway App is a Cytoscape (version 3) plugin designed to provide easy query access to the BioGateway Resource Description Framework triple store, which contains functional and interaction information for proteins from several curated resources. For explorative network building, we have added a comprehensive dataset with regulatory relationships of mammalian DNA-binding transcription factors and their target genes, compiled both from curated resources and from a text mining effort. Query results are visualized using the inherent flexibility of the Cytoscape framework, and network links can be checked against curated database records or against the original publication.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Install through the Cytoscape application manager or visit www.biogateway.eu for download and tutorial documents.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary information is available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz835","type":"journal-article","created":{"date-parts":[[2019,11,8]],"date-time":"2019-11-08T17:30:16Z","timestamp":1573234216000},"page":"1966-1967","source":"Crossref","is-referenced-by-count":14,"title":["The Cytoscape BioGateway App: explorative network building from an RDF store"],"prefix":"10.1093","volume":"36","author":[{"given":"Stian","family":"Holm\u00e5s","sequence":"first","affiliation":[{"name":"Semantic Systems Biology Group , Department of Biology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rafel","family":"Riudavets Puig","sequence":"additional","affiliation":[{"name":"Semantic Systems Biology Group , Department of Biology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcio Luis","family":"Acencio","sequence":"additional","affiliation":[{"name":"Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology , 7491 Trondheim, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir","family":"Mironov","sequence":"additional","affiliation":[{"name":"Semantic Systems Biology Group , Department of Biology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1171-9876","authenticated-orcid":false,"given":"Martin","family":"Kuiper","sequence":"additional","affiliation":[{"name":"Semantic Systems Biology Group , Department of Biology"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,11,9]]},"reference":[{"key":"2023060912020574800_btz835-B1","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2105-10-S10-S11","article-title":"BioGateway: a semantic systems biology tool for the life sciences","volume":"10","author":"Antezana","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023060912020574800_btz835-B2","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/1471-2164-13-405","article-title":"HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions","volume":"13","author":"Bovolenta","year":"2012","journal-title":"BMC Genomics"},{"key":"2023060912020574800_btz835-B3","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/2041-1480-4-S1-S1","article-title":"Ontology-based querying with Bio2RDF\u2019s linked open data","volume":"4","author":"Callahan","year":"2013","journal-title":"J. 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