{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T13:40:54Z","timestamp":1758894054716},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources. However, there are no resources to integrate these data automatically or to provide a \u2018one-stop shop\u2019 experience for users seeking information essential for deciphering and modeling gene regulatory networks.<\/jats:p>\n               <jats:p>Results: IntegromeDB, a semantic graph-based \u2018deep-web\u2019 data integration system that automatically captures, integrates and manages publicly available data concerning transcriptional regulation, as well as other relevant biological information, is proposed in this article. The problems associated with data integration are addressed by ontology-driven data mapping, multiple data annotation and heterogeneous data querying, also enabling integration of the user's data. IntegromeDB integrates over 100 experimental and computational data sources relating to genomics, transcriptomics, genetics, and functional and interaction data concerning gene transcriptional regulation in eukaryotes and prokaryotes.<\/jats:p>\n               <jats:p>Availability: IntegromeDB is accessible through the integrated research environment BiologicalNetworks at http:\/\/www.BiologicalNetworks.org<\/jats:p>\n               <jats:p>Contact: \u00a0baitaluk@sdsc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq231","type":"journal-article","created":{"date-parts":[[2010,4,29]],"date-time":"2010-04-29T02:34:16Z","timestamp":1272508456000},"page":"1651-1661","source":"Crossref","is-referenced-by-count":14,"title":["Semantic integration of data on transcriptional regulation"],"prefix":"10.1093","volume":"26","author":[{"given":"Michael","family":"Baitaluk","sequence":"first","affiliation":[{"name":"1 San Diego Supercomputer Center and 2 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"}]},{"given":"Julia","family":"Ponomarenko","sequence":"additional","affiliation":[{"name":"1 San Diego Supercomputer Center and 2 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"},{"name":"1 San Diego Supercomputer Center and 2 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,4,28]]},"reference":[{"key":"2023012507555360900_B1","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.cyto.2008.08.013","article-title":"Diagnostic utility of APOE, soluble CD40, CD40L, and Abeta1-40 levels in plasma in Alzheimer's disease","volume":"44","author":"Ait-ghezala","year":"2008","journal-title":"Cytokine"},{"key":"2023012507555360900_B2","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/1471-2105-7-55","article-title":"PathSys: integrating molecular interaction graphs for systems biology","volume":"7","author":"Baitaluk","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012507555360900_B3","doi-asserted-by":"crossref","first-page":"W466","DOI":"10.1093\/nar\/gkl308","article-title":"BiologicalNetworks: visualization and analysis tool for systems biology","volume":"34","author":"Baitaluk","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012507555360900_B4","first-page":"75","article-title":"Plasma beta amyloid and cytokine profile in women with Alzheimer's disease","volume":"29","author":"Baranowska-Bik","year":"2008","journal-title":"Neuro Endocrinol. 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