{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T09:39:58Z","timestamp":1766137198724},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"S10","license":[{"start":{"date-parts":[[2019,5,1]],"date-time":"2019-05-01T00:00:00Z","timestamp":1556668800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T00:00:00Z","timestamp":1559088000000},"content-version":"vor","delay-in-days":28,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,5]]},"DOI":"10.1186\/s12859-019-2812-7","type":"journal-article","created":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T00:02:50Z","timestamp":1559088170000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["CODA-ML: context-specific biological knowledge representation for systemic physiology analysis"],"prefix":"10.1186","volume":"20","author":[{"given":"Mijin","family":"Kwon","sequence":"first","affiliation":[]},{"given":"Soorin","family":"Yim","sequence":"additional","affiliation":[]},{"given":"Gwangmin","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Saehwan","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Chungsun","family":"Jeong","sequence":"additional","affiliation":[]},{"given":"Doheon","family":"Lee","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,5,29]]},"reference":[{"issue":"Database issue","key":"2812_CR1","doi-asserted-by":"publisher","first-page":"D470","DOI":"10.1093\/nar\/gku1204","volume":"43","author":"A Chatr-Aryamontri","year":"2015","unstructured":"Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, et al. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2015;43(Database issue):D470\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"2812_CR2","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.1101\/gr.216721.116","volume":"27","author":"A Saha","year":"2017","unstructured":"Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, Consortium GT, Engelhardt BE, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res. 2017;27(11):1843\u201358.","journal-title":"Genome Res"},{"issue":"D1","key":"2812_CR3","doi-asserted-by":"publisher","first-page":"D754","DOI":"10.1093\/nar\/gkx1098","volume":"46","author":"DR Zerbino","year":"2018","unstructured":"Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Giron CG, et al. Ensembl 2018. Nucleic Acids Res. 2018;46(D1):D754\u201361.","journal-title":"Nucleic Acids Res"},{"key":"2812_CR4","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27.","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"2812_CR5","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/ng.3259","volume":"47","author":"CS Greene","year":"2015","unstructured":"Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, et al. Understanding multicellular function and disease with human tissue-specific networks. Nat Genet. 2015;47(6):569\u201376.","journal-title":"Nat Genet"},{"key":"2812_CR6","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/nrm1054","volume":"4","author":"PJ Hunter","year":"2003","unstructured":"Hunter PJ, Thomas K. Borg: integration from proteins to organs: the Physiome project. Nat Rev Mol Cell Biol. 2003;4:237.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2812_CR7","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/1752-0509-8-49","volume":"8","author":"J D\u00f6nitz","year":"2014","unstructured":"D\u00f6nitz J, Wingender E. EndoNet: an information resource about the intercellular signaling network. BMC Syst Biol. 2014;8:49.","journal-title":"BMC Syst Biol"},{"issue":"3","key":"2812_CR8","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1007\/s10549-009-0640-6","volume":"121","author":"S Jeon","year":"2010","unstructured":"Jeon S, Choi JY, Lee KM, Park SK, Yoo KY, Noh DY, Ahn SH, Kang D. Combined genetic effect of CDK7 and ESR1 polymorphisms on breast cancer. Breast Cancer Res Treat. 2010;121(3):737\u201342.","journal-title":"Breast Cancer Res Treat"},{"key":"2812_CR9","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/S0893-133X(01)00395-5","volume":"26","author":"JG Hensler","year":"2002","unstructured":"Hensler JG. Differential regulation of 5-HT1A receptor-G protein interactions in brain following chronic antidepressant administration. Neuropsychopharmacology. 2002;26:565.","journal-title":"Neuropsychopharmacology"},{"key":"2812_CR10","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1186\/1752-0509-7-135","volume":"7","author":"C Chaouiya","year":"2013","unstructured":"Chaouiya C, et al. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol. 2013;7:135.","journal-title":"BMC Syst Biol"},{"issue":"9","key":"2812_CR11","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1038\/nbt.1666","volume":"28","author":"E Demir","year":"2010","unstructured":"Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010;28(9):935\u201342.","journal-title":"Nat Biotechnol"},{"key":"2812_CR12","series-title":"Proceedings of the 7th international workshop on Data and text mining in biomedical informatics","doi-asserted-by":"publisher","DOI":"10.1145\/2512089.2512097","volume-title":"BSML: bio-synergy modeling language for multi-component and multi-target analysis","author":"W Hwang","year":"2013","unstructured":"Hwang W, et al.: BSML: bio-synergy modeling language for multi-component and multi-target analysis. Proceedings of the 7th international workshop on Data and text mining in biomedical informatics 2013."},{"issue":"D1","key":"2812_CR13","doi-asserted-by":"publisher","first-page":"D710","DOI":"10.1093\/nar\/gkv1157","volume":"44","author":"A Yates","year":"2015","unstructured":"Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L. Ensembl 2016. Nucleic Acids Res. 2015;44(D1):D710\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2812_CR14","doi-asserted-by":"publisher","first-page":"D380","DOI":"10.1093\/nar\/gkv1277","volume":"44","author":"D Szklarczyk","year":"2015","unstructured":"Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein\u2013chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 2015;44(D1):D380\u20134.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2812_CR15","first-page":"D258","volume":"32","author":"MA Harris","year":"2004","unstructured":"Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, et al. The gene ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32(Database issue):D258\u201361.","journal-title":"Nucleic Acids Res"},{"issue":"suppl_1","key":"2812_CR16","doi-asserted-by":"publisher","first-page":"D267","DOI":"10.1093\/nar\/gkh061","volume":"32","author":"O Bodenreider","year":"2004","unstructured":"Bodenreider O. The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004;32(suppl_1):D267\u201370.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2812_CR17","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1136\/jamia.2001.0080317","volume":"8","author":"MH Coletti","year":"2001","unstructured":"Coletti MH, Bleich HL. Medical subject headings used to search the biomedical literature. J Am Med Inform Assoc. 2001;8(4):317\u201323.","journal-title":"J Am Med Inform Assoc"},{"key":"2812_CR18","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1038\/sj.onc.1204073","volume":"20","author":"S Fan","year":"2001","unstructured":"Fan S, et al. Role of direct interaction in BRCA1 inhibition of estrogen receptor activity. Oncogene. 2001;20:77.","journal-title":"Oncogene"},{"issue":"D1","key":"2812_CR19","doi-asserted-by":"publisher","first-page":"D972","DOI":"10.1093\/nar\/gkw838","volume":"45","author":"AP Davis","year":"2017","unstructured":"Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The comparative Toxicogenomics database: update 2017. Nucleic Acids Res. 2017;45(D1):D972\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2812_CR20","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1016\/j.bbagen.2013.10.023","volume":"1840","author":"TH Kim","year":"2014","unstructured":"Kim TH, Shin YJ, Won AJ, Lee BM, Choi WS, Jung JH, Chung HY, Kim HS. Resveratrol enhances chemosensitivity of doxorubicin in multidrug-resistant human breast cancer cells via increased cellular influx of doxorubicin. Biochim Biophys Acta. 2014;1840(1):615\u201325.","journal-title":"Biochim Biophys Acta"},{"issue":"4","key":"2812_CR21","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1093\/bioinformatics\/btx660","volume":"34","author":"CT Hoyt","year":"2017","unstructured":"Hoyt CT, Konotopez A, Ebeling C. PyBEL: a computational framework for biological expression language. Bioinformatics. 2017;34(4):703\u20134.","journal-title":"Bioinformatics"},{"key":"2812_CR22","doi-asserted-by":"publisher","first-page":"2905","DOI":"10.1158\/1078-0432.CCR-14-0816","volume":"21","author":"T VanArsdale","year":"2015","unstructured":"VanArsdale T, Boshoff C, Arndt KT, Abraham RT. Molecular pathways: targeting the cyclin D-CDK4\/6 axis for cancer treatment. Clin Cancer Res. 2015;21:2905 clincanres. 0816.2014.","journal-title":"Clin Cancer Res"},{"issue":"4","key":"2812_CR23","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1002\/wrna.1283","volume":"6","author":"SU Rehman","year":"2015","unstructured":"Rehman SU, Husain MA, Sarwar T, Ishqi HM, Tabish M. Modulation of alternative splicing by anticancer drugs. Wiley Interdiscip Rev. 2015;6(4):369\u201379.","journal-title":"Wiley Interdiscip Rev"},{"issue":"1","key":"2812_CR24","doi-asserted-by":"publisher","first-page":"4223","DOI":"10.1038\/s41598-018-22351-4","volume":"8","author":"H Yu","year":"2018","unstructured":"Yu H, Jung J, Yoon S, Kwon M, Bae S, Yim S, Lee J, Kim S, Kang Y, Lee D. Publisher correction: CODA: integrating multi-level context-oriented directed associations for analysis of drug effects. Sci Rep. 2018;8(1):4223.","journal-title":"Sci Rep"},{"issue":"9","key":"2812_CR25","doi-asserted-by":"publisher","first-page":"e1003194","DOI":"10.1371\/journal.pcbi.1003194","volume":"9","author":"E Demir","year":"2013","unstructured":"Demir E, Babur \u00d6, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, S\u00fcmer OS, Bader GD, Sander C. Using biological pathway data with paxtools. PLoS Comput Biol. 2013;9(9):e1003194.","journal-title":"PLoS Comput Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2812-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2812-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2812-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T23:06:22Z","timestamp":1590620782000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2812-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5]]},"references-count":25,"journal-issue":{"issue":"S10","published-print":{"date-parts":[[2019,5]]}},"alternative-id":["2812"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2812-7","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5]]},"assertion":[{"value":"29 May 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"248"}}