{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T01:33:06Z","timestamp":1775698386728,"version":"3.50.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T00:00:00Z","timestamp":1769731200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T00:00:00Z","timestamp":1771891200000},"content-version":"vor","delay-in-days":25,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Korea Institute of Oriental Medicine, South Korea","award":["KSN2235120"],"award-info":[{"award-number":["KSN2235120"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genom Data"],"DOI":"10.1186\/s12863-026-01409-7","type":"journal-article","created":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T11:34:57Z","timestamp":1769772897000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["KORE-Map 1.1: Korean medicine omics resource extension map on transcriptome data of dyspepsia herbal medicine"],"prefix":"10.1186","volume":"27","author":[{"given":"Eun-Hye","family":"Seo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Musun","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Su-Jin","family":"Baek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haeseung","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sang-Min","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aeyung","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"No Soo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A. Yeong","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu Ri","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin-Mu","family":"Yi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seongwon","family":"Cha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,1,30]]},"reference":[{"issue":"4A","key":"1409_CR1","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1017\/S1368980000000525","volume":"3","author":"VE Tyler","year":"2000","unstructured":"Tyler VE. Herbal medicine: from the past to the future. Public Health Nutr. 2000;3(4A):447\u201352.","journal-title":"Public Health Nutr"},{"issue":"2","key":"1409_CR2","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1142\/S0192415X13500183","volume":"41","author":"J Wang","year":"2013","unstructured":"Wang J, Wang Q, Li L, Li Y, Zhang H, Zheng L, Yang L, Zheng Y, Yang Y, Peng G, et al. Phlegm-dampness constitution: genomics, susceptibility, adjustment and treatment with traditional Chinese medicine. Am J Chin Med. 2013;41(2):253\u201362.","journal-title":"Am J Chin Med"},{"issue":"1","key":"1409_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s11684-012-0173-y","volume":"6","author":"Q Wang","year":"2012","unstructured":"Wang Q. Individualized medicine, health medicine, and constitutional theory in Chinese medicine. Front Med. 2012;6(1):1\u20137.","journal-title":"Front Med"},{"key":"1409_CR4","doi-asserted-by":"publisher","first-page":"112748","DOI":"10.1016\/j.biopha.2022.112748","volume":"148","author":"SJ Baek","year":"2022","unstructured":"Baek SJ, Lee H, Park SM, Park M, Yi JM, Kim NS, Kim A, Cha S. Identification of a novel anticancer mechanism of paeoniae radix extracts based on systematic transcriptome analysis. Biomed Pharmacother. 2022;148:112748.","journal-title":"Biomed Pharmacother"},{"key":"1409_CR5","doi-asserted-by":"publisher","first-page":"1010520","DOI":"10.3389\/fphar.2022.1010520","volume":"13","author":"SM Park","year":"2022","unstructured":"Park SM, Kim A, Lee H, Baek SJ, Kim NS, Park M, Yi JM, Cha S. Systematic transcriptome analysis reveals molecular mechanisms and indications of bupleuri radix. Front Pharmacol. 2022;13:1010520.","journal-title":"Front Pharmacol"},{"issue":"3","key":"1409_CR6","doi-asserted-by":"publisher","first-page":"e0150460","DOI":"10.1371\/journal.pone.0150460","volume":"11","author":"H Lee","year":"2016","unstructured":"Lee H, Kang S, Kim W. Drug repositioning for cancer therapy based on Large-Scale Drug-Induced transcriptional signatures. PLoS ONE. 2016;11(3):e0150460.","journal-title":"PLoS ONE"},{"issue":"1","key":"1409_CR7","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1038\/s41597-024-03734-x","volume":"11","author":"M Park","year":"2024","unstructured":"Park M, Park SM, Lee H, Kim A, Kim NS, Kim YR, Yi JM, Cha S. KORE-Map 1.0: Korean medicine omics resource extension map on transcriptome data of tonifying herbal medicine. Sci Data. 2024;11(1):974.","journal-title":"Sci Data"},{"key":"1409_CR8","doi-asserted-by":"crossref","unstructured":"Wang JH, Han SY, Kim J, Lim S, Jeong C, Wu L, Kim H. Comparative assessment of the anti-helicobacter pylori activity and gastroprotective effects of three herbal formulas for functional dyspepsia in vitro. Cells. 2024;13(11).","DOI":"10.3390\/cells13110901"},{"issue":"34","key":"1409_CR9","doi-asserted-by":"publisher","first-page":"7778","DOI":"10.3748\/wjg.v22.i34.7778","volume":"22","author":"MC Lee","year":"2016","unstructured":"Lee MC, Ha W, Park J, Kim J, Jung Y, Kim BJ. Effects of Lizhong Tang on Gastrointestinal motility in mice. World J Gastroenterol. 2016;22(34):7778\u201386.","journal-title":"World J Gastroenterol"},{"issue":"1","key":"1409_CR10","first-page":"9","volume":"35","author":"MH Kim","year":"2022","unstructured":"Kim MH, Lee SH, Hwang DY, Park YB, Ham SH, Yang WM. Protective effects of Banhasasim-tang, a herbal medicine, against cold restraint stress-induced gastric ulcers. Pak J Pharm Sci. 2022;35(1):9\u201313.","journal-title":"Pak J Pharm Sci"},{"key":"1409_CR11","doi-asserted-by":"crossref","unstructured":"Kim K, Ko SJ, Cho SH, Kim J, Park JW. Herbal medicine, Banxia-xiexin tang, for functional dyspepsia: a systematic review and meta-analysis. Front Pharmacol. 2023;14.","DOI":"10.3389\/fphar.2023.1130257"},{"issue":"2","key":"1409_CR12","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1016\/j.jep.2012.04.043","volume":"142","author":"MY Lee","year":"2012","unstructured":"Lee MY, Shin IS, Jeon WY, Seo CS, Ha H, Huh JI, Shin HK. Protective effect of Bojungikki-tang, a traditional herbal formula, against alcohol-induced gastric injury in rats. J Ethnopharmacol. 2012;142(2):346\u201353.","journal-title":"J Ethnopharmacol"},{"key":"1409_CR13","doi-asserted-by":"crossref","unstructured":"Lee B, Ahn EK, Yang C. Herbal medicine prescriptions for functional dyspepsia: a nationwide population-based study in Korea. Evid Based Complement Alternat Med. 2022;2022:3306420.","DOI":"10.1155\/2022\/3306420"},{"key":"1409_CR14","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.3389\/fphar.2020.01337","volume":"11","author":"E Ji","year":"2020","unstructured":"Ji E, Wang T, Xu J, Fan J, Zhang Y, Guan Y, Yang H, Wei J, Zhang G, Huang L. Systematic investigation of the efficacy of Sinitang Decoction against ulcerative colitis. Front Pharmacol. 2020;11:1337.","journal-title":"Front Pharmacol"},{"key":"1409_CR15","doi-asserted-by":"crossref","unstructured":"Won J, Lee BH, Jung WM, Chae Y, Lee H. Herbal medicine for inflammatory bowel diseases: development of pattern identification algorithms by retrospective analysis of case series data. Eur J Integr Med. 2020;36.","DOI":"10.1016\/j.eujim.2020.101114"},{"issue":"16","key":"1409_CR16","first-page":"1889","volume":"122","author":"FP Chen","year":"2009","unstructured":"Chen FP, Chen FJ, Jong MS, Tsai HL, Wang JR, Hwang SJ. Modern use of Chinese herbal formulae from Shang-Han Lun. Chin Med J (Engl). 2009;122(16):1889\u201394.","journal-title":"Chin Med J (Engl)"},{"key":"1409_CR17","doi-asserted-by":"publisher","unstructured":"KORE-Map 1. 1: Data files. https:\/\/doi.org\/10.6084\/m9.figshare.30215833.v4.","DOI":"10.6084\/m9.figshare.30215833.v4"},{"issue":"1","key":"1409_CR18","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15\u201321.","journal-title":"Bioinformatics"},{"key":"1409_CR19","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"1409_CR20","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1016\/j.cell.2017.10.049","volume":"171","author":"A Subramanian","year":"2017","unstructured":"Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, et al. A next generation connectivity map: L1000 platform and the first 1,000,000 profiles. Cell. 2017;171(6):1437\u201352. e1417.","journal-title":"Cell"},{"key":"1409_CR21","unstructured":"Digital transformation of herbal medicine. Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549. https:\/\/identifiers.org\/GEO:GSE252820."},{"key":"1409_CR22","unstructured":"Digital transformation of herbal medicine. Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2. https:\/\/identifiers.org\/GEO:GSE248976."},{"key":"1409_CR23","unstructured":"Digital transformation of herbal medicine. Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29. https:\/\/identifiers.org\/GEO:GSE250627."},{"key":"1409_CR24","unstructured":"Digital transformation of herbal medicine. Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783. https:\/\/identifiers.org\/GEO:GSE254458."},{"key":"1409_CR25","doi-asserted-by":"publisher","unstructured":"KORE-Map 1.1 RNA processing and analysis script. https:\/\/doi.org\/10.5281\/zenodo.17568315.","DOI":"10.5281\/zenodo.17568315"}],"container-title":["BMC Genomic Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12863-026-01409-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12863-026-01409-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12863-026-01409-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T10:32:21Z","timestamp":1771929141000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12863-026-01409-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,30]]},"references-count":25,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1409"],"URL":"https:\/\/doi.org\/10.1186\/s12863-026-01409-7","relation":{},"ISSN":["2730-6844"],"issn-type":[{"value":"2730-6844","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,30]]},"assertion":[{"value":"30 September 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 January 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 January 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"24"}}