{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T23:08:34Z","timestamp":1792796914918,"version":"4.5.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T00:00:00Z","timestamp":1669248000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Kazusa DNA Research Institute Foundation"},{"DOI":"10.13039\/501100010462","name":"National Institute of Genetics","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010462","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002241","name":"Japan Science and Technology Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"KAKENHI","doi-asserted-by":"publisher","award":["17K07810"],"award-info":[{"award-number":["17K07810"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JPMJCR17O2"],"award-info":[{"award-number":["JPMJCR17O2"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007173","name":"Bio-oriented Technology Research Advancement Institution","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007173","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003382","name":"Core Research for Evolutional Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003382","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The identification of unknown chemicals has emerged as a significant issue in untargeted metabolome analysis owing to the limited availability of purified standards for identification; this is a major bottleneck for the accumulation of reusable metabolome data in systems biology. Public resources for discovering and prioritizing the unknowns that should be subject to practical identification, as well as further detailed study of spending costs and the risks of misprediction, are lacking. As such a resource, we released databases, Food-, Plant-\u00a0and Thing-Metabolome Repository (http:\/\/metabolites.in\/foods, http:\/\/metabolites.in\/plants, and http:\/\/metabolites.in\/things, referred to as XMRs) in which the sample-specific localization of unknowns detected by liquid chromatography\u2013mass spectrometry in a wide variety of samples can be examined, helping to discover and prioritize the unknowns. A set of application programming interfaces for the XMRs facilitates the use of metabolome data for large-scale analysis and data mining. Several applications of XMRs, including integrated metabolome and genome analyses, are presented. Expanding the concept of XMRs will accelerate the identification of unknowns and increase the discovery of new knowledge.<\/jats:p>","DOI":"10.1093\/nar\/gkac1058","type":"journal-article","created":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T00:09:48Z","timestamp":1669248588000},"page":"D660-D677","source":"Crossref","is-referenced-by-count":13,"title":["The Thing Metabolome Repository\u00a0family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5861-6228","authenticated-orcid":false,"given":"Nozomu","family":"Sakurai","sequence":"first","affiliation":[{"name":"Bioinformation and DDBJ Center, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan"},{"name":"Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan"},{"name":"Sakura Scientific Co. Ltd. , 35 Horinouchi, Odawara, Kanagawa 250-0853, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shinichi","family":"Yamazaki","sequence":"additional","affiliation":[{"name":"Tohoku Medical Megabank Organization, Tohoku University , 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunihiro","family":"Suda","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ai","family":"Hosoki","sequence":"additional","affiliation":[{"name":"Bioinformation and DDBJ Center, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nayumi","family":"Akimoto","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3182-2894","authenticated-orcid":false,"given":"Haruya","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daisuke","family":"Shibata","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuichi","family":"Aoki","sequence":"additional","affiliation":[{"name":"Tohoku Medical Megabank Organization, Tohoku University , 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan"},{"name":"Graduate School of Information Sciences, Tohoku University , 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8679, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,24]]},"reference":[{"key":"2023010804254866400_B1","doi-asserted-by":"crossref","first-page":"72","DOI":"10.3390\/metabo9040072","article-title":"CFM-ID 3.0: significantly improved ESI-MS\/MS prediction and compound identification","volume":"9","author":"Djoumbou-Feunang","year":"2019","journal-title":"Metabolites"},{"key":"2023010804254866400_B2","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s13321-017-0207-1","article-title":"Critical assessment of small molecule identification 2016: automated methods","volume":"9","author":"Schymanski","year":"2017","journal-title":"J. Cheminform."},{"key":"2023010804254866400_B3","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nbt.3597","article-title":"Sharing and community curation of mass spectrometry data with global natural products social molecular networking","volume":"34","author":"Wang","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2023010804254866400_B4","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.copbio.2018.01.008","article-title":"Advances in computational metabolomics and databases deepen the understanding of metabolisms","volume":"54","author":"Tsugawa","year":"2018","journal-title":"Curr. Opin. Biotechnol."},{"key":"2023010804254866400_B5","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nmeth.4512","article-title":"Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics","volume":"15","author":"Lai","year":"2018","journal-title":"Nat. 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