{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T01:04:42Z","timestamp":1790039082663,"version":"4.0.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,6,5]],"date-time":"2017-06-05T00:00:00Z","timestamp":1496620800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,6,5]],"date-time":"2017-06-05T00:00:00Z","timestamp":1496620800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U01 CA180940"],"award-info":[{"award-number":["U01 CA180940"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM\/ITEM_GROUP pattern defined in the latest CIMI Reference Model is used to represent reusable model elements (mini-Archetypes).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We produced a metadata repository with 38 clinical cancer genome study domains, comprising a rich collection of mini-Archetype pattern instances. We performed a case study of the domain \u201cclinical pharmaceutical\u201d in the TCGA data dictionary and demonstrated enriched data elements in the metadata repository are very useful in support of building detailed clinical models.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Our informatics approach leveraging Semantic Web technologies provides an effective way to build a CIMI-compliant metadata repository that would facilitate the detailed clinical modeling to support use cases beyond TCGA in clinical cancer study domains.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13326-017-0130-4","type":"journal-article","created":{"date-parts":[[2017,6,5]],"date-time":"2017-06-05T11:41:03Z","timestamp":1496662863000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies"],"prefix":"10.1186","volume":"8","author":[{"given":"Deepak K.","family":"Sharma","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harold R.","family":"Solbrig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cui","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunhua","family":"Weng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher G.","family":"Chute","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2940-0019","authenticated-orcid":false,"given":"Guoqian","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,6,5]]},"reference":[{"issue":"2-3","key":"130_CR1","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1016\/S1386-5056(02)00103-X","volume":"69","author":"JF Coyle","year":"2003","unstructured":"Coyle JF, Mori AR, Huff SM. Standards for detailed clinical models as the basis for medical data exchange and decision support. International journal of medical informatics. 2003;69(2-3):157\u201374. Epub 2003\/06\/18.","journal-title":"International journal of medical informatics"},{"key":"130_CR2","unstructured":"HL7 Detailed Clinical Models 2014 [May 15, 2016]. Available from: http:\/\/wiki.hl7.org\/index.php?title=Detailed_Clinical_Models."},{"key":"130_CR3","first-page":"238","volume":"96","author":"T Beale","year":"2003","unstructured":"Beale T. Archetypes and the EHR. Studies in health technology and informatics. 2003;96:238\u201344. Epub 2004\/04\/06.","journal-title":"Studies in health technology and informatics."},{"key":"130_CR4","unstructured":"Clinical Element Model 2014 [May 15, 2016]. 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PubMed PMID: 22195076, PubMed Central PMCID: PMC3243296, Epub 2011\/12\/24.","journal-title":"AMIA Annual Symposium proceedings\/AMIA Symposium AMIA Symposium."},{"issue":"e2","key":"130_CR8","doi-asserted-by":"publisher","first-page":"e341","DOI":"10.1136\/amiajnl-2013-001939","volume":"20","author":"J Pathak","year":"2013","unstructured":"Pathak J, Bailey KR, Beebe CE, Bethard S, Carrell DC, Chen PJ, et al. Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. Journal of the American Medical Informatics Association. 2013;20(e2):e341\u20138. doi:10.1136\/amiajnl-2013-001939. PubMed PMID: 24190931, PubMed Central PMCID: PMC3861933, Epub 2013\/11\/06.","journal-title":"Journal of the American Medical Informatics Association"},{"key":"130_CR9","volume-title":"SHARE Project 2014 [May 15","author":"CDISC","year":"2016","unstructured":"CDISC. SHARE Project 2014 [May 15. 2016]. 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AMIA Annu Symp Proc. 2003;982."},{"key":"130_CR25","unstructured":"Shape Expressions [May 15, 2016]. http:\/\/www.w3.org\/2013\/ShEx\/Primer."}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0130-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13326-017-0130-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0130-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:22:40Z","timestamp":1790036560000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13326-017-0130-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,5]]},"references-count":25,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["130"],"URL":"https:\/\/doi.org\/10.1186\/s13326-017-0130-4","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6,5]]},"assertion":[{"value":"16 May 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 June 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"19"}}