{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:39:48Z","timestamp":1772138388273,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,1,16]],"date-time":"2017-01-16T00:00:00Z","timestamp":1484524800000},"content-version":"vor","delay-in-days":81,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DB1054964"],"award-info":[{"award-number":["DB1054964"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA194547"],"award-info":[{"award-number":["R01CA194547"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hirschl Trust"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5,1]]},"abstract":"<jats:p>Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https:\/\/pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations.<\/jats:p>\n                  <jats:p>Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically.<\/jats:p>\n                  <jats:p>Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB\u2019s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API.<\/jats:p>\n                  <jats:p>Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology.<\/jats:p>\n                  <jats:p>Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API.<\/jats:p>","DOI":"10.1093\/jamia\/ocw148","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T15:06:19Z","timestamp":1475161579000},"page":"513-519","source":"Crossref","is-referenced-by-count":96,"title":["The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations"],"prefix":"10.1093","volume":"24","author":[{"given":"Linda","family":"Huang","sequence":"first","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Institute for Computational Biomedicine"}]},{"given":"Helen","family":"Fernandes","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Hamid","family":"Zia","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Peyman","family":"Tavassoli","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Hanna","family":"Rennert","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"David","family":"Pisapia","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Marcin","family":"Imielinski","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Andrea","family":"Sboner","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Institute for Computational Biomedicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Mark A","family":"Rubin","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Michael","family":"Kluk","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA"}]},{"given":"Olivier","family":"Elemento","sequence":"additional","affiliation":[{"name":"Institute for Precision Medicine"},{"name":"Institute for Computational Biomedicine"}]}],"member":"286","published-online":{"date-parts":[[2016,10,27]]},"reference":[{"issue":"111","key":"2020110612362207600_ocw148-B1","doi-asserted-by":"crossref","first-page":"111ra21","DOI":"10.1126\/scitranslmed.3003161","article-title":"Personalized oncology through integrative high-throughput sequencing: a pilot study","volume":"3","author":"Roychowdhury","year":"2011","journal-title":"Sci Trans Med."},{"issue":"6","key":"2020110612362207600_ocw148-B2","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/nm.3559","article-title":"Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine","volume":"20","author":"Van Allen","year":"2014","journal-title":"Nat Med."},{"issue":"4","key":"2020110612362207600_ocw148-B3","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1001\/jamaoncol.2015.1313","article-title":"Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response","volume":"1","author":"Beltran","year":"2015","journal-title":"JAMA Onco.l"},{"issue":"1","key":"2020110612362207600_ocw148-B4","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl Variant Effect Predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"issue":"2","key":"2020110612362207600_ocw148-B5","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly."},{"issue":"16","key":"2020110612362207600_ocw148-B6","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2020110612362207600_ocw148-B7","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","article-title":"ClinVar: public archive of relationships among sequence variation and human phenotype","volume":"42","author":"Landrum","year":"2014","journal-title":"Nucleic Acids Res."},{"issue":"6","key":"2020110612362207600_ocw148-B8","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1002\/humu.22981","article-title":"HGVS Recommendations for the Description of Sequence Variants: 2016 Update","volume":"37","author":"den Dunnen","year":"2016","journal-title":"Hum Mutat."},{"issue":"1","key":"2020110612362207600_ocw148-B9","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1093\/bioinformatics\/btu613","article-title":"The Ensembl REST API: Ensembl Data for Any Language","volume":"31","author":"Yates","year":"2015","journal-title":"Bioinformatics."},{"key":"2020110612362207600_ocw148-B10","doi-asserted-by":"crossref","first-page":"D805","DOI":"10.1093\/nar\/gku1075","article-title":"COSMIC: exploring the world's knowledge of somatic mutations in human cancer","volume":"43","author":"Forbes","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020110612362207600_ocw148-B11","doi-asserted-by":"crossref","first-page":"D1079","DOI":"10.1093\/nar\/gku1071","article-title":"Genenames.org: the HGNC resources in 2015","volume":"43","author":"Gray","year":"2015","journal-title":"Nucleic Acids Res."}],"container-title":["Journal of the American Medical Informatics Association"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/24\/3\/513\/34148189\/ocw148.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/24\/3\/513\/34148189\/ocw148.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,6]],"date-time":"2020-11-06T12:43:36Z","timestamp":1604666616000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamia\/article\/24\/3\/513\/2418181"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10,27]]},"references-count":11,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2016,10,27]]},"published-print":{"date-parts":[[2017,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jamia\/ocw148","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/059824","asserted-by":"object"}]},"ISSN":["1067-5027","1527-974X"],"issn-type":[{"value":"1067-5027","type":"print"},{"value":"1527-974X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,5]]},"published":{"date-parts":[[2016,10,27]]}}}