This information is over 2 years old. Information was current at time of publication.{"id":13810,"date":"2021-07-20T13:07:28","date_gmt":"2021-07-20T17:07:28","guid":{"rendered":"https:\/\/info.hsls.pitt.edu\/updatereport\/?p=13810"},"modified":"2021-07-28T15:41:04","modified_gmt":"2021-07-28T19:41:04","slug":"share-human-variant-data-with-new-ncbi-clinvar-api","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/updatereport\/share-human-variant-data-with-new-ncbi-clinvar-api\/","title":{"rendered":"Share Human Variant Data with New NCBI ClinVar API"},"content":{"rendered":"<p>Do you work with human genetic variants? Have you sought out relevant publications, clinically significant evidence, and\/or publicly available data? Are you ready to contribute to the scientific and patient-care community by sharing your own research output?<\/p>\n<p>You likely already know about and use <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/\">ClinVar<\/a>, the go-to resource for the clinical genetics community that aggregates information about genomic variation and its relationship to human health. ClinVar recently reached the significant milestone of including <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/06\/04\/clinvar-reaches-one-million-variants\/\">1 million unique variants<\/a> in its database. Over 1,800 organizations from 82 countries have submitted almost 1.5 million records in ClinVar, including more than 11,000 curated variants from 14 expert panels.<\/p>\n<p>Now it is easier than ever to reciprocate and be a supportive community member by submitting your human genetic variant data using the new <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/06\/11\/automate-workflow-clinvar-submission-api\/\">ClinVar Submission API<\/a>. The workflow for submissions is fast and automated, thanks to a <a href=\"https:\/\/mlsdev.com\/blog\/81-a-beginner-s-tutorial-for-understanding-restful-api\">RESTful API<\/a>\u2014a particular architectural style for an application program interface (API) allowing two software programs to communicate with each other to access and use data.<!--more--><\/p>\n<p>There are three one-time activities for the ClinVar Submission API setup:<\/p>\n<ol>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/docs\/submission_portal\/\">Create\/update your profile<\/a> and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/docs\/submission_portal\/#register-the-submitting-organiza\">register your organization with ClinVar.<\/a><\/li>\n<li>Request a service account with an <a href=\"mailto:clinvar@ncbi.nlm.nih.gov\">email to ClinVar<\/a>.<\/li>\n<li>Create a new API key in the <a href=\"https:\/\/submit.ncbi.nlm.nih.gov\/clinvar\/\">ClinVar Submission Portal<\/a>.<\/li>\n<\/ol>\n<p>Submission occurs by uploading <a href=\"https:\/\/www.json.org\/json-en.html\">JSON<\/a> data. System errors or basic validation issues are reported immediately, with any data validation errors available via a status request. After successful processing, the ClinVar accession numbers become available and the records are published within a week.<\/p>\n<p>Join your Pittsburgh research colleagues who are already active members of the ClinVar community and submit your own variant data. To see examples, check out submissions from: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/submitters\/506557\/\">Magee-Womens Research Institute<\/a>, <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/submitters\/507465\/\">Pittsburgh Clinical Genomics Laboratory<\/a>, <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/submitters\/506882\/\">Pittsburgh Institute for Neurodegenerative Disease\/Palladino Lab<\/a>, and the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/submitters\/500303\/\">University of Pittsburgh\/Rajkovic Lab<\/a>.<\/p>\n<p>If you have questions about how to search ClinVar and understanding its data display, explore the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/docs\/faq\/\">ClinVar FAQ<\/a> or <a href=\"https:\/\/www.hsls.pitt.edu\/data-services\/contact\">contact HSLS Data Services<\/a>.<\/p>\n<p>~Carrie Iwema<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Do you work with human genetic variants? Have you sought out relevant publications, clinically significant evidence, and\/or publicly available data? Are you ready to contribute to the scientific and patient-care community by sharing your own research output? You likely already know about and use ClinVar, the go-to resource for the clinical genetics community that aggregates [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"issue-archives","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[167],"tags":[80,-1],"class_list":["post-13810","post","type-post","status-publish","format-standard","hentry","category-august-2021","tag-data-management","avhec_catgroup-issue-archives"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/13810","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/comments?post=13810"}],"version-history":[{"count":4,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/13810\/revisions"}],"predecessor-version":[{"id":13843,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/13810\/revisions\/13843"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/media?parent=13810"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/categories?post=13810"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/tags?post=13810"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}