{"action":"created","issue":{"url":"https://api.github.com/repos/ResearchSoftwareInstitute/greendatatranslator/issues/114","repository_url":"https://api.github.com/repos/ResearchSoftwareInstitute/greendatatranslator","labels_url":"https://api.github.com/repos/ResearchSoftwareInstitute/greendatatranslator/issues/114/labels{/name}","comments_url":"https://api.github.com/repos/ResearchSoftwareInstitute/greendatatranslator/issues/114/comments","events_url":"https://api.github.com/repos/ResearchSoftwareInstitute/greendatatranslator/issues/114/events","html_url":"https://github.com/ResearchSoftwareInstitute/greendatatranslator/issues/114","id":301525628,"node_id":"MDU6SXNzdWUzMDE1MjU2Mjg=","number":114,"title":"Green Team - NIEHS Collaboration","user":{"login":"karafecho","id":26254388,"node_id":"MDQ6VXNlcjI2MjU0Mzg4","avatar_url":"https://avatars1.githubusercontent.com/u/26254388?v=4","gravatar_id":"","url":"https://api.github.com/users/karafecho","html_url":"https://github.com/karafecho","followers_url":"https://api.github.com/users/karafecho/followers","following_url":"https://api.github.com/users/karafecho/following{/other_user}","gists_url":"https://api.github.com/users/karafecho/gists{/gist_id}","starred_url":"https://api.github.com/users/karafecho/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karafecho/subscriptions","organizations_url":"https://api.github.com/users/karafecho/orgs","repos_url":"https://api.github.com/users/karafecho/repos","events_url":"https://api.github.com/users/karafecho/events{/privacy}","received_events_url":"https://api.github.com/users/karafecho/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"stevencox","id":306971,"node_id":"MDQ6VXNlcjMwNjk3MQ==","avatar_url":"https://avatars0.githubusercontent.com/u/306971?v=4","gravatar_id":"","url":"https://api.github.com/users/stevencox","html_url":"https://github.com/stevencox","followers_url":"https://api.github.com/users/stevencox/followers","following_url":"https://api.github.com/users/stevencox/following{/other_user}","gists_url":"https://api.github.com/users/stevencox/gists{/gist_id}","starred_url":"https://api.github.com/users/stevencox/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stevencox/subscriptions","organizations_url":"https://api.github.com/users/stevencox/orgs","repos_url":"https://api.github.com/users/stevencox/repos","events_url":"https://api.github.com/users/stevencox/events{/privacy}","received_events_url":"https://api.github.com/users/stevencox/received_events","type":"User","site_admin":false},"assignees":[{"login":"stevencox","id":306971,"node_id":"MDQ6VXNlcjMwNjk3MQ==","avatar_url":"https://avatars0.githubusercontent.com/u/306971?v=4","gravatar_id":"","url":"https://api.github.com/users/stevencox","html_url":"https://github.com/stevencox","followers_url":"https://api.github.com/users/stevencox/followers","following_url":"https://api.github.com/users/stevencox/following{/other_user}","gists_url":"https://api.github.com/users/stevencox/gists{/gist_id}","starred_url":"https://api.github.com/users/stevencox/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stevencox/subscriptions","organizations_url":"https://api.github.com/users/stevencox/orgs","repos_url":"https://api.github.com/users/stevencox/repos","events_url":"https://api.github.com/users/stevencox/events{/privacy}","received_events_url":"https://api.github.com/users/stevencox/received_events","type":"User","site_admin":false},{"login":"cpschmitt","id":572797,"node_id":"MDQ6VXNlcjU3Mjc5Nw==","avatar_url":"https://avatars1.githubusercontent.com/u/572797?v=4","gravatar_id":"","url":"https://api.github.com/users/cpschmitt","html_url":"https://github.com/cpschmitt","followers_url":"https://api.github.com/users/cpschmitt/followers","following_url":"https://api.github.com/users/cpschmitt/following{/other_user}","gists_url":"https://api.github.com/users/cpschmitt/gists{/gist_id}","starred_url":"https://api.github.com/users/cpschmitt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cpschmitt/subscriptions","organizations_url":"https://api.github.com/users/cpschmitt/orgs","repos_url":"https://api.github.com/users/cpschmitt/repos","events_url":"https://api.github.com/users/cpschmitt/events{/privacy}","received_events_url":"https://api.github.com/users/cpschmitt/received_events","type":"User","site_admin":false},{"login":"cbizon","id":10744350,"node_id":"MDQ6VXNlcjEwNzQ0MzUw","avatar_url":"https://avatars2.githubusercontent.com/u/10744350?v=4","gravatar_id":"","url":"https://api.github.com/users/cbizon","html_url":"https://github.com/cbizon","followers_url":"https://api.github.com/users/cbizon/followers","following_url":"https://api.github.com/users/cbizon/following{/other_user}","gists_url":"https://api.github.com/users/cbizon/gists{/gist_id}","starred_url":"https://api.github.com/users/cbizon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cbizon/subscriptions","organizations_url":"https://api.github.com/users/cbizon/orgs","repos_url":"https://api.github.com/users/cbizon/repos","events_url":"https://api.github.com/users/cbizon/events{/privacy}","received_events_url":"https://api.github.com/users/cbizon/received_events","type":"User","site_admin":false},{"login":"karafecho","id":26254388,"node_id":"MDQ6VXNlcjI2MjU0Mzg4","avatar_url":"https://avatars1.githubusercontent.com/u/26254388?v=4","gravatar_id":"","url":"https://api.github.com/users/karafecho","html_url":"https://github.com/karafecho","followers_url":"https://api.github.com/users/karafecho/followers","following_url":"https://api.github.com/users/karafecho/following{/other_user}","gists_url":"https://api.github.com/users/karafecho/gists{/gist_id}","starred_url":"https://api.github.com/users/karafecho/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karafecho/subscriptions","organizations_url":"https://api.github.com/users/karafecho/orgs","repos_url":"https://api.github.com/users/karafecho/repos","events_url":"https://api.github.com/users/karafecho/events{/privacy}","received_events_url":"https://api.github.com/users/karafecho/received_events","type":"User","site_admin":false}],"milestone":null,"comments":8,"created_at":"2018-03-01T19:15:49Z","updated_at":"2018-11-12T17:37:44Z","closed_at":null,"author_association":"NONE","body":"This issue involves a new collaboration with Charles Schmitt and Shepherd Schurman of NIEHS to Investigate the use of the Translator/Reasoner architecture in the context of NIEHS clinical data sources (i.e., EPR, CRU), knowledge sources (i.e., Tox21, DrugMatrix), and new toxicology use cases. "},"comment":{"url":"https://api.github.com/repos/ResearchSoftwareInstitute/greendatatranslator/issues/comments/437967489","html_url":"https://github.com/ResearchSoftwareInstitute/greendatatranslator/issues/114#issuecomment-437967489","issue_url":"https://api.github.com/repos/ResearchSoftwareInstitute/greendatatranslator/issues/114","id":437967489,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNzk2NzQ4OQ==","user":{"login":"karafecho","id":26254388,"node_id":"MDQ6VXNlcjI2MjU0Mzg4","avatar_url":"https://avatars1.githubusercontent.com/u/26254388?v=4","gravatar_id":"","url":"https://api.github.com/users/karafecho","html_url":"https://github.com/karafecho","followers_url":"https://api.github.com/users/karafecho/followers","following_url":"https://api.github.com/users/karafecho/following{/other_user}","gists_url":"https://api.github.com/users/karafecho/gists{/gist_id}","starred_url":"https://api.github.com/users/karafecho/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karafecho/subscriptions","organizations_url":"https://api.github.com/users/karafecho/orgs","repos_url":"https://api.github.com/users/karafecho/repos","events_url":"https://api.github.com/users/karafecho/events{/privacy}","received_events_url":"https://api.github.com/users/karafecho/received_events","type":"User","site_admin":false},"created_at":"2018-11-12T17:37:44Z","updated_at":"2018-11-12T17:37:44Z","author_association":"NONE","body":"Update on Green/Gamma collaboration with NIEHS (Charles Schmitt), 11/2/2018:\r\n\r\n1. EPR asthma use case - tagged EPR participants in CDWH for incorporation into ICEES; goal is to replicate a prior study; genome-wide sequencing of all EPR participants is expected to be complete by Fall 2019; targeting overlapping population initially (roughly 5000 patients)\r\n2. EPR immune-mediated disease use case - common risk factors and biological processes across immune-mediated diseases; SMEs to determine risk factors and biological processes; EPR for validation; CTD for clustering on genes, chemicals, diseases/phenotypes; ROBOKOP and neo4j for identifying additional genes, pathway, diseases/phenotypes; ??? tool for visualizing and curating bipartite graphs\r\n3. Tox21 Enricher - associations between chemicals and Tox21 chemicals (10,000), assays (300); includes Drug Matrix, Leadscope; chemical structure similarity capability; toxicity predictions; need to map assays to ontologies; data to be stored at RENCI, NIEHS to develop API and send dictionary of desired data elements\r\n4. Not discussed, but referred to during the meeting: Ilya Baldin’s NSF ImPACT award and ICEES as a use case for secure multiparty computation\r\n\r\n Modification to approved Green Team IRB protocol on asthma-like patients:\r\n \r\nGoal: We seek to add additional patient level data elements to inform the existing research study. The new data elements will include a limited set of genotype calls and responses to two survey questions (EPR Health and Exposure Survey, EPR Exposome Survey) that relate to the current Asthma use case.  The data elements are available from the Environmental Polymorphism Registry (EPR), a longitudinal research study being conducted by the NIEHS.  The EPR has enrolled around 19,000 subjects in North Carolina which includes approximately 5000 subjects who are in the UNC CDW-H (as determined from a prior UNC-NIEHS study).   We plan to add data elements from the EPR to only those subjects that are in the EPR and are in the cohort for this study. \r\n  \r\nThe genotype data is focused on a small set of variants (4 total) that relate to the TLR4 pathway.  The survey questions include a broad range of questions related to environmental exposures and general health.  In a prior EPR-based study, we found significant differences in suspectibility to Asthma for patients based on distance to roadways and based upon their genotype for these variants.  Under this modification, we will extend the existing Asthma analysis to include these genotypes and attempt to confirm the prior findings. We also plan to incorporate the survey questions and genotype data into the existing study analysis in order to uncover potential relationships between Asthma outcomes, clinical data, environmental exposure measures, survey responses, and genotypes.  We note that this work is only meant to extend the set of data elements in the existing study and not to pursue additional research goals.\r\n  \r\nSafeguards:\r\nIn prior work between UNC and EPR, we have developed a method to link records from patients seen at both institutions based upon the use of one way hash codes.  The hash codes are derived from identifying information (age, sex, name, address), although once computed the identifying information is no longer needed and cannot be regenerated from the hash codes.  We plan to use the hash codes to allow linking the existing UNC study data with the EPR data elements.  As UNC and EPR share identical hash codes, we can add the EPR data elements to existing de-identified study data at UNC, thus the EPR data elements will not be added to identified patient records and the NIEHS will not to transfer identifying information to UNC.  EPR will provide the data elements with the hash codes using secure file transfer.\r\n"}}
{"actor":{"display_login":"karafecho"}}