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  1. Ontology Representation

    Genomics ontology presents the genetic variants as query-able concepts in the i2b2 web-client. Creating this queryable ontology is a 3-step process: Create … can be queried by rs identifier or by gene name, thus giving a total of 4 concepts. Sample scripts to insert theses 4 concepts in the concept_dimension table can
    i2b2 on Genomics Data • Feb 21, 2018

  2. Analysis Tools

    all Workplace items / objects (folders, queries, patient sets, etc.) containing the terms provided (in either their annotations or their names … the usage of smaller queries of patient subgroups (from a large patient set) iteratively, in place of one single large query of that huge patient set
    i2b2 Web Client • Mar 03, 2019

  3. i2b2 on Genomics Data

    This community project extends the current i2b2 query functionality by providing the ability to query for genotyped subjects by specific annotations related to genetic variants. Also, new query widgets have been built in the i2b2 web client that leverages existing i2b2 infrastructure for querying large strings of text
    i2b2 on Genomics Data • Feb 21, 2018

  4. Roles

    they can run the same query within a specified time period. If the user exceeds the maximum number of times then their account will be locked and only the Admin … are not obfuscated and the user is not limited to the number of times they can run the same query. DATA_LDS LDS = Limited Data Set The user can see
    Server (Cells) Architecture Home • Sep 04, 2018

  5. User Roles

    they can run the same query within a specified time period. If the user exceeds the maximum number of times then their account will be locked and only … are not obfuscated and the user is not limited to the number of times they can run the same query. DATA_LDS LDS = Limited Data Set The user can
    Server (Cells) Architecture Home • Sep 04, 2018

  6. User Role

    is limited on the number of times they can run the same query within a specified time period. If the user exceeds the maximum number of times then their account … . The results are not obfuscated and the user is not limited to the number of times they can run the same query. DATA_LDS LDS = Limited
    Server (Cells) Architecture Home • Sep 04, 2018

  7. i2b2-workshop at AMIA Nov-2020

    Survey 20,000 feet view: Shawn (20 mins) (slides) Data Model and Query Tool:  Jeff (45 minutes) + QA 10  Intro to i2b2 Query Tool Ontologies  Data Model Community Project Highlights (ACT, genomics, etc. Medco?) - i2b2 on OMOP / OMOP to i2b2 Exercise 1: Building a query (demo data) [15 minutes] Ontology
    Additional Tutorials and Documentation • Nov 18, 2020

  8. 6.6.4 Project User Roles

    ). The user is limited on the number of times they can run the same query within a specified time period. If the user exceeds the maximum number of times … the patient count. The results are not obfuscated and the user is not limited to the number of times they can run the same query. DATA_LDS LDS
    Developers Getting Started With i2b2 • Jan 03, 2020

  9. 1.7.09c Release Notes

    contain at least two important fixes that are necessary for you to run SHRINE queries without any issues. Date constraints on SHRINE queries are not save on the local i2b2 side. This causes a problem when users re-run the query as they will receive different results because the constraint no longer exists. Error
    Release Management • May 09, 2018

  10. Loading Genomic VCF Files into i2b2

    genomics_i2b2.png Project Summary   This community project extends the current i2b2 query functionality by providing the ability to query for genotyped subjects by specific annotations related to genetic variants. Also, new query widgets have been built in the i2b2 web client that leverages existing i2b2
    i2b2 on Genomics Data • Feb 21, 2018