The Informatics Workgroup's dbGaP Data Submission Subgroup has completed work on eleMAP.
This dynamic tool allows researchers to harmonize their local phenotype data dictionaries to existing
metadata and terminology standards such as the caDSR (Cancer Data Standards Registry and Repository),
NCIT (NCI Thesaurus) and SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms). Use this free, online tool to search/browse metadata related to different studies, create new studies (and the related
metadata), and export metadata in Microsoft Excel format. Video and pdf tutorials about eleMAP are available on the eleMAP Tutorial page.
Phenotype KnowledgeBase (PheKB)
The Phenotype Knowledgebase website, PheKB, is a collaborative environment to building and validating electronic phenotype algorithms. The PheKB has both a public component that allows you to view existing phenotypes and implementations and a collaborative component that allows you to submit phenotypes, provide detail about implementations of a phenotype or add to existing phenotypes. For the collaborative component, you will need to register with the site. For additional information on the PheKB, refer to the following slides.
VDART: Demographic Analysis of Risk Toolkit
eMERGE investigator Brad Malin (VU) and his team have completed work on VDART - Vanderbilt Demographic Analysis of Risk Toolkit. This software analyzes the re-identification risk of demographic information remaining in de-identified microdata.
Phenome-Wide Association Studies (PheWAS)
PheWAS methods leverage EMR billing data (ICD9s) to derive case and controls populations. Using this data, a large number of disease phenotypes can be investigated simultaneously against a specified variant or variants. The software and code translation file can be downloaded here.
AMIA CRI Panel on Informatics Activities
During the AMIA CRI Summit on March 10, 2011, eMERGE presented a panel on informatics activities. The panel presentations are publically available:
- "Cross-Institutional Systems to Support Phenotyping in Biomedical Research: Experiences from the eMERGE Network." Panelist: Luke Rasmussen, Marshfield Clinic.
- "Clinical Text Exploration Tools." Panelist: David Carrell, Group Health Cooperative.
- "Clinical Text Processing with Open Source Software." Panelist: Will Thompson, Northwestern University.
- "Portability of NLP Systems - Lessons Learned from MedEx." Panelist: Hua Xu, Vanderbilt University.
- "eleMAP: A Toolkit for Data Dictionary Harmonization and Standardized Representation of Phenotype Data Extracted from Electronic Medical Records." Panelist: Jyoti Pathak, Mayo Clinic.
Additional Network Resources
- Natural Language Processing (NLP) - Survey of Tools and Resources
- eMERGE library - The eMERGE Network has been prolific during its short time as a consortium. Manuscripts currently in publication and involving eMERGE work are being tracked by the eMERGE Coordinating Center. A Zotero library containing all eMERGE manuscripts that have been published since the launch of the network through to the present has been created and is now accessible via the new online eMERGE library. The Coordinating Center will add new entries for additional manuscripts as they are published.
For additional details on how to access and navigate the eMERGE library please view the following user guide.