Genomic Epidemiology Entity Mart (GEEM)
The Genomic Epidemiology Entity Mart is a portal we are developing for examining and downloading ontology-driven specifications for standardized data components. The portal aims to provide term reviewers and software developers with ways to utilize application ontology contents without the need to be trained in ontology curation or querying.
- Ontology curators are responsible for crafting the standards within ontology editing platforms like Protege. They periodically provide the resulting OWL files to GEEM for processing.
- Ontology implementers and reviewers view, download, and/or create custom packages of selected ontology defined entities for inclusion in their ontology-driven content and data management software.
- Initially GEEM will offer a few application ontologies for selecting components to make user packages from which can be shared to others on the net. GEEM can also be run as a stand-alone docker package within an agency for internal use only.
The GEEM portal enables an ontology’s categorical and numeric datums and more complex data entities to be viewed as HTML form elements, including term preferred name, definition, synonyms, database cross-references, categorical selection lists, and numeric data entry and validation fields. Specifications for these elements can be generated for reuse by software developers; logged-in users will be able to save selected elements in packages that can be updated and downloaded later in JSON, YAML, or Microsoft Excel format; and finally, a form viewer is provided to show how such specifications can be used to drive data entry and reporting.
GEEM itself does not currently provide a data storage platform – this is left as an implementation detail that will vary among agencies. A future direction for GEEM is to provide conversion tools to enable data management platforms like RedCap and the Cedar Project to benefit from reusable standard definitions for domain specific data collection needs.
View GEEM at https://watson.bccdc.med.ubc.ca/geem/portal.html
A stand-alone GEEM specification form viewer is at https://watson.bccdc.med.ubc.ca/geem/form.html
The development site for GEEM is https://github.com/GenEpiO/geem/
Our poster presentation at ICBO2019 summarizes the current functionality of the platform. Click on image for enlarged PDF view.