Project in the Spotlight
In this section, we will highlight one of the Workshop projects. This time, it is the project Data Standards Hackathon coordinated by Martin Maiers.
Detailed project description:
Historically, there have been few standards regarding HLA and KIR genotyping data, and associated meta-data, and very few public tools for the management of these data. Recognizing the tremendous potential of NGS for immunogenomics, and the need for coordinated consolidation of the data for such a broad field, we have organized a series of collaborative software-development events (“hackathons”) focused on the creation of novel tools, standards and services that will maximize the utility of immunogenomic data for clinical and basic research science. These meetings have been supported by the National Marrow Donor Program (NMDP) and several commercial vendors.
During previous Data Standards Hackathon events, participants helped finalize specifications for MIRING, worked on tools implementing it (e.g., HML 1.0, HL7-FHIR), and considered ways how to express novel polymorphisms without human curation (e.g., Gene Feature Enumeration).
We have held 6 hackathons before the 17th IHIW, and have held 3 since then. We have also organized smaller, more focused hackathons to address issues specific to donor registries, in collaboration with the World Marrow Donor Association (WMDA), and focused on Electronic Health Records integration with HL7-FHIR (Health Level 7 – Fast Healthcare Interoperability Resources).
HL7-FHIR is emerging as global standard for health IT and we want to collaborate with laboratories and industry partners to roll out its use for HLA. Getting HLA data in/out of the Electronic Medical Record is a dream that is starting to come true. Not only does it reduce manual entry effort and errors, but it allows us to move from “typing” to “sequencing” by accurately and securely transmitting consensus sequence data to better inform research and medical decision making. Recent work has focused on developing secure “apps” using the SMART-on-FHIR specification (OAuth2) that can plug-in to electronic medical records system to allow secure transmission of complex data (like HLA).
Since the first hackathon in 2014, this project has delivered a number of standards, systems, manuscripts and tools.
There are a number of open problems to be addressed. We have identified a few that are central to the goals of the 17th and 18th IHIWS efforts as they relate to the communication of NGS results.
Suggested topics for this event include
Development of tools for translating between proprietary formats and open standards; specifically: HL7-FHIR and semantic validation.
Automated annotation and curation of sequence variation. Specifically use the GFE system to annotate the consensus sequence data collected as part of the 18th IHIWS.
Validation of population genetics tools. Specifically haplotype frequency estimation (pyPop, Hapl-o-Mat, haplostats, others) and extension to analysis of GFE encoded data
Support for incorporation of HLA into smartphone apps
Software for analysis of MHC and KIR region genomics
Milestones in years:
Data standards Hackathon: WMDA Office, Leiden, Mar 23-24, 2019
Data standards Hackathon: Denver, Colorado May 30-31, 2019
HLA/HL7-FHIR Data Standards Symposium and Hackathon
Minneapolis, MN Aug 21-23, 2019
HL7-FHIR development at HL7-working group meetings and connectathons.