2019-06-19 JUN
Research with Medical Records
A few of us (particularly those in Connect) may be at Creating Connections: Advances in the Research Use of Electronic Health Records this Wednesday, so we have an open agenda for those at the hackaton.
Useful data resources discussed at the meeting:
- https://mimic.physionet.org ... or not, notice interoperability model does not support REST API.
Cloud4Bio Gitter
Enough people are attending the weekly hackaton now that we could use a messaging service. Here we go, https://gitter.im/cloud4bio/community, let's make sure everybody is set up (Bhaumik).
We need to pick a log tool to integrate with gitter and other dev tools ...
To Jira or not to Jira
That is the question Geeta will explore with us.
...
Linked data
As Connect develops questionnaires, it needs to abide by a referential framework. Instead of conventional ontologies of old, we'll give linked data a try. A bit of historic reference by the same TBL that invented the Web
https://www.w3.org/DesignIssues/LinkedData.html
RDF has since given way to JSON as a preferred serialization
Two important things to explore:
- JSON-LD's Playground: https://json-ld.org/playground
- https://schema.org
Open agenda ... (i.e. fill it or adjourn early :-) )
One small thing...
NBDC/DBCLS BioHackathon 2019 Team Proposal (Accepted)
We will create a cloud-native server instance that translates background genetic screening arrays to common haplotypes/haploblocks, annotates variants from those haplotypes, and records them in EMRs as rdf or json in a fhir-compliant reports.
Global Screening Arrays and similar platforms are becoming ubiquitous and even available on the consumer market (23 and me, ancestry.com), and exonic and whole genome sequencing are becoming more common in the medical arena. I propose to lead a team to build a FHIR compatible server instance that takes in bam or vcf files and assigns population-level haploblocks to them, then returning them to FHIR-compliant EMRs as observations, with variant annotations, when and where appropriate. We will use the personal genome project (https://pgp.med.harvard.edu/data) as example data to initiate this project.
Previous work in this area includes:
https://github.com/NCBI-Hackathons/PrecisionMedicineToolkit
https://github.com/NCBI-Hackathons/TheHumanPangenome
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071752/ **
http://www.hl7.org/special/committees/clingenomics/ **
https://github.com/NCBI-Hackathons/HaploCravat
As you can see, it'd be cool to build this on some of @jonas' work with TCGA. Let me know if anyone wants in on this project.
