2019-05-08 MAY
GETex (Oscar)
review of last week's session at ATC ... (Oscar?)
Observable Notebook ready for ATC's notebooks exploring the API: https://observablehq.com/@episphere/gtex
Problem - assemble multi-variable structures for samples and donors.
Oscar found sampleId in histology (https://gtexportal.org/home/api-docs/#!/histology/image), i.e. https://gtexportal.org/rest/v1/histology/image?format=json
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AllofUs (Jonas)
What
1 million participant NIH All-of-Us has announced a data portal: https://databrowser.researchallofus.org/. It is still in Beta and I couldn't find documentation on the API. We can however hacking it out of dev tools: we see the AoU API exists and is RESTful. The data portal is fully decoupled from the data layer :-). See for example https://public.api.researchallofus.org/v1/databrowser/survey-results?survey_concept_id=1586134. Shall we probe further?
Who
This is what WhoIs knows about their API backend: http://whois.domaintools.com/researchallofus.org. Note it is registered by Vanderbilt University through Network Solutions, LLC. It is not a NIH domain.
Questionnaire Commons
Note questionnaire structure in the API call (right). It looks like we have standards for Commons emerging already :-).
Video
One year review of the project at NIH May 7th, 2019: https://videocast.nih.gov/summary.asp?Live=31677&bhcp=1
DCEG API (Praful)
Praful has been developing an API for data ingestion in large cohort studies at DCEG, from demographics to clinical phenotypes, from genomics to images. This will be hosted in Google Cloud Platform so this will be the perfect excuse to review, and try, all that is involved in going from an serverless API to a DSL that operates a large Cloud Platform.
API documentation: https://documenter.getpostman.com/view/3282203/S1LsXq2E
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Computational Medicine Hackathon (Ben)
June 10-11 at Hopkins --
Potential Topics:
Potential topics include:
- Coherent-phenotype mapping to haplotypes
- Mapping haplotype blocks to ontologies
- Structural Variants in Health and Disease
- Haplotypes and RNA-seq
- Complex Variant Structure
- Annotation Structures for Complex Variants
- Visualization of Complex Variants
Announcement and application: https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/08/computational-medicine-in-the-cloud-june-10-11-2019/
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For those wanting to test DCEG's API and write your own analysis and/or interactive dashboards, you can ask for your own key from Praful. Nicole is developing documentation for a connector from SAS, anyone for an R connector?
