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cancerDHC / tools

A repository for the work of the Tools workstream for CCDH
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specify formats for data adhering to CRDC-H model #28

Closed balhoff closed 3 years ago

balhoff commented 3 years ago

This issue can be closed after creating some documentation on how to create structured formats which can be validated with CRDC-H.

Examples should go in the repository created for #27.

This issue is covered by two issues:

balhoff commented 3 years ago

See also #15. It may turn out these issues are the same, but for now this one is specifically about CRDC-H and linkml.

gaurav commented 3 years ago

GDC supports exporting query results as XML and TSV. I think the JSON representation is easier to read, but it's useful to know that these options exist.

PDC does not appear to support this, but it does allow lists of results to be exported as TSV/CSV on their website, so there's probably an API endpoint I haven't found yet to do this.

balhoff commented 3 years ago

A JSON format is produced in https://github.com/cancerDHC/example-data. We have some more work to do formalizing the format possibilities in Phase 3.

gaurav commented 3 years ago

There is a LinkML-CSV package in development for converting instance data from a LinkML model in and out of CSV format, which might be really useful here.

gaurav commented 3 years ago

For our immediate needs, the LinkML instance format (in YAML) seems to be a good representation, and has been developed into some exemplars by the CCDH Data Model Harmonization team as part of the CCDH Pilot. Future formats will probably be supported by adding generators to LinkML, so that data from any LinkML model can be converted into that format (e.g. see the issue tracking an Avro/PFB generator for LinkML). Given that, I think we can close this issue until specific use-cases emerge from CDA and the CRDC nodes.