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monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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Define a set of basic principles for all source ingests #2

Open matentzn opened 3 years ago

matentzn commented 3 years ago
  1. A QC check for the output (what properties are used, reasoner coherence, etc)
  2. A GitHub action (#104) that runs once per X to update the source
  3. A Makefile that can be fully executed inside the ODK docker container to generate the output
  4. The final output is milled through ROBOT merge/convert (to RDF/XML)
  5. An exclude list for terms we don't want (txt)
  6. An exclude query for terms we don't want (sparql)
matentzn commented 3 years ago

After a nice discussion on slack, we will aim for adding all ingests directly into this repo here, rather than having separate repos for all ingests.

joeflack4 commented 2 years ago

Where shall we write these principles or drafts of them? There's an empty "mondo ingest wiki" where that can be done, but maybe elsewhere is good?

matentzn commented 2 years ago

We do not use Wikis anymore due to their lack of portability, but we can open a section in the Mondo docs?

joeflack4 commented 2 years ago

I think GH wiki can be portable, but probably not easy. Mondo docs sounds good tho.

joeflack4 commented 1 year ago

Note to self: (1) is maybe not strictly needed when I/we are creating these initial ingests. Currently, we have some intermediate/indirect way of doing '1', e.g. Mondo has a coherence checker. We may at some point use OAK validate for the pipelines we've written. And Nico may have some other things in mind, but not something to prioritize at this time, and may not be something that I personally will be delegated to work on.