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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Duplicate "nodes" element in JSON serializtion #897

Closed pnrobinson closed 3 years ago

pnrobinson commented 4 years ago

According to https://github.com/geneontology/obographs the JSON serialization should only contain one "nodes" element, and yet monod.json contains two. The second element seems to contain non-Mondo terms. See line 1570594. 

    "nodes" : [ {
      "id" : "http://purl.obolibrary.org/obo/CHEBI_25699",
joeflack4 commented 3 years ago

I've labeled this needs clarification for now; I'm still not too familiar with this code base.

Questions

  1. @pnrobinson What are you doing (i.e. specific commands) when this happens? That will help me know where to look.
  2. @cmungall @matentzn Or if you guys can point me in a specific direction, that would be helpful. I searched the codebase for "serialization" and "json", but didn't find much outside of some makefile targets.
matentzn commented 3 years ago

This problem is too complicated for the Mondo team to solve, this needs to be moved here: https://github.com/geneontology/obographs/issues

There was a lot of work recently on obographs by @julesjacobsen maybe this issue is solved now.