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Need taxonomic rank ontology #6
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@scottcain helpfully provided the following alternative in IRC: https://raw.githubusercontent.com/oborel/obo-relations/master/subsets/ro-chado.obo unfortunately this crashes as well with
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Finally got around to extracting the project. https://github.com/erasche/chado-schema-builder It could? should? move to GMOD probably, but I'm happy to maintain it. |
Thanks! I've enabled debug log (DBSTAG_TRACE env var) and it seems to be related to the "is_a stanza" in ro-chado.obo The error goes away (both in chado 1.23 and 1.31) if I just remove it (and the OBO_REL:is_a appears to be created in the db anyway) : https://raw.githubusercontent.com/abretaud/obo-relations/master/subsets/ro-chado.obo This "is_a" stuff was somewhat discussed in oborel/obo-relations#68 |
@abretaud well....let's use that. Got a copy building now. |
great work @abretaud! :) |
https://cpt.tamu.edu/jenkins/job/Chado-Prebuilt-Schemas/62/console I'm restarting the jobs... hopefully with this fix we'll start being able to use the latest builds instead of ancient ones :D |
Let's cross fingers! Is there a particular reason to use the master branch from chado? Its status looks like it's in-between the 1.23 and 1.31 releases (more than 1.23, but less than 1.31) |
Mostly because it was what I always did. I was just looking into automatically using the version in the output filenames, couldn't figure out why I couldn't find 1.31 anywhere. Glad you noticed this :) |
on master just now. Switching to 1.31 and trying again. |
That's worrying if it fails too on GO... |
Getting closer...
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Builds are now working on https://cpt.tamu.edu/jenkins/job/Chado-Prebuilt-Schemas This is the latest error if anyone has comments on how to grok it.
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Is it possible that another cv added a term called "is_a" and the code you've written is inadvertently using it rather than the one that should be* coming from relationship? That has happened to me in the past. *I'm using "should be" here in the pre-relations ontology sense--when a canonical "is_a" came from the relationship ontology. |
Back! For the oborel/obo-relations#115, the comment from @cybersiddhu is interesting, there would be an additional "is_a" added by the perl obo parser while converting from obo to xml. Could there be a way for stag-storenode.pl to just ignore the duplicate key violations? |
@abretaud ok, server is back too. Sorry about that. Some of the errors were fixed by re-running and removing the is_a/magic statements from scott, but unfortunately did not fix all of them. |
This is done! |
Tripal needs the taxonomic rank ontology to be loaded in chado (required to create an organism from the tripal loader), it's available there: http://purl.obolibrary.org/obo/taxrank.obo
Maybe it could be added to the Chado-Prebuilt-Schemas ?
Also we could replace http://www.obofoundry.org/ro/ro.obo by http://purl.obolibrary.org/obo/ro.obo to fix the 404 error?
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