Comments (12)
Hi @matentzn
I checked the latest indexer run and these seem to be the OBO ontologies we still have a problem with:
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I manually checked most of these. I personally would suggest to restrict OLS to only active ontologies in OBO:
All of these ones you listed here (or most of them, didn't check all) are obsolete, or inactive. OBO Foundry does not recommend the use of non-active ontologies (i.e. they are hidden on https://obofoundry.org/)
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@udp, can you confirm that RO is not having issues anymore, please?
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For that 6.5 GB JSON file, json2csv took 3 minutes and generated 765 MB of CSV
This seems a suspiciously large difference, but I tried gzipping them to see how much ACTUAL data there was and not just repetition:
- The 6.5 GB JSON file compressed to 322 MB.
- The 765 MB of CSV compressed to 285 MB
Those numbers are firmly in the same ballpark so I think no data has been lost, so all of obo foundry is actually pretty tiny depending on how you represent it.
I also tried gzipping ALL of the OLS “downloads” folder from noah, so that’s all the OWL files from OBO and OLS’s ontologies, which also includes lots of obsolete stuff I didn’t index above. That compressed to 886 MB. So all of the data in OLS is actually only 886 MB when compressed!
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For
doid
cto
cvdo
mfmo
ons
ro
upheno
mamo
vario
can you list the import URLs that are not rdfxml? I may be able to fix these with a bit of a sledge hammer.
ogi OBOFoundry/OBOFoundry.github.io#1942
ero (inactive on obo, URL of ontology redirects to website) OBOFoundry/OBOFoundry.github.io#1942
rnao Resolves: http://purl.obolibrary.org/obo/rnao.owl
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@matentzn they were manually checked by me too to make the table. I didn't realise they were obsolete/inactive. However they will be completely absent (= 404) from OLS when we ship OLS4 if we do not load them. Will this an issue?
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In general I am happy with not loading inactive ontologies. However, even if an ontology is inactive, it can still be used and we can not drop its availability - particularly when there seems to be no other alternative. I think MAMO is a good example of this and is used in EBI by the BioModels team.
A way around this is to not load inactive OBO ontologies. In a case like MAMO we can add it to the EBI OLS config with the URL pointing to the file system.
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@henrietteharmse I think your suggestion is the way to go.
Maybe be a bit more conservative for now and only exclude obsolete ontologies from OBO to start with. If you supply me with a list @udp with the remaining (non obsolete, breaking ones), I can maybe reach out to the groups and use OLS inclusions to up their game a bit and fix their ontology.
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@matentzn We currently have an issue with RO. Though the core file is RDF/XML:
https://raw.githubusercontent.com/oborel/obo-relations/master/ro.owl
it imports this file: https://raw.githubusercontent.com/oborel/obo-relations/master/chemical.owl which is in functional syntax.
Issue opened here: oborel/obo-relations#673
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This will be solved soon by @anitacaron, the solution is already there, we just need time to review and implement it.
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For the Human Disease Ontology (doid
), would loading the doid-merged.owl file (http://purl.obolibrary.org/obo/doid/doid-merged.owl), which has all imports loaded in, fix this issue?
@lschriml, fyi.
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The doid file that isn't RDF/XML was our ext.owl file (in OFN). We recently switched it to RDF/XML because other people were experiencing parsing issues (DiseaseOntology/HumanDiseaseOntology#1112).
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