obo stats

[ebispot]

obo stats

[udp]

Hi @matentzn

I checked the latest indexer run and these seem to be the OBO ontologies we still have a problem with:

ontology id	purl	problem
mamo	http://purl.obolibrary.org/obo/mamo.owl	OWL XML
vario	http://purl.obolibrary.org/obo/vario.owl	OWL ??
gaz	http://purl.obolibrary.org/obo/gaz.obo	OBO
dinto	http://purl.obolibrary.org/obo/dinto.owl	Redirects to the github repo
eo	http://purl.obolibrary.org/obo/eo.owl	Redirects to https://raw.githubusercontent.com/Planteome/plant-environment-ontology/master/plant-environment-ontology.obo.owl which is 404
epo	http://purl.obolibrary.org/obo/epo.owl	Redirects to https://epidemiology-ontology.googlecode.com/files/epidemiology_ontology.owl which is 404
ero	http://purl.obolibrary.org/obo/ero.owl	Redirects to https://open.catalyst.harvard.edu/products/eagle-i/ which is a HTML page not an ontology
flu	http://purl.obolibrary.org/obo/flu.owl	Imports http://purl.obolibrary.org/obo/ido/2010-12-02/ido-main-workaround.owl which is 404
mfo	http://purl.obolibrary.org/obo/mfo.owl	Redirects to https://obofoundry.org/ not an ontology
mirnao	http://purl.obolibrary.org/obo/mirnao.owl	Redirects to http://mirna-ontology.googlecode.com/svn/trunk/src/ontology/mirnao.owl which is 404
mo	http://purl.obolibrary.org/obo/mo.owl	Redirects to http://ontologies.berkeleybop.org/ which is not an ontology
nmr	http://purl.obolibrary.org/obo/nmr.owl	Redirects to http://ontologies.berkeleybop.org/ which is not an ontology
ogi	http://purl.obolibrary.org/obo/ogi.owl	Redirects to https://ontology-for-genetic-interval.googlecode.com/svn/trunk/src/OGI.owl which is 404
sep	http://purl.obolibrary.org/obo/sep.owl	Redirects to http://ontologies.berkeleybop.org/sep.owl NoSuchKey
vhog	http://purl.obolibrary.org/obo/vhog.owl	Redirects to http://ontologies.berkeleybop.org/vhog.owl NoSuchKey

[matentzn]

I manually checked most of these. I personally would suggest to restrict OLS to only active ontologies in OBO:

https://obofoundry.org/

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/)

[anitacaron]

@udp, can you confirm that RO is not having issues anymore, please?

[udp]

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!

[matentzn]

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

[udp]

@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?

[henrietteharmse]

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.

[matentzn]

@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.

[udp]

@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

[matentzn]

This will be solved soon by @anitacaron, the solution is already there, we just need time to review and implement it.

[allenbaron]

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.

[allenbaron]

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).