#2462 purl library updates

[Carrine E. Blank]

Hi Gareth,

Thanks so much to you and your team for incorporating all of my term requests into ChEBI!

I am now trying to use OntoFox to extract parts of ChEBI into my own working ontology (on microbial phenotypic traits and metabolic traits).

I just contacted Oliver He who manages the OntoAnimals and he said that the uses the following purl libraries to keep the ChEBI libraries up-to-date in the OntoAnimal universe:

(Copied from an email from Oliver:)

This appears to be release version:
http://purl.obolibrary.org/obo/chebi.owl
which points to:
http://www.berkeleybop.org/ontologies/chebi.owl
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI Release version 125</rdfs:comment>

So, it appears that the most recent version of ChEBI in the purl libraries is version 125 (and you folks are now on version 131).

Do you know when the purl libraries for ChEBI are to be updated? (Or is there a different address for the purl libraries that Oliver should use?)

Thanks so much for your assistance!

[Gareth Owen]

Hi Carrine,

I have forwarded your message to our developers, who will be able to come up with a more authoritative answer than me!

Best regards,
Gareth

[Chris Mungall]

Carrine,

http://purl.obolibrary.org/obo/chebi.owl now points to the most recent ontology. It should never lag by more than a day

Gareth, you can close this

[Chris Mungall]

Here is text I sent to chebi-dev earlier via email.

Let me explain how this works so you're able to handle this yourself in future. The OBO Foundry documentation is not great but we're working on this.

You can read about OBO purls here:
http://obofoundry.github.io/docs/PURLGuide.html

The chebi-devs should be able to access and edit their purls, and redirect them as you please, you don't need to rely on our jenkins job. You could have the owl purl redirect to the purl on your FTP site. However please don't do this, at least not yet because your modeling and IRI choices are not consistent with GO and this will break things for us. You should be using the official obo to owl translation. This is available as part of the OWL API, or in various command line tools such as ROBOT: https://github.com/ontodev/robot/issues

Currently your .obo and .owl purl redirects to berkeleybop.org/ontologies and you're welcome to keep doing this. You are in control of what gets placed here. If you go to your metadata entry:

• http://obofoundry.github.io/ontology/chebi.html

And then click "View" or "Edit" on the bottom left you can see and edit your metadata entry. In it you will see this chunk:

build:
  source_url: http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip
  path: archive/main
  method: archive
  infallible: 1

This tells the OBO central build to get the obo and owl files from this job: http://build.berkeleybop.org/job/build-chebi/ This job polls your ftp site daily (this was stalled but now fixed).

For more, see the FAQ entry:
http://obofoundry.github.io/faq/what-is-the-build-field.html

So you can intercept this anywhere you please. You can redirect at the purl level and ignore the rest. But don't do this until your comfortable with standard releases. I think you should just keep using what's in place for now, I just wanted to make what is happening more transparent.

[Gareth Owen]

Hi Chris,

Thanks for sorting this out and for explaining how it all works!

Kind regards,
Gareth