some links still pointed to googlecode, need to be fixed

[zhengj2007]

In ogms.owl (http://purl.obofoundry.org/obo/ogms.owl, redirect to https://raw.githubusercontent.com/OGMS/ogms/master/src/ontology/ogms.owl), its xml namespace and base still pointed to googlecode: <rdf:RDF xmlns="http://ogms.googlecode.com/svn/trunk/src/ontology/ogms.owl#" xml:base="http://ogms.googlecode.com/svn/trunk/src/ontology/ogms.owl" xmlns:dc="http://purl.org/dc/elements/1.1/" ...

It causes problem when ontobee server load the ontology. It needs to be fixed. In addition, I think the link shown above (https://raw.githubusercontent.com/OGMS/ogms/master/src/ontology/ogms.owl) suppose to be development version. The links should point to a release version.

In addition, OGMS purl configuration files also have many googlecode links need to be updated (https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/ogms.yml).

The release directory is empty. The release version of OGMS files migrated from google code need to be added in. So, the PURL versionIRI can be updated and solved on OGMS github project site.

[cmungall]

In ogms.owl (http://purl.obofoundry.org/obo/ogms.owl, redirect to

I think you mean http://purl.obolibrary.org/obo/ogms.owl

its xml namespace and base still pointed to googlecode:

This should not be a problem, as the base tag is not actually used. The ontology parses file using OWLAPI and RDF libs. Is ontobee doing some dark magic with XML parsing? If so this should be documented.

The OGMS RDF/XML should probably still be fixed for aesthetic reasons, but it's important we don't have undocumented dependencies in tools like ontobee.

In addition, OGMS purl configuration files also have many googlecode links need to be updated

+1

[e4ong1031]

@cmungall

The Ontobee script uses OWLAPI to merge ontology imports. When loading OGMS with OWLAPI version 4.1.4, the following error returned: java.io.FileNotFoundException: http://ogms.googlecode.com/svn/trunk/src/ontology/ogms.owl

After changing the XML namespace and base, the script proceeds without error.

[cmungall]

Hmm, this isn't making much sense.

This works fine:

owltools http://purl.obolibrary.org/obo/ogms.owl

Which is as predicted, as the xml:base isn't used. The error your seeing should only happen if there is a problem with the imports, and the imports are:

   <!ENTITY obo "http://purl.obolibrary.org/obo/" >
 ...
        <owl:imports rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
        <owl:imports rdf:resource="&obo;bfo.owl"/>
        <owl:imports rdf:resource="&obo;iao/dev/ontology-metadata.owl"/>

Can you point to the loading code?

[e4ong1031]

@zhengj2007 I re-run the Ontobee upload script with the downloaded OGMS source file without modifying the XML namespace, and the script actually runs smoothly without any error. The real cause of the upload failure is this file: https://github.com/OGMS/ogms/blob/master/src/ontology/catalog-v001.xml.

@cmungall You are right, it is not the XML namespace causing the problem.

The Ontobee uploading script will look for possible mapping before merging the ontologies.

Using OGMS as an example: The OWL source file is here: https://raw.githubusercontent.com/OGMS/ogms/master/src/ontology/ogms.owl. So the script also tries to download this file for mapping: https://raw.githubusercontent.com/OGMS/ogms/master/src/ontology/catalog-v001.xml.

In the catalog-v001.xml, there is a line: <uri id="Automatically generated entry, Timestamp=1445396160362" name="http://ogms.googlecode.com/svn/trunk/src/ontology/ogms.owl" uri="ogms.owl"/>

This will create a mapping from "ogms.owl" to googlecode, and overwrite the GitHub URL when the script loads the ontology.

[zhengj2007]

@e4ong1031 Thanks for investigating it.

I will bring the issue for discussion in next OGMS call. If no objection, I will update catalog-v001.xml, ogms.owl and ogms.yml files.

[zhengj2007]

@BAevermann Could you please update the ontology information in the ogms.owl for this release?

For example, The OGMS developer site is http://code.google.com/p/ogms/ need to update to GitHub repo.

Besides, Could you please also update OGMS purl configuration file ogms.yml on this release?

The OGMS version IRI still pointed to google project files. So, all these version IRIs do not work, for example, http://purl.obolibrary.org/obo/ogms/2011-09-20/ogms.owl

Thanks!

[BAevermann]

I think most of these tasks have been handled. The developer version has not been officially formulated yet, but I think that is in the offing. Can I close ticket?