Import of different versions of same ontology causes issues

[GoogleCodeExporter]

[reported by Mauricio Almeida at 
http://groups.google.com/group/information-ontology/msg/7e135221bb037eda]

Opening the IAO file on its own doesn't present any issue, problems start when 
I try to import IDO for example.
I believe the issue to be caused by IDO and IAO both importing 
ontology-metadata.owl, but different versions. This creates a problem when 
Protege tries and load the second one, thus an exception "Could not rename 
ontology, an ontology by that name already exists"

IDO gets  http://purl.obolibrary.org/obo/iao/2010-10-26/ontology-metadata.owl
IAO gets  http://purl.obolibrary.org/obo/iao/2009-11-06/ontology-metadata.owl 
(via iao-main.owl)
OGMS gets http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl 
(directly from the dev trunk) 

Would it be possible to update your released files to consistently use 
http://purl.obolibrary.org/obo/iao/ontology-metadata.owl?

Thanks,
Melanie

Original issue reported on code.google.com by mcour...@gmail.com on 17 Aug 2011 at 6:04

[GoogleCodeExporter]

This issue has been resolved.  The current version of OGMS now imports from: 
http://purl.obolibrary.org/obo/iao/ontology-metadata.owl

Also, the script that generates the OWL file from the OBO has been updated 
accordingly.

Original comment by albertgo...@gmail.com on 17 Aug 2011 at 6:40

• Changed state: Fixed

[GoogleCodeExporter]

The IAO/OGMS imports still don't work well together in OWL-API and Protege, see 
[1] for a simple owl file that shows the issue. 

The problem is that "Stable IAO" imports the metadata ontology by using the URL:

http://purl.obolibrary.org/obo/iao/2009-11-06/ontology-metadata.owl

while OGMS now imports it from:

http://purl.obolibrary.org/obo/iao/ontology-metadata.owl

Both of the above URLs resolve (through redirection) to:

http://information-artifact-ontology.googlecode.com/svn/releases/2009-11-06/merg
ed/ontology-metadata.owl

but the OWL-API and Protege can't deal with importing the same ontology from 
two different URLs. There is a bug filed for this [2] but for now no one can 
import IAO and OGMS together in a single ontology because of this issue.  

One solution, I think, is to import the metadata file the same way IAO does it 
in the current stable release. This means that OGMS should import:

http://purl.obolibrary.org/obo/iao/2009-11-06/ontology-metadata.owl

instead of

http://purl.obolibrary.org/obo/iao/ontology-metadata.owl

and then update this import to a newer URL if there is new stable metadata 
release. This will obviously cause problems for other people's ontologies if 
they use another URL for the metadata ontology but, for now, everyone could at 
least import the metadata the same way IAO does it. Hopefully the OWL-API will 
fix this issue soon.

Another option is to not import the metadata ontology directly and either use 
an external owl file, or just let end users import the metadata file if needed.

The workaround for now, as stated in [1], is to first load the metadata file 
from either URLs into Protege (or into OWLOntologyManager if doing this 
programatically) and then load IAO and OGMS. I tried this and it works but end 
users have to know about this trick.

[1] 
https://mailman.stanford.edu/pipermail/p4-feedback/2011-September/004078.html
[2] 
http://sourceforge.net/tracker/?func=detail&aid=3403855&group_id=90989&atid=5955
34

Thanks,
Shahim

Original comment by sha...@essaid.com on 13 Oct 2011 at 8:37