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[bioontology-support] [bioportal-announce] BioPortal 2.5 Released

Natasha F. Noy noy at stanford.edu
Mon Aug 9 17:17:44 PDT 2010


>>
>> We are not providing public access to the instances themselves,  
>> mostly for security reasons. Of course you can access all the  
>> information that we store in those instances through our REST  
>> services for accessing ontologies:
>> http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Services_to_access_ontologies_and_ontology_versions
>>
>
> I have seen that documentation on the REST services to access  
> ontologies and ontology versions. However, what I would like to  
> obtain is the metadata about a particular ontology. In other words,  
> I would like to obtain the information corresponding to the Ontology  
> Metadata Vocabular (OMV) as part of the BioPortalMetadata.owl  
> corresponding to a particular ontology. As far as I understand from  
> the link you sent me, there is no service to retrieve the ontology  
> metadata. Or is there?

The service returns you the *content* of the metadata, but not tagged  
with the same properties as in OMV. For instance, we may have  
<versionNumber> in http://rest.bioontology.org/bioportal/ontologies/42838
but internally it was stored as OMV:version...

>>
>> Can I ask you why do you need the instances?
>
>
> I wanted to access the instances of BioPortalMetadata.owl (or  
> instances of the OMV ontology) for two reasons: 1)  I would like to  
> see examples on how this metadata is built and follow the example to  
> build the metadata for an ontology I am working on, 2) I would like  
> to be able to access the metadata of different ontologies  
> programmatically, allowing the user to select what ontology is  
> better from them.

you can do (2) from  the information that you get in the REST service  
results: those give you exactly the information in the metadata --  
just in the different format. As for (1), you can sort of infer the  
same information from the RESt service response. You don't have to  
have it in the form of OWL instances.

>>  Also, on the error that you are getting when trying to open  
>> BioPortalMetadata.owl: which tool are you using? Note that the file  
>> is RDF/OWL 1 file.
>
>
> I am using Protege 4.1. beta. Does Protege 4.1. beta only reads OWL2  
> files and that is the reason of the problem?

No, shouldn't be a problem. And I seem to be able  to open it with  
Protege 4. Could you please, specify where exactly you get the OWL  
file and which version of Protege 4.1 you are using?

>
>> On the mappings: take a look at a page that we recently added to  
>> our wiki:
>> http://www.bioontology.org/wiki/index.php/BioPortal_Mappings
>
>
> Thank you very much for that link - I had not seen it before and it  
> is really useful.
>
> Related to the mappings, I have read the wiki page [1] and your  
> paper [2] on the Lexical OWL Ontology Matcher (LOOM).
> I am interested in using LOOM to create mappings between ontologies.
>
> However, it seems that LOOM also works with Protege 3, as it  
> requires the pprj file.
>
> Could you please let me know what version of Protege should I used  
> for LOOM?
>
> I guess I will not  be able to load ontologies
> developed with Protege 4.1 Beta or the OWLAPI, right?
>
> I do not think I am using any constructs corresponding only to OWL2,  
> but if I am, will this be a problem?


I  think you should be able to load such OWL2 ontology in the protege  
3 API. Write to Amir (the first author on that paper) for details  
about running LOOM.

Natasha





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