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

Alejandra Gonzalez-Beltran a.gonzalezbeltran at
Tue Aug 10 12:12:56 PDT 2010

Thanks again for your prompt reply. I am including answers to your
questions below.

On 10/08/2010 01:17, Natasha F. Noy wrote:
>>> 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:
>> 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
> but internally it was stored as OMV:version...

I see. I will work with the information retrieved, then.

>>> 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?

I downloaded the file from:

which I accessed from:

I am using Protege 4.1. beta - the latest version I found.

I am still having the same problem and cannot open the file. I will try
with a previous version of Protege.

>>> On the mappings: take a look at a page that we recently added to our
>>> wiki:
>> 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.

I had contacted Amir a couple of days ago, so I will wait for the response.

Thank you very much for your help.


> Natasha

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