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

Alejandra Gonzalez Beltran a.gonzalezbeltran at
Mon Aug 9 11:37:59 PDT 2010

Dear Natasha,

Thank you very much for your reply. Please, see my answers in-line below.

On 9 August 2010 18:59, Natasha F. Noy <noy at> wrote:

> Dear Alejandra,
> 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?

> 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.

> 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?

> 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?

Kind regards,


[2] Creating Mappings For Ontologies in Biomedicine: Simple Methods Work
   A. Ghazvinian, N. F. Noy, M. A. Musen
   2009 AMIA Annual Symposium, San Francisco, CA. Published in 2009

> Hope this helps.
> Natasha
> On Aug 8, 2010, at 3:05 AM, Alejandra Gonzalez Beltran wrote:
>  Dear Trish and/or BioPortal support,
>> I am writing to you with respect to BioPortal and in particular, the
>> BioPortal metadata.
>> I have been read your paper [1] and the information I found online on the
>> BioPortal website and the NCBO wiki, about the different functionalities on
>> the website and REST services.
>> In particular, I am interested in the metadata maintained for each of the
>> ontologies and read the information at
>> and I am
>> investigating the BioPortalMetadata.owl.
>> I have not found how I could retrieve the metadata for a particular
>> ontology. Could you please point me to documentation about that? I would
>> like to be able to retrieve the individuals for the BioPortalMetadata
>> ontology for each ontology available in BioPortal.
>> Also, I would like to understand better how you deal with the mappings
>> between ontologies. I have been looking at mappings.rdfs, the mappings
>> through the web interface and the REST service retrieving the mappings. For
>> example, I would like to have more information on the relationship types. Is
>> there any documentation describing mappings.rdfs?
>> Best regards,
>> Alejandra
>> [1] Nucleic Acids Research, 2009, Vol. 37. Web Server Issue.
>>  --
>> Alejandra González-Beltrán, PhD
>> Wolfson Institute of Biomedical Research & Department of Computer Science
>> University College London
>> London WC1E 6BT
>> United Kingdom
>> E-mail: A.GonzalezBeltran at
>> Tel: +44 (0)20 7679 0975 (Direct Dial)
>> Internal:  40975
>> Fax:  +44 (0)20 7209 0470
>> Web:
>> Project Web:
>> On 9 June 2010 20:30, Trish Whetzel <whetzel at> wrote:
>> The National Center for Biomedical Ontology is pleased to announce the
>> release of BioPortal 2.5, a Web-based platform for browsing, visualizing,
>> mapping, and commenting on biomedical ontologies and terminologies.  Our new
>> release of BioPortal includes many new features, Web services, and bug
>> fixes.  BioPortal ( is a comprehensive
>> repository of biomedical ontologies that enables users to access and share
>> ontologies that are actively used in biomedical communities. Users can
>> publish their ontologies in BioPortal, link ontologies to each other, review
>> ontologies and comment on specific terms, list projects that use ontologies,
>> annotate textual metadata with ontologies, and use Web services to
>> incorporate ontologies or their components into their software applications.
>> Major new features in this release include the following:
>> -       Support for structured notes and term requests: Users can now use
>> BioPortal to request that content developers add new terms.  BioPortal
>> provides a structured template for making such requests, allowing users to
>> suggest preferred names, synonyms, and definitions for the requested terms.
>> BioPortal stores the requests as structured notes that are attached to the
>> ontology and that other ontology tools, such as Protégé, will be able to
>> use.
>> -       Support for email notifications to interested parties whenever a
>> BioPortal user creates new notes for an ontology of interest. (If you would
>> like to subscribe to notifications about a particular ontology, please send
>> email to support at  We will have an interactive form to
>> sign-up for notifications shortly.)
>> -       A set of prototype Web services to generate RDF representation for
>> terms in ontologies in BioPortal (see documentation [1] for details).
>> -       A prototype end-point for SPARQL access to all ontologies in
>> BioPortal:
>> -       A set of Web services for retrieving instance information for OWL
>> ontologies [1]. We are planning to release a user interface for viewing
>> instances shortly.
>> -       New ontology widgets that developers can embed on their Web sites,
>> including an ontology tree widget that allows Web-site authors to present a
>> display of an ontology or an ontology subtree for any BioPortal ontology in
>> any Web page.
>> -       A preview release of Bio-Mixer, a mashup tool that provides
>> extremely flexible browsing and exploration of ontologies and their mappings
>>  [1]
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> whetzel at
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>> bioportal-announce at
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Alejandra González-Beltrán, PhD
Wolfson Institute of Biomedical Research & Department of Computer Science
University College London
London WC1E 6BT
United Kingdom

E-mail: A.GonzalezBeltran at
Tel: +44 (0)20 7679 0975 (Direct Dial)
Internal:  40975
Fax:  +44 (0)20 7209 0470
Project Web:
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