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

Natasha F. Noy noy at
Mon Aug 9 10:59:12 PDT 2010

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:

Can I ask you why do you need the 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.

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

Hope this helps.


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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