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

Alejandra Gonzalez Beltran a.gonzalezbeltran at
Sun Aug 8 03:05:53 PDT 2010

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,


[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
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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