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[bioontology-support] FW: BioPortal 2.5 Released

Baker, Nathan Nathan.Baker at
Wed Jun 16 19:25:57 PDT 2010

Hi Paul --

Thanks a lot for your help. Would you mind changing my email address to nathan.baker at

Thanks again,


From: Paul R Alexander <palexander at>
To: Baker, Nathan
Cc: support at <support at>
Sent: Wed Jun 16 18:24:32 2010
Subject: Re: [bioontology-support] FW: BioPortal 2.5 Released


We've just activated notifications and have added you to the subscription list for NPO. The account we have for you is registered with an email address of baker at<mailto:baker at>, so you may want to login to BioPortal to change that if it should be different (or let us know if you have problems and we can change it for you).

Currently we're only sending email notifications when users add notes to an ontology. Please let us know if there are other types of notifications that you would like to receive and we'll see if we can add them.

Let me know if you have any questions.

Paul Alexander
Web / UI Developer
NCBO BioPortal

On 6/9/10 12:37 PM, Baker, Nathan wrote:
Hi All –

I would like to sign up for notifications of new notes/changes for the NanoParticle Ontology.


From: ncbo-everyone-bounces at<mailto:ncbo-everyone-bounces at> [mailto:ncbo-everyone-bounces at] On Behalf Of Trish Whetzel
Sent: Wednesday, June 09, 2010 12:23 PM
To: ncbo-everyone at<mailto:ncbo-everyone at>
Subject: BioPortal 2.5 Released

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<mailto: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

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at<mailto:whetzel at>

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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