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

Trish Whetzel whetzel at
Tue Jun 15 18:17:39 PDT 2010

Hi Uday,

The issue is now resolved.


On Jun 11, 2010, at 3:19 PM, Trish Whetzel wrote:

> Hi Uday,
> I reported this as an urgent bug for the developers to investigate  
> further. We'll let you know when this is resolved.
> Trish
> On Jun 11, 2010, at 8:09 AM, Uday Shanker Evani wrote:
>> Hi Trish,
>> This is Uday Evani from the Buck Institute. We noticed that  
>> BioPortal text annotator is not returning back gene ontology terms.  
>> Do you know what's going on?
>> Thanks
>> Uday
>> Trish Whetzel 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 <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
>>> [1]
>>> Trish Whetzel, PhD
>>> Outreach Coordinator
>>> The National Center for Biomedical Ontology
>>> Ph: 650-721-2378
>>> whetzel at <mailto:whetzel at>
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