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

Trish Whetzel whetzel at
Fri Jun 11 15:19:53 PDT 2010

Hi Uday,

I reported this as an urgent bug for the developers to investigate  
further. We'll let you know when this is resolved.


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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