Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Trish Whetzel whetzel at
Fri Jun 18 16:10:02 PDT 2010

Hi Emily,

SNOMED is being re-processed and is not currently available due to the  
previous error.  We'll keep you posted on when that will be available.


On Jun 18, 2010, at 3:37 PM, Emily Howe wrote:

> Hi Trish,
> We also noticed Snomed is not an option on the BioPortal text  
> annotator.  Is that a bug or on purpose?
> Thanks
> Emily
> ________________________________________
> From: Trish Whetzel [whetzel at]
> Sent: Friday, June 11, 2010 3:19 PM
> To: Uday Evani
> Cc: Emily Howe; support
> Subject: Re: [bioportal-announce] BioPortal 2.5 Released
> 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>

More information about the bioontology-support mailing list