Re: [bioportal-announce] NCBO BioPortal 4.0 Released

On 9/25/13 10:49 PM, Ray Fergerson wrote:
>
> We are very happy to finally announce, after a year of planning and 
> development work, the release of the reengineering of BioPortal. 
> Because this is a huge change we care labeling this release BioPortal 4.0.
>
> The primary distinguishing feature of this release is the replacement 
> of several backend storage and caching mechanisms with a single 
> triple-store based backend built with on the open source 4store 
> platform.  In addition we are simultaneously releasing a new version 
> of the BioPortal REST API. This API is also built on top of the triple 
> store. It provides a much more uniform and REST-full interface to the 
> underlying BioPortal data than our previous REST API.
>
> The old API will continue to function through the end of 2013. This 
> API will only be able to access "old content" (that is, ontologies 
> submitted or updated before today).  We encourage API users to 
> transition as quickly as possible to the new API. The new API is the 
> only way to access both new content (submitted after today) and old 
> content. The reports from beta users of the new API have been 
> uniformly positive.  Draft documentation for the new API is available at
>
> http://data.bioontology.org/documentation
>
> BioPortal users will note a few changes from the previous version. 
> Some of these changes are temporary (we didn't quite get everything 
> done...) while others are permanent. There are also a number of minor 
> and cosmetic changes. The list of the more important changes is 
> available below.
>
> With a release of this size, it is inevitable that some bugs have 
> crept in. Please report any that you run across to the 
> support@bioontology.org <mailto:support@bioontology.org> mailing list. 
> Have confidence that we will be working diligently to prioritize and 
> fix the problems that arise.
>
> The NCBO Team
>
> --------------------------
>
> Temporary Changes
>
> -All handling of obsolete classes in UI and API is not supported yet. 
> Obsolete classes are currently indistinguishable from normal classes.
>
> -"Slices" and ontology sets (user defined lists of ontologies of 
> interest) are not supported yet
>
> -The tree browse UI does not yet distinguish between is-a and part-of 
> relations for OBO ontologies. Previously (and probably in the future) 
> icons next to the class name indicated the relationship type.
>
> -We do not yet have a VM version for this release. We expect to 
> produce a new VM version by the end of the year. This VM will include 
> the triple-store based storage mechanism. In addition VM users will be 
> able to query the VM triple-store directly with SPARQL.
>
> -Parsing of new ontologies and new versions remains disabled for the 
> next few days. We will re-enable parsing by early next week.
>
> Permanent Additions
>
> -New ontologies and new versions of ontologies will be typically 
> available for text annotation the next day after submission. 
> Previously the process took several weeks to several months.
>
> -We now have the latest versions UMLS ontologies. Previously we 
> updated UMLS ontologies on request only, which left us with some very 
> old versions. Going forward we will try to update our set of UMLS 
> ontologies within a month of the UMLS release.
>
> Permanent Subtractions
>
> -Programmatic and browse access to classes in non-current versions of 
> ontologies is removed. We still retain metadata about older versions 
> of ontologies and we still allow you to download the source files for 
> old versions.
>
> -We no longer support Protégé Frames format ontologies. Owners of 
> these ontologies will need to convert them to OWL or OBO to load them.
>
> -We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL 
> and OBO ontologies. This API supports OWL version 2.0. For almost all 
> features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases 
> though where ontologies that marginally parsed with an OWL 1.0 parser 
> will not parse at all with the OWL 2.0 parser. We leave it to OWL 
> ontology owners to provide valid OWL 2.0 ontologies.
>
>

Am I correct in assuming that this still isn't a Linked Data offering? I 
say that because of what I get back from:

curl -iLH "Accept: text/turtle" 
http://purl.bioontology.org/ontology/SNOMEDCT/154501005

That returns HTML.

Our Vapour variant for Linked Data verification reports:
http://linkeddata.uriburner.com:8000/vapour?uri=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F154501005&validateRDF=1&defaultResponse=dontmind&userAgent=vapour.sourceforge.net 
.


Re. SPARQL access, what's the SPARQL endpoint URL? I couldn't find that 
in your documentation (of course, I might have just missed it).

-- 

Regards,

Kingsley Idehen	
Founder & CEO
OpenLink Software
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