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Re: Fwd: [bioportal-announce] BioPortal 3.7 Released

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Fri, 13 Apr 2012 16:20:38 -0400
Message-ID: <4F888A96.7020706@openlinksw.com>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
CC: public-semweb-lifesci@w3.org
On 4/13/12 4:13 PM, M. Scott Marshall wrote:
> Looks like you found it. For others interested, it can be found as a
> New Account link on this page:
> http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal

I do have a concern though, when writing SPARQL-FED I now have to figure 
out URL patterns for every SPARQL endpoint that does this. Why hasn't 
this been presented to the SPARQL group as a potential tweak of the 
SPARQL protocol? In addition, if you adopt WebID as an authentication 
mechanism you won't even have this problem at all i.e., no spec changes 
to SPARQL, it will just work, and you can control or track usage of the 
endpoint.

Link:

1. http://www.openlinksw.com/dataspace/dav/wiki/Main/VirtAuthFOAFSSLACL 
-- example of WebID protecting a SPARQL endpoint


Kingsley
>
> -Scott
>
> On Fri, Apr 13, 2012 at 10:10 PM, Kingsley Idehen
> <kidehen@openlinksw.com>  wrote:
>> On 4/12/12 6:12 PM, M. Scott Marshall wrote:
>>> Hi Kingsley,
>>>
>>> Quick tip from Trish:
>>>
>>> Using the example, add the API Key to this line:
>>> SERVICE<http://sparql.bioontology.org/sparql?apikey=YourAPIKey
>>>
>>> NCBO started to require a (free on request) APIKey to use their
>>> services some time ago (I think that the announcement was sent to this
>>> list). It helps them track how their services are being used and, of
>>> course, prevents Denial of Service attacks. Come to think of it, they
>>> might be interested in considering how to use WebID instead.
>>>
>>> Hope that helps,
>>> Scott
>>
>> Okay!
>>
>> Found the API Key following account creation.
>>
>> Link: http://bioportal.bioontology.org/accounts/new .
>>
>> Kingsley
>>
>>> On Thu, Apr 12, 2012 at 10:33 PM, Kingsley Idehen
>>> <kidehen@openlinksw.com>    wrote:
>>>> On 4/10/12 5:06 PM, M. Scott Marshall wrote:
>>>>> Note that the BioPortal SPARQL endpoint has moved into beta. It has a
>>>>> (web) user interface, documentation, and example queries:
>>>>>
>>>>> http://sparql.bioontology.org/
>>>>>
>>>>> Nice!
>>>>>
>>>>> -Scott
>>>>
>>>> Do I need an API Key to access the SPARQL endpoint?
>>>>
>>>> Please try this SPARQL-FED from: http://uriburner.com/sparql .
>>>>
>>>> PREFIX meta:<http://bioportal.bioontology.org/metadata/def/>
>>>> SELECT DISTINCT *
>>>> WHERE { SERVICE<http://sparql.bioontology.org/sparql>
>>>>           {
>>>>             SELECT DISTINCT ?vrtID ?graph
>>>>             WHERE {
>>>>                     ?vrtID meta:hasVersion ?version .
>>>>                     ?version meta:hasDataGraph ?graph .
>>>>                   }
>>>>            LIMIT 5
>>>>          }
>>>>       }
>>>>
>>>>
>>>> Actual SPARQL Protocol URL: http://uriburner.com/c/IHLEVT .
>>>>
>>>> It returns: 403 FORBIDEN - Apikey not provided .
>>>>
>>>> Am I doing something wrong e.g., not actually talking to a SPARQL
>>>> endpoint
>>>> etc?
>>>>
>>>>
>>>> Kingsley
>>>>
>>>>> ---------- Forwarded message ----------
>>>>> From: Ray Fergerson<ray.fergerson@stanford.edu>
>>>>> Date: Tue, Apr 10, 2012 at 10:01 PM
>>>>> Subject: [bioportal-announce] BioPortal 3.7 Released
>>>>> To: announce@bioontology.org
>>>>>
>>>>>
>>>>> We are pleased to announce the release of BioPortal 3.7. The major new
>>>>> features in this release are:
>>>>>
>>>>>
>>>>>
>>>>> ·         The term search web service and UI now supports some simple
>>>>> Boolean logic. The format is backwards compatible with our previous
>>>>> format so entering “heart attack” still results in terms which contain
>>>>> both words (a logical AND). Negation is indicated with a minus sign
>>>>> prefix (as in Google search). For example, searching on “heart attack
>>>>> –fear –anxiety” returns terms containing both “heart” and “attack” but
>>>>> not those that refer to a “fear of a heart attack” or “anxiety about a
>>>>> heart attack”. A logical OR is achieved by enclosing words in
>>>>> parenthesis. For example “(heart attack)” returns terms which contain
>>>>> either “heart” or “attack”. *
>>>>>
>>>>>
>>>>>
>>>>> ·         We have regenerated all lexical mappings (“LOOM mappings”)
>>>>> between all terms in all ontologies. The mapping algorithm creates a
>>>>> mapping between two terms if the names of the two terms are identical
>>>>> except for case and spacing. LOOM mappings are created between terms
>>>>> if there is a match between the preferred name of one term and the
>>>>> preferred name or synonym of another term. *
>>>>>
>>>>>
>>>>>
>>>>> ·         We now have a beta version of an RDF triple store up and
>>>>> available for use. (The alpha version is no longer available.) This
>>>>> service provides direct SPARQL access to the ontologies in BioPortal.
>>>>> A demonstration user interface with SPARQL examples is available at
>>>>> http://sparql.bioontology.org. This triple store contains all
>>>>> ontologies available in BioPortal (updated nightly). *
>>>>>
>>>>> * This item was requested via the User Support mailing list and the
>>>>> NCBO User Group. Thank you for your comments and suggestions!
>>>>>
>>>>> Ray
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> bioportal-announce mailing list
>>>>> bioportal-announce@lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioportal-announce
>>>>>
>>>>>
>>>> --
>>>>
>>>> Regards,
>>>>
>>>> Kingsley Idehen
>>>> Founder&      CEO
>>>> OpenLink Software
>>>> Company Web: http://www.openlinksw.com
>>>> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
>>>> Twitter/Identi.ca handle: @kidehen
>>>> Google+ Profile: https://plus.google.com/112399767740508618350/about
>>>> LinkedIn Profile: http://www.linkedin.com/in/kidehen
>>
>>
>> --
>>
>> Regards,
>>
>> Kingsley Idehen
>> Founder&    CEO
>> OpenLink Software
>> Company Web: http://www.openlinksw.com
>> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
>> Twitter/Identi.ca handle: @kidehen
>> Google+ Profile: https://plus.google.com/112399767740508618350/about
>> LinkedIn Profile: http://www.linkedin.com/in/kidehen


-- 

Regards,

Kingsley Idehen	
Founder&  CEO
OpenLink Software
Company Web: http://www.openlinksw.com
Personal Weblog: http://www.openlinksw.com/blog/~kidehen
Twitter/Identi.ca handle: @kidehen
Google+ Profile: https://plus.google.com/112399767740508618350/about
LinkedIn Profile: http://www.linkedin.com/in/kidehen








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