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

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Fri, 13 Apr 2012 17:53:08 -0400
Message-ID: <4F88A044.30707@openlinksw.com>
To: public-semweb-lifesci@w3.org
On 4/13/12 4:38 PM, Michel Dumontier wrote:
> Hi Kingsley,
>   Ya, at the NCBO hackathon i tried a variety of tools with the NCBO 
> SPARQL endpoint, and the addition of the api_key=x parameter in the 
> SPARQL URL wasn't always welcome (e.g. Relfinder would automatically 
> append a '?' to whatever you put as a URL), but others like SILK 
> either accept the extended URL or have an explicit parameter field.
>   So, with the webid - do you have examples where this can be used 
> programmatically (e.g. with a perl/java/php script)? You see, there's 
> no need for the apikey if you use their interface.

A WebID will challenge you to present an X.509 certificate that holds 
your personal URI in its SAN, re. human driving browser making SPARQL 
calls.

Via cURL you simply use a .pem file in your call, that's it.

The above applies all the time, the SPARQL calls are just over HTTPS as 
opposed to HTTP. 100% unobtrusive, webby, and follow-your-nose friendly :-)


Kingsley
>
> m.
>
> On Fri, Apr 13, 2012 at 2:20 PM, Kingsley Idehen 
> <kidehen@openlinksw.com <mailto:kidehen@openlinksw.com>> wrote:
>
>     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 <mailto: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
>                 <mailto: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
>                         <mailto:ray.fergerson@stanford.edu>>
>                         Date: Tue, Apr 10, 2012 at 10:01 PM
>                         Subject: [bioportal-announce] BioPortal 3.7
>                         Released
>                         To: announce@bioontology.org
>                         <mailto: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
>                         <mailto: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
>                     <http://www.openlinksw.com/blog/%7Ekidehen>
>                     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
>             <http://www.openlinksw.com/blog/%7Ekidehen>
>             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
>     <http://www.openlinksw.com/blog/%7Ekidehen>
>     Twitter/Identi.ca handle: @kidehen
>     Google+ Profile: https://plus.google.com/112399767740508618350/about
>     LinkedIn Profile: http://www.linkedin.com/in/kidehen
>
>
>
>
>
>
>
>
>
> -- 
> Michel Dumontier
> Associate Professor of Bioinformatics, Carleton University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest 
> Group
> http://dumontierlab.com
>


-- 

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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