- From: Kingsley Idehen <kidehen@openlinksw.com>
- Date: Fri, 13 Apr 2012 17:53:08 -0400
- To: public-semweb-lifesci@w3.org
- Message-ID: <4F88A044.30707@openlinksw.com>
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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Received on Friday, 13 April 2012 21:53:33 UTC