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 <kide...@openlinksw.com <mailto:kide...@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 <kide...@openlinksw.com <mailto:kide...@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 <kide...@openlinksw.com <mailto:kide...@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.ferger...@stanford.edu <mailto:ray.ferger...@stanford.edu>> Date: Tue, Apr 10, 2012 at 10:01 PM Subject: [bioportal-announce] BioPortal 3.7 Released To: annou...@bioontology.org <mailto:annou...@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-annou...@lists.stanford.edu <mailto:bioportal-annou...@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 UniversityChair, W3C Semantic Web for Health Care and the Life Sciences Interest Grouphttp://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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