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

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Fri, 13 Apr 2012 14:38:22 -0600
Message-ID: <CALcEXf6ozkJwmDK2hrQeNFEZHA-wGMee6M9EprNOy3jq6J3Xtw@mail.gmail.com>
To: Kingsley Idehen <kidehen@openlinksw.com>
Cc: "M. Scott Marshall" <mscottmarshall@gmail.com>, public-semweb-lifesci@w3.org
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.

m.

On Fri, Apr 13, 2012 at 2:20 PM, Kingsley Idehen <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<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<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<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<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/<http://bioportal.bioontology.org/metadata/def/>
>>>>> >
>>>>> SELECT DISTINCT *
>>>>> WHERE { SERVICE<http://sparql.**bioontology.org/sparql<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<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<bioportal-announce@lists.stanford.edu>
>>>>>> https://mailman.stanford.edu/**mailman/listinfo/bioportal-**announce<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/~kidehen>
>>>>> Twitter/Identi.ca handle: @kidehen
>>>>> Google+ Profile: https://plus.google.com/**112399767740508618350/about<https://plus.google.com/112399767740508618350/about>
>>>>> LinkedIn Profile: http://www.linkedin.com/in/**kidehen<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/~kidehen>
>>> Twitter/Identi.ca handle: @kidehen
>>> Google+ Profile: https://plus.google.com/**112399767740508618350/about<https://plus.google.com/112399767740508618350/about>
>>> LinkedIn Profile: http://www.linkedin.com/in/**kidehen<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/~kidehen>
> Twitter/Identi.ca handle: @kidehen
> Google+ Profile: https://plus.google.com/**112399767740508618350/about<https://plus.google.com/112399767740508618350/about>
> LinkedIn Profile: http://www.linkedin.com/in/**kidehen<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
Received on Friday, 13 April 2012 20:39:25 GMT

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