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Re: LODD: new ChEMBL SPARQL end point, requirements for embedding in LODD?

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Tue, 09 Feb 2010 10:40:30 -0500
Message-ID: <4B7181EE.9090408@openlinksw.com>
To: Egon Willighagen <egon.willighagen@gmail.com>
CC: public-semweb-lifesci <public-semweb-lifesci@w3.org>
Egon Willighagen wrote:
> Hi all,
>
> as indicated on the LODD call, I had some trouble getting the ChEMBL
> SPARQL end point somewhat faster. The end point has move to a new more
> powerful Virtuoso server, also with more sane server settings:
>
> http://chem-bla-ics.blogspot.com/2010/02/chembl-rdf-1sparql-end-point.html
>
> The RDF graph links out to Bio2RDF, and the obvious next step is link
> to in the LODD network...
>
> However, I do not really seem to find requirements... I assume the
> regular LD [0] rules apply? The ChEMBL data is only available as
> SPARQL right now, but it a start... (the rest is a bit of PHP
> wrapping. BTW, anyone aware of a simple PHP lib for that? It's not
> much code, but I rather reuse anyway.)...
>
> Second thing is how to provide links... the InChI is mentioned
> (mis-capatalized at [1], which makes me wonder who I should ask for
> permission to make (minor) changes to the wiki), but many DBs do not
> have URIs which include the InChI, making it rather difficult to link
> to that resource in a general, independent way... that is, there is no
> [2] matching http://www4.wiwiss.fu-berlin.de/drugbank/snorql/?describe=http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00010.
>
> More general, is there a requirement and/or policy on how the
> resources should be linked up?
>
> Looking forward to hearing from you,
>
> Egon
>
> 0.http://www.w3.org/DesignIssues/LinkedData.html
> 1.http://esw.w3.org/topic/HCLSIG/LODD/Data/
> 2.http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/InChI=1/C149H246N44O42S/c1-20-77(13)116(191-122(211)81(17)168-132(221)104(66-113(204)205)178-121(210)79(15)167-123(212)88(152)62-84-39-43-86(198)44-40-84)145(234)185-102(63-83-32-23-22-24-33-83)138(227)193-118(82(18)197)146(235)186-103(65-111(155)202)137(226)189-108(71-196)142(231)182-101(64-85-41-45-87(199)46-42-85)136(225)175-93(38-31-56-165-149(161)162)126(215)174-91(35-26-28-53-151)131(220)190-115(76(11)12)143(232)184-97(58-72(3)4)124(213)166-68-112(203)170-94(47-49-109(153)200)128(217)180-100(61-75(9)10)135(224)188-106(69-194)140(229)169-80(16)120(209)172-92(37-30-55-164-148(159)160)125(214)173-90(34-25-27-52-150)127(216)179-99(60-74(7)8)134(223)181-98(59-73(5)6)133(222)176-95(48-50-110(154)201)129(218)183-105(67-114(206)207)139(228)192-117(78(14)21-2)144(233)177-96(51-57-236-19)130(219)187-107(70-195)141(230)171-89(119(156)208)36-29-54-163-147(157)158/h22-24,32-33,39-46,72-82,88-108,115-118,194-199H,20-21,25-31,34-38,47-71,150-152H2,1-19H3,(H2,153,200)(H2,154,201)(H2,155,202)(H2,156,208)(H,166,213)(H,167,212)(H,168,221)(H,169,229)(H,170,203)(H,171,230)(H,172,209)(H,173,214)(H,174,215)(H,175,225)(H,176,222)(H,177,233)(H,178,210)(H,179,216)(H,180,217)(H,181,223)(H,182,231)(H,183,218)(H,184,232)(H,185,234)(H,186,235)(H,187,219)(H,188,224)(H,189,226)(H,190,220)(H,191,211)(H,192,228)(H,193,227)(H,204,205)(H,206,207)(H4,157,158,163)(H4,159,160,164)(H4,161,162,165)/f/h157,159,161,163-193,204,206H,153-156,158,160,162H2
>
>   
Egon,

Nice to see the progress you're making.

BTW - have you considered installing the Faceted Browser Engine VAD 
[1][2][3]? Once installed you will have this interface [4] added to you 
Linked Data Space -- basically, allowing you to perform some really 
powerful queries using a variety of approaches with Type and Property 
pivoting at your disposal.

Links:

1. 
http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VirtFacetBrowserInstallConfig 
-- installation and config
2. 
http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VirtuosoFacetsViewsLinkedData  
-- Details about Entity Rank feature and pivoting
3. 
http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VirtuosoFacetsWebService  
-- Web Service
4. http://lod.openlinksw.com/fct -- this instance demonstrates how we 
can perform live EAV model pivoting (or faceted navigation) atop an 8.5 
Billion+ quad store (includes: Bio2RDF, NeuroCommons, LODD, DBpedia, and 
other data sets from the LOD cloud), it also allows you conditionally 
enable and apply inference rules (we provide some pre-built rules, and 
can add others on request).


-- 

Regards,

Kingsley Idehen	      
President & CEO 
OpenLink Software     
Web: http://www.openlinksw.com
Weblog: http://www.openlinksw.com/blog/~kidehen
Twitter/Identi.ca: kidehen 
Received on Tuesday, 9 February 2010 15:41:00 GMT

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