reactome

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Alexander Garcia Castro

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Jun 26, 2017, 11:51:49 AM6/26/17
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Is the reactome bio2rdf endpoint alive? I cant access it. 

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Michel Dumontier

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Jun 26, 2017, 6:29:21 PM6/26/17
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no, the laval site was hosting reactome, and it not functional. Does reactome not have an RDF endpoint?

m.

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Simon Jupp

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Jun 26, 2017, 9:38:39 PM6/26/17
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Yes, reactome is available from here http://www.ebi.ac.uk/rdf/services/reactome/sparql

The version in there is a little bit out of date, but you can get the latest version in the new consolidated SPARQL endpoint that will be released very soon - beta is available here http://wwwdev.ebi.ac.uk/rdf/services/sparql

Simon

Kingsley Idehen

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Jun 27, 2017, 9:53:51 AM6/27/17
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On 6/26/17 9:38 PM, Simon Jupp wrote:
Yes, reactome is available from here http://www.ebi.ac.uk/rdf/services/reactome/sparql

The version in there is a little bit out of date, but you can get the latest version in the new consolidated SPARQL endpoint that will be released very soon - beta is available here http://wwwdev.ebi.ac.uk/rdf/services/sparql

Simon

Simon,

Note that the doc identified by <http://wwwdev.ebi.ac.uk/services/sparql> doesn't include an actual listing of SPARQL endpoints.

Are you are part of EMBL-EBI ?

Kingsley
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Simon Jupp

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Jun 27, 2017, 10:42:34 AM6/27/17
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Hi Kingsley, 

Yes, I'm at the EBI and responsible for the RDF platform, what are you looking for exactly? We are moving to a model where we only have a single sparql endpoint with multiple datasets loaded, you can find the list of datasets here http://wwwdev.ebi.ac.uk/rdf/datasets/.  We also have full HCLS VoID for all 
datasets loaded into the platform. 


Simon 

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Kingsley Idehen

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Jun 27, 2017, 11:34:17 AM6/27/17
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On 6/27/17 10:42 AM, Simon Jupp wrote:
Hi Kingsley, 

Yes, I'm at the EBI and responsible for the RDF platform, what are you looking for exactly? We are moving to a model where we only have a single sparql endpoint with multiple datasets loaded, you can find the list of datasets here http://wwwdev.ebi.ac.uk/rdf/datasets/.  We also have full HCLS VoID for all 
datasets loaded into the platform. 


Simon

Simon,

If you only have a single SPARQL endpoint, there is nothing to change bar possibly listing the relevant named graphs used to partition the datasets :)

Kingsley
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Kingsley Idehen

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Jun 27, 2017, 11:40:26 AM6/27/17
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On 6/27/17 10:42 AM, Simon Jupp wrote:
Hi Kingsley, 

Yes, I'm at the EBI and responsible for the RDF platform, what are you looking for exactly? We are moving to a model where we only have a single sparql endpoint with multiple datasets loaded, you can find the list of datasets here http://wwwdev.ebi.ac.uk/rdf/datasets/.  We also have full HCLS VoID for all 
datasets loaded into the platform. 


Simon 

On Tue, Jun 27, 2017 at 9:53 AM, Kingsley Idehen <kid...@openlinksw.com> wrote:
On 6/26/17 9:38 PM, Simon Jupp wrote:
Yes, reactome is available from here http://www.ebi.ac.uk/rdf/services/reactome/sparql

The version in there is a little bit out of date, but you can get the latest version in the new consolidated SPARQL endpoint that will be released very soon - beta is available here http://wwwdev.ebi.ac.uk/rdf/services/sparql

Simon

 Simon,

Note that the doc identified by <http://wwwdev.ebi.ac.uk/services/sparql> doesn't include an actual listing of SPARQL endpoints.

Are you are part of EMBL-EBI ?

Kingsley

Looking further, given the following at <http://wwwdev.ebi.ac.uk/rdf/datasets/#BulkDownloads> .

Bulk Download

Our RDF datasets can be downloaded via ftp. The exact paths can be obtained with SPARQL queries over the dataset descriptions (VoID files).

Would it be possible to add any of the following to the HTML content?

1. <link/> relation in <head/> that has URI identifying each VoID documents as object of xhv:related (or schema:relatedLink or skos:related) relation?

2. <script/> rendition of the above using JSON-LD or RDF-Turtle -- nothing wrong with both, for maximum compatibility with data consumers.

Simon Jupp

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Jun 27, 2017, 12:09:42 PM6/27/17
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The datasets page is dynamically generated based on the datasets present, the SPARQL endpoint also has a tab called "named graphs" that lists these, but the list is quite long as some of the datasets are partitioned into multiple graphs e.g ensembl is split by species. 

Simon Jupp

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Jun 27, 2017, 12:23:13 PM6/27/17
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Yep, we're also looking at providing JSON-LD in webpages for describing datasets as part of bioschemas.org


Thanks
Simon


Kingsley Idehen

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Jun 30, 2017, 3:24:50 PM6/30/17
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Simon and others,

If you have a sizeable Virtuoso instance (i.e., 2 Billion+ Triples),
please notify me about your desire to add your config to the spreadsheet at:
https://docs.google.com/spreadsheets/d/1-stlTC_WJmMU3xA_NxA1tSLHw6_sbpjff-5OITtrbFw/edit#gid=812792186


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