Question regarding evidence information in GlyGen RDF data

[ReneRanzinger]

Hi Jeet and Rene,

We've been trying to organize the evidence information for glycoproteins and were as such trying to use the SPARQL endpoint to query the GlyGen data. GlycoRDF (GlycoCoO) has the glycan:published_in predicate for this purpose, to indicate evidence for a particular glycosylation site to be glycosylated by a particular glycan structure. However, we couldn't find any such triples, and instead found many Evidence classes in your triples which only were found as Objects to Subjects that were Proteins, and not Sites. Could you tell me if you have such data in GlyGen (publication evidence for glycans at particular sites), and if so, how we could obtain them from your RDF endpoint?

Thanks in advance, Kiyoko

[ReneRanzinger]

It looks like the data model has to change and add additional glycan:has_evidence predicate that connects gco:Glyosylation_Site and glycan:Evidence. Best, Robel

[ReneRanzinger]

Hi Kiyoko,

Hope you are doing well.

There is a big chunk of data that is yet to be RDFised and because of that, there are several triples currently missing in the current triple store. We had briefly discussed this before, but it did not make it to the release priority task list. However, this is a priority now and will be a part of the 2.1 release (to be released June-July). We are towards the end of 2.0 release and cannot accommodate this big task of updating the triple store. The information you are looking for is available to access via the APIs. I can provide you with additional details of the API if needed.

I am also attaching the current GlyGen RDF datamodel.

[ReneRanzinger]

This will be updated in 2.1 as part of #248 .