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I swimming the huge sea of semantic Web and Linked Open Data (LOD) to use these knowledge bases for annotating semantically biological experiment of my organisation.

My idea consists of:

  1. RDF-izing my local biological experiment data in my triple store
  2. linking them to references which point to LOD
  3. If some concepts are not available as LOD, completing my virtual KB locally, by creating other types and properties in my triple store linked to the LOD cloud.
  4. Analyzing data through federated SPARQL queries, to leverage my virtual KB (= local data of points 1,2 plus external LOD of point 3)

In principle, that's is exactly one of the use cases LOD were created for but, practically speaking, there are some issues to tackle.

Issue 1: are federated queries scalable for the real world problems?

Issue 2: There are many linked data vocabularies out there in the LOD Cloud. In this day and age, it is very huge and covers many fields of Life Sciences, but some of such datasets are out-of-date or do not have a SPARQL endpoint to perform federated queries. They seem not very stable.

One alternative, is using semantic stable hub like Wikidata as the principal external KB. Wikidata is a general purpose KB but it seems very active.

Could be a valid opportunity or are there other design patterns for LOD usage?

  • Can you show a piece of your data (and probably a piece of their DSP White Paper)? – Stanislav Kralin Jul 15 '17 at 6:30
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    I cannot provide a piece of my data on the fly. But they do just describe biological samples with genomic and pharmacological annotations. I provided the link to the semantic annotations just as an example (link operational data to a KB is exactly what I need). Anyway, I think the white paper should be found here: londonbookfair.co.uk/__novadocuments/… – floatingpurr Jul 15 '17 at 15:27
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    Well, there are many events dedicated to SW and LD applications in Life Sciences (the latest one). Probably you should consult their proceedings for the current best practices in this particular field… – Stanislav Kralin Jul 17 '17 at 10:53
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    BTW, Wikidata exampe queries page contains many examples related to this field. Just press "Ctrl+F" and type "gene" or "genes" on this page. Also, you might be interested in another solution of the same vendor. – Stanislav Kralin Jul 23 '17 at 8:34
  • @StanislavKralin, thank you once again. I've already checked out vendor solutions such as linked life data or also Bio2Rdf but they seem no longer updated. – floatingpurr Jul 24 '17 at 9:36

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