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Knowledge-Graph-Hub / kg-covid-19

An instance of KG Hub to produce a knowledge graph for COVID-19 response.
https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki
BSD 3-Clause "New" or "Revised" License
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All but one of the SPARQL queries are broken (for MS submission) #342

Closed justaddcoffee closed 3 years ago

justaddcoffee commented 3 years ago

Describe the bug

One of the reviewers remarked: I could only get one of your example queries to return something on http://kg-hub-rdf.berkeleybop.io/blazegraph/#query I'm not sure if this is expected

To Reproduce

SPARQL queries are here: https://github.com/Knowledge-Graph-Hub/kg-covid-19/tree/master/queries/sparql

Endpoint is here: kg-hub-rdf.berkeleybop.io/blazegraph/p

Expected behavior

All SPARQL queries should return something - the title of each describes what it should return

Version

https://github.com/Knowledge-Graph-Hub/kg-covid-19/commit/9fd270e1b141487ee422d138cd74add87118f669

matentzn commented 3 years ago

All but one work:

Seems like interaction links are no longer available in their reified form. I will change the query to use direct linking instead.

matentzn commented 3 years ago

IGNORE THIS READ ON

Justin, can you review this:

whether it is acceptable. Note: it is now missing the p (see old query above)! (the way in which the interaction worked previously)

matentzn commented 3 years ago

Sorry there was a mistake now fixed.

matentzn commented 3 years ago

Thanks to @deepakunni3 here the correct version:

fixed query-03-sars-cov-2-interactors

deepakunni3 commented 3 years ago

To add more context to this ticket, In earlier versions of our KG-COVID-19 N-Triples export (and the SPARQL endpoint) we used to have biolink:subject, biolink:object, biolink:predicate as predicates of a reified association. But this was incorrect since Biolink should not mint predicates for core RDF predicates. So subsequent versions of our export, which happened after these SPARQL Queries were written, has the following changes: