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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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Add query for drug -> drug targets #388

Closed justaddcoffee closed 3 years ago

justaddcoffee commented 3 years ago

Adding sparql query for drug -> drug targets per convo with @callahantiff

@matentzn could you have a look at this sparql query and 1) confirm it's okay and 2) maybe give some advice about why it's timing out? It should return at most 30k things, so it doesn't seem too demanding

justaddcoffee commented 3 years ago

This query now works, but only yields 2,082 rows - should be more like 30,000. Some targets might not be classified as 9606/human, and/or some drug or proteins might have >1 category

justaddcoffee commented 3 years ago

Now at 3,474 drug -> drug target edges, by casting a wider net for drug and target bl categories (bl:Drug | bl:ChemicalSubstance for drug categories, and bl:Protein | bl:Gene | bl:NamedThing for target categories)

sonarcloud[bot] commented 3 years ago

Kudos, SonarCloud Quality Gate passed!

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

justaddcoffee commented 3 years ago

3,372 drug -> target edges when I remove targets with catefory of bl:NamedThing, which seems to broad.

@callahantiff could we chat briefly at some point before Thursday? I think that this query will work for your purposes, but want to confirm

callahantiff commented 3 years ago

3,372 drug -> target edges when I remove targets with catefory of bl:NamedThing, which seems to broad.

@callahantiff could we chat briefly at some point before Thursday? I think that this query will work for your purposes, but want to confirm

Absolutely! Will slack you about a time.

justaddcoffee commented 3 years ago

@callahantiff - just a quick note that this SPARQL query for drug -> drug target has moved here: https://github.com/Knowledge-Graph-Hub/kg-covid-19/blob/master/queries/query-07-drug-to-drug-target.rq (b/c of this PR)

I don't think you were actually using this rq file - just making sure things don't break on your end

callahantiff commented 3 years ago

@callahantiff - just a quick note that this SPARQL query for drug -> drug target has moved here: https://github.com/Knowledge-Graph-Hub/kg-covid-19/blob/master/queries/query-07-drug-to-drug-target.rq (b/c of this PR)

I don't think you were actually using this rq file - just making sure things don't break on your end

Thanks @justaddcoffee - I made sure to update things on my end!