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RobokopU24 / ORION

Code that parses datasets from various sources and converts them to load graph databases.
MIT License
12 stars 13 forks source link

No labels on taxon nodes #20

Closed cbizon closed 3 years ago

cbizon commented 4 years ago

This may be a nodenormalization problem.

PhillipsOwen commented 4 years ago

when you say "label" do you really mean "name"? here is an example for viral proteome KGX output:

{"id":"NCBITaxon:1923255", "name":"Hubei tombus-like virus 1", "category":["organism_taxon", "named_thing", "ontology_class"], "equivalent_identifiers":["NCBITaxon:1923255"]},

I can add checks to node normalization to throw a warning if the name is missing.

PhillipsOwen commented 4 years ago

Presuming that this data was discovered on the covid graph, I ran this query which did not return any rows:

match (n1) where n1.id=~".NCBITaxon." and (n1.name=null or n1.name="") return n1 limit 10

cbizon commented 3 years ago

Hmm, I noticed this in the browser. Looking around, it appears that the. nodes do have names, the browser was just not displaying them.

FWIW, I suspect that this query would be faster: match (n1:organism_taxon) where (n1.name = null or n1.name="") return n1 limit 10