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VirtualFlyBrain / VFB2

Virtual Fly Brain Documentation Site
https://virtualflybrain.org
MIT License
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Add pub query #367

Open dosumis opened 10 months ago

dosumis commented 10 months ago

3 sources of pubs:

  1. Curation of expression: 

    MATCH p=(n:Cell)<-[:INSTANCEOF]-()-[r:part_of]->() 
OPTIONAL MATCH (pub:pub) where pub.short_form = r.pub 
RETURN pub.label, n.label limit 100

  2. NLP

    MATCH p=()-[r:has_reference]->() WHERE r.typ = ['nlp'] RETURN p LIMIT 25

  3. Ontology 

    MATCH p=()-[r:has_reference]->() WHERE r.typ = 'def' or r.typ  = 'syn' RETURN p LIMIT 25

Query should combine all 3 sources and have a column to distinguish between them.

Query should be on site an on VFB_connect

dosumis commented 10 months ago

Note - there is an issue with inconsistency of pub edges that should be fixed.

3 sources of these links:

  1. kb - kb2 all attributes should be lists
  2. side loading by https://github.com/VirtualFlyBrain/VFB_neo4j/blob/master/src/uk/ac/ebi/vfb/neo4j/flybase2neo/expression_runner.py - or something it calls
  3. NLP pipeline.

These should all be made into lists and all code that depends on this should expect lists (side loading and queries).

(related issue - review code for dealing with synonym and def refs on ontology terms)