Make scRNAseq queries live (EPIC)

[dosumis]

Pushing scRNAseq data queries live: Can we do it this week?

• Data live in DB
  • [x] pdb-dev has all data (aim to use this for first release of queries)
  • [x] pdb-ug loading latest (the way dataset is referred to in queries will need to be fixed for this release)
    • [ ] Make PR with tweaked queries
  • [x] Working queries in place](https://github.com/VirtualFlyBrain/VFB_json_schema/pull/114)
  • Add query hooks to neurons (driven by scRNAseq flag)
  • [x] Hack in hasScRNAseq tag via Cypher. Don't wait for another DB build. MATCH (primary:Class:Anatomy)<-[r:SUBCLASSOF*0..]-(a:Class:Anatomy)<-[r1:composed_primarily_of]-(c:Cluster:Individual)-[r3:has_source]->(ds:scRNAseq_DataSet:Individual) SET primary:hasScRNAseq
  • [x] Add query text for query for clusters: "Single cell transcriptomics data for {%anatomy}"
  • [x] Add Query details to XMI - run subClassOf query in OWLERY to generate input
  • [x] Hack in DataSet label to node with scRNAseqDataSet => fix queries for data and license on cluster TermInfo. @Robbie1977 (Note - this will be fixed in new database load)
  • [ ] Implement suppression of display of relationship edges for all edges in Relationship TermInfo with hide_in_term_info: ['True']. see https://github.com/VirtualFlyBrain/VFB_json_schema/issues/115 & linked PR
  • Cluster->gene query
  • Query hook for clusters - can just use "Cluster" for now - but in future it would be better to have an scRNAseq label as we may well re use cluster for other purposes. QUery tet: Genes expressed in ${cluster}
  • [x] Changes to XMI - direct neo4j query - just takes ID of cluster (Individual)
  • [x] Code needed to translate queries to results tables
    • @Robbie1977 has written - will link PR to this ticket.
    • columns as in https://github.com/VirtualFlyBrain/VFB_json_schema/issues/112#issuecomment-1283675439 - bit first table has publication and second table has cell_type.
  • Can we make sure code edits are not held up by clashing updates for other purposes?

[Robbie1977]

MATCH (primary:Class:Anatomy)<-[r:SUBCLASSOF*0..]-(a:Class:Anatomy)<-[r1:composed_primarily_of]-(c:Cluster:Individual)-[r3:has_source]->(ds:scRNAseq_DataSet:Individual) SET primary:hasScRNAseq

[dosumis]

@hkir-dev to work on moving anatomy -> cluster query to SOLR. Not urgent.

[dosumis]

Items for follow-on sprint(s):

• Update to latest build
  • Fix queries to cope with schema change
  • Fix xref-roller so that it generates multiple xrefs when accession is list with n > 1.