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bulk RNAseq queries #391

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Clare72 opened this issue Dec 5, 2024 · 0 comments
Open

bulk RNAseq queries #391

Clare72 opened this issue Dec 5, 2024 · 0 comments
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@Clare72
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Clare72 commented Dec 5, 2024

Add queries for displaying bulk sequencing data (similar to scRNAseq queries)
Might also need bulk_seq (or similar) node label to determine which pages to add to?

On DataSet page

  • 'List all Samples for ___' query (might want to say expression patterns rather than samples?)
match (s:Sample)-[:has_source]->(ds:DataSet) 
where ds.iri = 'http://www.ncbi.nlm.nih.gov/bioproject/PRJNA480794' 
optional match (s)-[:INSTANCEOF]->(e:Expression_pattern)
optional match (ds)-[:has_reference]->(p:pub)
return s.label AS Name, e.label AS `Expression Pattern`, p.miniref[0] AS Reference

Would be nice to also get anatomy by linking up to exp curation

On Sample page

  • 'Genes expressed in ___' query
match (s:Sample)-[r:expresses]->(g:Gene) 
where s.iri = 'http://www.ncbi.nlm.nih.gov/biosample/SAMN09650153'
match (s)-[:INSTANCEOF]->(ep:Expression_pattern)
return g.label AS Gene, ep.label AS `Expression Pattern`, r.expression_level[0] AS Level

NB - no extent for bulk seq data

  • Query for anatomy that the driver is expressed in (same as on parent expression pattern class)

On Expression pattern page (and maybe also Anatomy pages?)

  • Bulk RNA sequencing data for ___' query
match (ep:Expression_pattern)<-[:INSTANCEOF]-(s:Sample)
where ep.iri = 'http://virtualflybrain.org/reports/VFBexp_FBtp0093500FBtp0093501'
match (s)-[:has_source]->(ds:DataSet)
optional match (ds)-[:has_reference]->(p:pub)
return s.label AS Sample, ep.label AS `Expression pattern`, ds.label AS Dataset, p.miniref[0] AS Reference

Not sure how to link from Anatomy

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