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Extend schema to allow recording genotypes of templates #239

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dosumis opened this issue Jun 8, 2021 · 0 comments
Open

Extend schema to allow recording genotypes of templates #239

dosumis opened this issue Jun 8, 2021 · 0 comments
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@dosumis
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dosumis commented Jun 8, 2021

genotypes can just be bags of alleles.

genotype has_part -> allele

nodes and edges can be added through VFB_neo4j uk.ac.ebi.vfb.neo4j.KB_tools

use feature_tools to add alleles:

https://github.com/VirtualFlyBrain/VFB_neo4j/blob/master/src/uk/ac/ebi/vfb/neo4j/flybase2neo/feature_tools.py - deals with typing.

VFB_neo4j uk.ac.ebi.vfb.neo4j.KB_tools edge writer to wire these up to genotype node via has_part. Add genotype

We already have a genotype node from GENO MATCH (n:Class { label: 'genotype'}) return n

We already have a has_genotype property:

MATCH (n:Property { label: 'has_genotype'}) return n

(has_genotype could be a simple extension on curation platform).

genotype node ID - recipe alphanumeric ordering of IDs to maker a new ID (as for splits)

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