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VirtualFlyBrain / pipeline

A repository for amalgamating pipeline issue tickets and general VFB pipeline doc
https://hub.docker.com/repository/docker/virtualflybrain/pipeline
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Implement generic typing system for neo nodes #43

Closed matentzn closed 4 years ago

matentzn commented 6 years ago

yaml or spreadsheet or key-value based: entity-iri:nodetype http://test.owl#Neuron:Neuron, meaning that all instances of Neuron should be typed as Neuron as well.

dosumis commented 4 years ago

MVP: list of classes - all instances and subclasses of which get a Neo:label default rdfs:label 'fu bar' => :Fu_bar. Optional spec over-ride on name.

Version2: Allows class expressions -> Neo:labels. In this case specification of neo:Label name is compulsory. TBD - implement by adding defined class or by using DL query.

matentzn commented 4 years ago

Note to self:

Allow configs like: 

- label:  Neuron_adult
   expressions:     
        - VFB:000002     
        - RO:0000060 some VFB:000001

label is optional; if not given, use recipes of David in comment above. expressions can be: CURIEs, IRIs, CURIE class expressions or IRI class expressions.

dosumis commented 4 years ago

The current list of labels from named classes is in this dict

https://github.com/VirtualFlyBrain/VFB_neo4j/blob/master/src/uk/ac/ebi/vfb/neo4j/neo2neo/add_constraints_and_redundant_labels.py#L33

Key = neo label, value = list of classes to which this applies (referred to by label)

Almost all follow the convention 'fu bar' => :Fu_bar.

Current class OWL expression queries:

https://github.com/VirtualFlyBrain/VFB_neo4j/blob/master/src/uk/ac/ebi/vfb/neo4j/owl2neo/add_labels_from_owl_queries.py#L19