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VirtualFlyBrain / VFB_neo4j

A python package for writing schema-compliant content to VFB neo4J DBs
Apache License 2.0
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Add function for making typing of neurons obsolete #272

Open dosumis opened 1 year ago

dosumis commented 1 year ago

We are beginning to get corrections to typing of images from major datasets. Rather than silently changing these, we have agreed that the old typing should be retained along with metadata. This needs to be outside of the indexing/query system - which can be most easily achieved by using and annotation property.

Function should take a list of tuples as an arg. Tuples have: individual ID, type ID (FBbt), comment. It should then convert the type edges specified to an annotation property 'oio:obsolete_type', annotated with the comment (rdfs:comment).

Adding new, corrected typing should be a second step using existing pipelines.

Limitation: If we get a major version update on a dataset, it would be useful to be able to assess what has changed in order to determine what to obsolete. This could be achieved via a function that wraps this one (which should be the subject of a separate ticket).

Clare72 commented 1 year ago

I can't find an existing property that fits what we want - shall we make this a neo property <http://n2o.neo/property/obsolete_type> or add something to vfb_ext? Also would it make most sense for this to be a method on the kb_owl_edge_writer class?