new version of go.obo has new bits

MoseleyBioinformaticsLab / GOcats

A tool for categorizing Gene Ontology into subgraphs of user-defined emergent concepts

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new version of go.obo has new bits #24

Open rmflight opened 4 months ago

rmflight commented 4 months ago

As of 2024-01-17 (latest go.obo release), there is a new typedef that causes gocats to choke.

[Typedef]
id: has_ontology_root_term
name: has ontology root term
namespace: external
xref: IAO:0000700
is_metadata_tag: true
is_class_level: true

This is used to define the roots of the three ontology namespaces: biological process, molecular function, cellular component. Which is neat. But the current version of gocats doesn't know about it, and crashes.

ehinderer commented 2 months ago

I noticed this a few months ago but have not gotten around to fixing the issue. I'm using the Jan 2019 go.obo version for the time being, but I will try to address this soon.