search

geneontology / minerva

BSD 3-Clause "New" or "Revised" License
6 stars 8 forks source link

Causal qualifiers with regulation terms are misleading in annotations #196

Open ukemi opened 6 years ago

ukemi commented 6 years ago

Chaining directional causal relation with regulation terms is leading to annotations like:

Cdc42 Mmus acts_upstream_of_negative_effect negative regulation of canonical Wnt signaling pathway PMID:16510873

These annotations are misleading, especially if the qualifiers are removed in the creation of a gaf file. Do we need new property chains so these relations are instead expressed as something similar to:

Cdc42 Mmus | acts_upstream_of_positive_effect | canonical Wnt signaling pathway | PMID:16510873

Is this correct? @vanaukenk any comments?

vanaukenk commented 6 years ago

@ukemi - can you paste the relevant model in this ticket? Thx.

ukemi commented 6 years ago

I believe the example is here: http://noctua.berkeleybop.org/editor/graph/gomodel:5ae3b0f600001114

vanaukenk commented 2 years ago

Need to check this again, as it doesn't look like the annotation above is still generated from the model. Could make another test case to double-check.