biolink-model-toolkit
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Error in get_descendents with curies
v. 1.1.2
If I lookup descendents of noncoding RNA product it works:
tk.get_descendants("noncoding RNA product")
['noncoding RNA product', 'microRNA', 'siRNA']
But if I use the curie form (which came from a response to tk.get_descendents(...,formatted=True)) then it fails:
tk.get_descendants("biolink:NoncodingRNAProduct")
Traceback (most recent call last):
File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/pydevconsole.py", line 364, in runcode
coro = func()
^^^^^^
File "<input>", line 1, in <module>
File "/opt/anaconda3/envs/redistpf/lib/python3.12/site-packages/bmt/toolkit.py", line 739, in get_descendants
raise ValueError("not a valid biolink component")
The types and predicates that I found that have this problem are:
Error with type: biolink:NoncodingRNAProduct
Error with type: biolink:MicroRNA
Error with type: biolink:SiRNA
Error with predicate: biolink:gene_fusion_with
Error with predicate: biolink:genetic_neighborhood_of
I think that on the type side it's not happy when there are consecutive capital letters and on the predicate side when there are underscores in the non-curie name of the predicate. That latter case should probably be changed in the model as well...?