Traceback (most recent call last):
File "/home/zeth/PycharmProjects/bionty-base/test.py", line 8, in <module>
Ontology("efo.owl")
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/ontology.py", line 283, in __init__
cls(self).parse_from(_handle) # type: ignore
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/rdfxml.py", line 119, in parse_from
self._process_axiom(axiom, curies)
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/rdfxml.py", line 819, in _process_axiom
for s in entity.synonyms
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/entity/__init__.py", line 465, in synonyms
return frozenset(Synonym(ontology, s) for s in termdata.synonyms)
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/entity/__init__.py", line 465, in <genexpr>
return frozenset(Synonym(ontology, s) for s in termdata.synonyms)
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/synonym.py", line 133, in __init__
raise ValueError(f"undeclared synonym type: {syndata.type}")
ValueError: undeclared synonym type: OMO:0003000
Since the 2.5.6 release and the changes to how synonyms are handled (https://github.com/althonos/pronto/issues/218), I run into
when trying to read the https://www.ebi.ac.uk/efo/ ontology.
Works with 2.5.5, does NOT work with 2.5.6 anymore.