althonos
Unable to create Pronto object since 2.5.6 (synonyms change)
Since the 2.5.6 release and the changes to how synonyms are handled (https://github.com/althonos/pronto/issues/218), I run into
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
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.
from pronto import Ontology
Ontology("efo.owl")
*(for those who may find this thread later)
Today pronto v2.5.5 works with v3.66.0 efo.owl version , but doesn't work with newer efo version, so you don't only need to downgrade pronto but to download older efo as well.
That's because the newer EFO version is broken. See: https://github.com/EBISPOT/efo/issues/2264 (also for a solution). I can read EFO 3.70+ by fixing the owl file as outlined in the thread.
Nevertheless, this issue is still open and relevant.