`ValueError: undeclared synonym type` with version 2.5.7

[ireneisdoomed]

Observed behaviour Version 2.5.7 is not capable of loading my OWL file, while 2.5.3 does.

Background I am one of the developers of Ontoma, a tool that processes the EFO ontology OWL file using pronto. We are having issues upgrading from version 2.5.3 to 2.5.7, the latest one. Every time I try loading the OWL file, I get this error: ValueError: undeclared synonym type: http://purl.obolibrary.org/obo/mondo#ABBREVIATION.

Steps to reproduce

1. Download EFO OWL file from https://github.com/EBISPOT/efo/releases/download/v3.68.0/efo_otar_slim.owl
2. Install pronto 2.5.7 with pip install pronto==2.5.7
3. Start iPython session
4. Import and try to load the ontology

   import pronto
   ont = pronto.Ontology("efo_otar_slim.owl")

5. See error

This is not a problem with the ontology, I've tried loading previous versions with the same result. In fact, it loads just fine when I use an older version of pronto:

1. Uninstall pronto 2.5.7 and install 2.5.3 pip install pronto==2.5.3
2. Start iPython session
3. Import and try to load the ontology

   import pronto
   ont = pronto.Ontology("efo_otar_slim.owl")

Full traceback is here:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[41], line 1
----> 1 ont = pronto.Ontology("efo_otar_slim.owl")

File /usr/local/lib/python3.11/site-packages/pronto/ontology.py:283, in Ontology.__init__(self, handle, import_depth, timeout, threads)
    281 for cls in BaseParser.__subclasses__():
    282     if cls.can_parse(typing.cast(str, self.path), buffer):
--> 283         cls(self).parse_from(_handle)  # type: ignore
    284         break
    285 else:

File /usr/local/lib/python3.11/site-packages/pronto/parsers/rdfxml.py:119, in RdfXMLParser.parse_from(self, handle, threads)
    117         self._extract_term(class_, curies)
    118     for axiom in tree.iterfind(_NS["owl"]["Axiom"]):
--> 119         self._process_axiom(axiom, curies)
    121 # Update lineage cache with symmetric of `subClassOf`
    122 self.symmetrize_lineage()

File /usr/local/lib/python3.11/site-packages/pronto/parsers/rdfxml.py:822, in RdfXMLParser._process_axiom(self, elem, curies)
    816     type_ = elem_type.text
    818 try:
    819     # recover existing synonym on the entity if there's one already
    820     synonym = next(
    821         s._data()
--> 822         for s in entity.synonyms
    823         if s.description == elem_target.text
    824         and s.scope == _SYNONYMS[property]
    825     )
    826     # update synonym type of existing synonym if we got one
    827     if type_ is not None:

File /usr/local/lib/python3.11/site-packages/pronto/entity/__init__.py:465, in Entity.synonyms(self)
    463 """`frozenset` of `Synonym`: A set of synonyms for this entity."""
    464 ontology, termdata = self._ontology(), self._data()
--> 465 return frozenset(Synonym(ontology, s) for s in termdata.synonyms)

File /usr/local/lib/python3.11/site-packages/pronto/entity/__init__.py:465, in <genexpr>(.0)
    463 """`frozenset` of `Synonym`: A set of synonyms for this entity."""
    464 ontology, termdata = self._ontology(), self._data()
--> 465 return frozenset(Synonym(ontology, s) for s in termdata.synonyms)

File /usr/local/lib/python3.11/site-packages/pronto/synonym.py:133, in Synonym.__init__(self, ontology, syndata)
    131 if syndata.type is not None:
    132     if not any(t.id == syndata.type for t in ontology.synonym_types()):
--> 133         raise ValueError(f"undeclared synonym type: {syndata.type}")
    134 self._data = weakref.ref(syndata)
    135 self.__ontology = ontology

ValueError: undeclared synonym type: http://purl.obolibrary.org/obo/mondo#ABBREVIATION