OboTermIncompleteError when processing mondo in specific directory

[kmanpearl]

Since I use multiple versions of the same datasets processed with different levels of label redundancy, I have multiple obnb data directories to store the processed data. When trying to load mondo within one directory using dat = MondoDiseaseOntology(root='../data/obnb/FullyRedundant') it works as expected. However when running dat = MondoDiseaseOntology(root='../data/obnb/NonRedundant') I got the following error. Not sure how to troubleshoot or what could be causing this. I also tried running MondoDiseaseOntology(root='../data/obnb/NonRedundant', redownload=True, reprocess=True) but got the same error so I assume its related to something in the directory.

OboTermIncompleteError                    Traceback (most recent call last)
Cell In[2], [line 1](vscode-notebook-cell:?execution_count=2&line=1)
----> [1](vscode-notebook-cell:?execution_count=2&line=1) non = MondoDiseaseOntology(root='../data/obnb/NonRedundant')

File [~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/mondo.py:16](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/mondo.py:16), in MondoDiseaseOntology.__init__(self, root, xref_prefix, **kwargs)
     [14](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/mondo.py:14) def __init__(self, root, xref_prefix=None, **kwargs):
     [15](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/mondo.py:15)     """Initialize MondoDiseaseOntology data object."""
---> [16](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/mondo.py:16)     super().__init__(root, xref_prefix=xref_prefix, **kwargs)

File [~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:31](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:31), in BaseOntologyData.__init__(self, root, xref_prefix, branch, **kwargs)
     [29](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:29) self.xref_prefix = xref_prefix
     [30](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:30) self.branch = branch
---> [31](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:31) super().__init__(root, **kwargs)

File [~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/base.py:101](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/base.py:101), in BaseData.__init__(self, root, version, redownload, reprocess, retransform, log_level, pre_transform, transform, cache_transform, download_cache, gene_id_converter, **kwargs)
     [98](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/base.py:98)     self._download_archive()
     [99](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/base.py:99)     self._process()  # FIX:
--> [101](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/base.py:101) self.load_processed_data()
    [102](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/base.py:102) self._apply_transform(transform)

File [~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:59](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:59), in BaseOntologyData.load_processed_data(self, path)
     [57](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:57) self.plogger.info(f"Load processed annodataion {path}")
     [58](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:58) ont = OntologyGraph(logger=self.plogger)
---> [59](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:59) self.xref_to_onto_ids = ont.read_obo(path, xref_prefix=self.xref_prefix)
     [60](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/data/ontology/base.py:60) self.data = ont if self.branch is None else ont.restrict_to_branch(self.branch)

File [~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:390](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:390), in OntologyGraph.read_obo(self, path, xref_prefix)
    [388](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:388) xref_to_term_id = defaultdict(set)
    [389](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:389) with open(path) as f:
--> [390](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:390)     for term in self.iter_terms(f):
    [391](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:391)         term_id, term_name, term_xrefs, term_parents = term
    [393](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:393)         self.add_node(term_id, exist_ok=True)

File [~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:314](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:314), in OntologyGraph.iter_terms(fp)
    [312](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:312) for _, stanza_lines in groups:
    [313](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:313)     if next(stanza_lines).startswith("[Term]"):
--> [314](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:314)         yield OntologyGraph.parse_stanza_simplified(stanza_lines)

File [~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:365](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:365), in OntologyGraph.parse_stanza_simplified(stanza_lines)
    [362](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:362)         term_parents.append(strip_key(line, key))
    [364](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:364) if term_id is None or term_name is None:
--> [365](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:365)     raise OboTermIncompleteError
    [367](https://vscode-remote+ssh-002dremote-002bv100.vscode-resource.vscode-cdn.net/mnt/research/compbio/krishnanlab/projects/net2onto/notebooks/~/anaconda3/envs/net2onto/lib/python3.10/site-packages/obnb/graph/ontology.py:367) return term_id, term_name, term_xrefs, term_parents

OboTermIncompleteError:

[falquaddoomi]

Hey @kmanpearl, just FYI I was able to replicate the issue when running dat = MondoDiseaseOntology(root='../data/obnb/FullyRedundant').

As far as I can tell the issue is occurring because the current version of mondo.obo includes the following stanza that's missing a name field:

[Term]
id: CHEBI:36684
is_obsolete: true
replaced_by: CHEBI:17792

The current implementation will throw OboTermIncompleteError if either the ID or name is missing.

I presume it's not occurring on your end for that particular folder, '../data/obnb/FullyRedundant', because you downloaded it back when it didn't contain the stanza above that's currently breaking it. When you try to use a new folder, e.g. '../data/obnb/NonRedundant', it downloads the new dataset and breaks.

Again just FYI, I'm currently looking into which, if any, of the following options make sense:

1. to skip entries with a missing ID or name,
2. perhaps use the ID as the name if the ID's there and the name isn't, or
3. in this case to use the replaced_by field to reference a different entity, i.e., CHEBI:17792, rather than trying and failing to use the incomplete CHEBI:36684 entry.

[kmanpearl]

@falquaddoomi I'm adding this here as well for continuity - not sure if this changes how you address the problem but the term CHEBI:36684 is originally from the Chemical Entities of Biological Interest Ontology. I am not exactly sure how mondo uses these other ontology nodes, but for the purpose of disease classification only nodes begining with MONDO: are actually relevant to the task