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```owl
has scope
oio:hasRelatedSynonym
genbank synonym
…
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I was reviewing the [ICD11 "lex" file](https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/lexmatch/unmapped_icd11foundation_lex.tsv) and there are 4 exact matches where the subj…
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**Describe the bug**
from discussion in https://github.com/linkml/linkml/pull/2303
related to, but seems distinct from: https://github.com/linkml/linkml/issues/1690
this is described in the docs …
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It's not very obvious how to do this at the moment. It's additionally confusing because vskit expansion is in OAK (this was intentional to avoid too many dependencies in linkml; however, it may be wor…
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```
def parse_from(self, handle, threads=None):
# Load the OBO graph into a syntax tree using fastobo
> doc = fastobo.load_graph(handle).compact_ids()
E File "", line 1
…
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A common use case is using an external ontology to map two other ontologies.
E.g uberon xrefs to two ssAOs. Those ssAOs do not xref to uberon
See the example ontology here:
- https://github.c…
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When running from poetry:
```
✗ runoak --help
Traceback (most recent call last):
File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/bin/runoak", line 2, in
from o…
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https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/lexmatch/unmapped_icd_lex_exact.tsv
subject_id | object_id | predicate_id | object_label | subject_label | mapping_justific…
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**Describe the bug**
PyDantic update causes pip dependency's imcompatibility.
with pydantic=2.5 (default pip behavior) raise error like:
`
... ...
File "/home/rnalab/zfdeng/miniconda3/envs/tm…