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When I run pheval, I see this stacktrace coming ultimately from linkml_runtime I think
`ImportError: cannot import name 're' from 'typing' (/opt/homebrew/Cellar/python@3.13/3.13.0_1/Frameworks/Pyt…
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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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```
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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Many ontology browsers such as OLS and BioPortal use the symbol "P" to show part-of edges - this has been common convention for decades. OboEdit also made use of a wider variety of symbols, e.g. "I" f…
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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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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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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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It is common practice to include a catalog-v001.xml file that determines how imports should be resolved,
e.g:
https://github.com/INCATools/ontology-access-kit/blob/20e82c06b53e414454f50ca9d9f824…