Merge branch 'main' into support-skos-mappings-for-simple-obo

INCATools · Jun 5, 2024 · fd9f23e · fd9f23e
2 parents eaaa173 + 8b25588
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diff --git a/docs/guide/associations.rst b/docs/guide/associations.rst
@@ -82,9 +82,9 @@ or any is-a :term:`Descendant`:
     runoak -i sqlite:obo:hp -G hpoa -g phenotype.hpoa associations -p i HP:0011482
 
 
-
 Further reading
 ---------------
 
+- `Ontogenesis article on associations <https://ontogenesis.knowledgeblog.org/50/>`_
 - `Gene Ontology: tool for the unification of biology <https://www.nature.com/articles/ng0500_25>`_
 - `On beyond Gruber: "Ontologies" in today's biomedical information systems and the limits of OWL <https://pubmed.ncbi.nlm.nih.gov/34384571/>`_.
diff --git a/docs/howtos/use-oak-expression-language.rst b/docs/howtos/use-oak-expression-language.rst
@@ -292,9 +292,21 @@ The ``.filter`` operator allows you to provide arbitrary python filters.
 NR
 ^^
 
-The ``.nr`` operator takes a set of terms are returns the non-redundant set of terms
+The ``.nr`` operator takes a set of terms and returns the non-redundant set of terms
 from that list (parameterized by a predicate or predicates).
 
+MRCA
+^^^^
+
+The ``.mrca`` operator takes a set of terms are returns the most recent common ancestors (:term:`MRCA`).
+Parameterized by a predicate or predicates.
+
+Example:
+
+.. code-block::
+
+   runoak -i sqlite:obo:uberon info .mrca//p=i,p .idfile my_terms.txt
+
 Others
 ^^^^^^
 

diff --git a/notebooks/CellType/LungEpithelialCell.ipynb b/notebooks/CellType/LungEpithelialCell.ipynb
diff --git a/notebooks/images/lung-cells-src.png b/notebooks/images/lung-cells-src.png
diff --git a/pyproject.toml b/pyproject.toml
@@ -93,7 +93,7 @@ reverse_relative = true
 [tool.codespell]
 skip = '.git,*.pdf,*.svg,poetry.lock,*.obo,*.ttl,*.ofn,*.gaf,*.tsv,*.json,input'
 ignore-regex = '(^\s*"image/\S+": ".*|[a-z]*\.\.\.)'
-ignore-words-list = 'ptd,ot,nd,ser,oger,gard,te,fo,fof,bu,ue,ois,processus,infarction,infarctions'
+ignore-words-list = 'ptd,ot,nd,ser,oger,gard,te,fo,fof,bu,ue,ois,processus,infarction,infarctions,assertIn,morpholgy'
 
 [tool.ruff]
 lint.extend-ignore = [

diff --git a/src/oaklib/__init__.py b/src/oaklib/__init__.py
@@ -6,6 +6,7 @@
 __version__ = "0.1.0"
 
 from oaklib.interfaces import BasicOntologyInterface  # noqa:F401
+from oaklib.query import onto_query  # noqa:F401  # noqa:F401
 from oaklib.resource import OntologyResource  # noqa:F401
 from oaklib.selector import get_adapter, get_implementation_from_shorthand  # noqa:F401