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Update docs
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cthoyt committed Nov 6, 2024
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2 changes: 1 addition & 1 deletion docs/source/custom.rst
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Expand Up @@ -84,4 +84,4 @@ as :class:`unittest` itself, :mod:`pytest`, or others. Therefore you can run the
.. code-block::
python -m pip install biomappings[tests]
python -m pytest biomappings_custom.py
python -m pytest biomappings_custom.py
7 changes: 4 additions & 3 deletions docs/source/predict.rst
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Expand Up @@ -27,10 +27,11 @@ The following examples have already been used to predict mappings
3. `generate_cl_mesh_mappings <https://github.com/biopragmatics/biomappings/blob/master/scripts/generate_cl_mesh_mappings.py>`_
implements a fully custom matching workflow, also built on Gilda (in case you want to roll your own)
4. `generate_mesh_uniprot_mappings <https://github.com/biopragmatics/biomappings/blob/master/scripts/generate_mesh_uniprot_mappings.py>`_
uses rule-based matching between MeSH and UniProt proteins that relies on the fact that the MeSH terms were generated from UniProt names.
uses rule-based matching between MeSH and UniProt proteins that relies on the fact that the MeSH terms were
generated from UniProt names.
5. `generate_wikipathways_orthologs <https://github.com/biopragmatics/biomappings/blob/master/scripts/generate_wikipathways_orthologs.py>`_
uses a rule-based method for matching orthologous pathways in WikiPathways that relies on the fact that the names are procedurally generated
with a certain template
uses a rule-based method for matching orthologous pathways in WikiPathways that relies on the fact that the names
are procedurally generated with a certain template

We also have a work-in-progress example using :mod:`pykeen` for generating mappings based on knowledge graph embeddings
(both in the transductive and inductive setting).
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