From 037b5de489656b90de93f3c96d98c371b63bfe71 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 6 Nov 2024 08:34:16 +0100 Subject: [PATCH] Update docs --- docs/source/custom.rst | 2 +- docs/source/predict.rst | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/source/custom.rst b/docs/source/custom.rst index 40ee454c..b1e20aac 100644 --- a/docs/source/custom.rst +++ b/docs/source/custom.rst @@ -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 \ No newline at end of file + python -m pytest biomappings_custom.py diff --git a/docs/source/predict.rst b/docs/source/predict.rst index cfd5eff2..b28006e3 100644 --- a/docs/source/predict.rst +++ b/docs/source/predict.rst @@ -27,10 +27,11 @@ The following examples have already been used to predict mappings 3. `generate_cl_mesh_mappings `_ implements a fully custom matching workflow, also built on Gilda (in case you want to roll your own) 4. `generate_mesh_uniprot_mappings `_ - 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 `_ - 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).