Moved Jupter notebooks to be part of sphinx docs (#816)

* Moved Jupter notebooks to be part of sphinx docs Fixes #758 * format * format * codespell * updated test to sync with labels being included * fixed test label
INCATools · Oct 18, 2024 · cec9d19 · cec9d19
1 parent 5152b39
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diff --git a/docs/conf.py b/docs/conf.py
@@ -42,6 +42,7 @@
     "sphinx.ext.intersphinx",
     "sphinx_copybutton",
     "sphinxcontrib.mermaid",
+    "nbsphinx",
 ]
 
 # The suffix(es) of source filenames.
@@ -82,3 +83,6 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
+
+#nbsphinx_allow_errors = True
+nbsphinx_execute = 'never'
diff --git a/notebooks/Ubergraph/Ubergraph.ipynb → ...apters/Ubergraph/Ubergraph-Tutorial.ipynb b/notebooks/Ubergraph/Ubergraph.ipynb → ...apters/Ubergraph/Ubergraph-Tutorial.ipynb
diff --git a/...graph/output/ubergraph-neuron-cl-only.png → ...graph/output/ubergraph-neuron-cl-only.png b/...graph/output/ubergraph-neuron-cl-only.png → ...graph/output/ubergraph-neuron-cl-only.png
diff --git a/...oks/Ubergraph/output/ubergraph-neuron.png → ...ers/Ubergraph/output/ubergraph-neuron.png b/...oks/Ubergraph/output/ubergraph-neuron.png → ...ers/Ubergraph/output/ubergraph-neuron.png
diff --git a/docs/examples/Adapters/index.rst b/docs/examples/Adapters/index.rst
@@ -0,0 +1,9 @@
+.. _adapters_examples:
+
+Adapter Examples
+================
+
+.. toctree::
+   :maxdepth: 2
+
+   Ubergraph/Ubergraph-Tutorial
diff --git a/notebooks/Command-Line-Examples.ipynb → docs/examples/Command-Line-Examples.ipynb b/notebooks/Command-Line-Examples.ipynb → docs/examples/Command-Line-Examples.ipynb
diff --git a/notebooks/Commands/Apply.ipynb → docs/examples/Commands/Apply.ipynb b/notebooks/Commands/Apply.ipynb → docs/examples/Commands/Apply.ipynb
diff --git a/notebooks/Commands/Associations.ipynb → docs/examples/Commands/Associations.ipynb b/notebooks/Commands/Associations.ipynb → docs/examples/Commands/Associations.ipynb
diff --git a/notebooks/Commands/DiffViaMappings.ipynb → docs/examples/Commands/DiffViaMappings.ipynb b/notebooks/Commands/DiffViaMappings.ipynb → docs/examples/Commands/DiffViaMappings.ipynb
diff --git a/notebooks/Commands/Disjoints.ipynb → docs/examples/Commands/Disjoints.ipynb b/notebooks/Commands/Disjoints.ipynb → docs/examples/Commands/Disjoints.ipynb
diff --git a/notebooks/Commands/Enrichment.ipynb → docs/examples/Commands/Enrichment.ipynb b/notebooks/Commands/Enrichment.ipynb → docs/examples/Commands/Enrichment.ipynb
diff --git a/notebooks/Commands/LogicalDefinitions.ipynb → ...xamples/Commands/LogicalDefinitions.ipynb b/notebooks/Commands/LogicalDefinitions.ipynb → ...xamples/Commands/LogicalDefinitions.ipynb
diff --git a/notebooks/Commands/Mappings.ipynb → docs/examples/Commands/Mappings.ipynb b/notebooks/Commands/Mappings.ipynb → docs/examples/Commands/Mappings.ipynb
diff --git a/notebooks/Commands/Obsoletes.ipynb → docs/examples/Commands/Obsoletes.ipynb b/notebooks/Commands/Obsoletes.ipynb → docs/examples/Commands/Obsoletes.ipynb
diff --git a/notebooks/Commands/Paths.ipynb → docs/examples/Commands/Paths.ipynb b/notebooks/Commands/Paths.ipynb → docs/examples/Commands/Paths.ipynb
diff --git a/notebooks/Lessons/PrefixMaps.ipynb → docs/examples/Commands/Prefixes.ipynb b/notebooks/Lessons/PrefixMaps.ipynb → docs/examples/Commands/Prefixes.ipynb
diff --git a/notebooks/Commands/Relationships.ipynb → docs/examples/Commands/Relationships.ipynb b/notebooks/Commands/Relationships.ipynb → docs/examples/Commands/Relationships.ipynb
diff --git a/notebooks/Commands/Rollup.ipynb → docs/examples/Commands/Rollup.ipynb b/notebooks/Commands/Rollup.ipynb → docs/examples/Commands/Rollup.ipynb
diff --git a/notebooks/Commands/Statistics.ipynb → docs/examples/Commands/Statistics.ipynb b/notebooks/Commands/Statistics.ipynb → docs/examples/Commands/Statistics.ipynb
diff --git a/notebooks/Commands/TaxonConstraints.ipynb → .../examples/Commands/TaxonConstraints.ipynb b/notebooks/Commands/TaxonConstraints.ipynb → .../examples/Commands/TaxonConstraints.ipynb
diff --git a/notebooks/Commands/TermsetSimilarity.ipynb → ...examples/Commands/TermsetSimilarity.ipynb b/notebooks/Commands/TermsetSimilarity.ipynb → ...examples/Commands/TermsetSimilarity.ipynb
diff --git a/notebooks/Commands/ValidateDefinitions.ipynb → ...amples/Commands/ValidateDefinitions.ipynb b/notebooks/Commands/ValidateDefinitions.ipynb → ...amples/Commands/ValidateDefinitions.ipynb
@@ -2166,7 +2166,7 @@
     }
    },
    "source": [
-    "# Using LLMs to validate definitions\n",
+    "## Using LLMs to validate definitions\n",
     "\n",
     "For this example we will use an LLM to validate this GO catalytic activity:\n",
     "\n",

diff --git a/notebooks/Commands/ValidateMappings.ipynb → .../examples/Commands/ValidateMappings.ipynb b/notebooks/Commands/ValidateMappings.ipynb → .../examples/Commands/ValidateMappings.ipynb
diff --git a/docs/examples/Commands/index.rst b/docs/examples/Commands/index.rst
@@ -0,0 +1,24 @@
+.. _commands_notebooks:
+
+Commands
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   Apply
+   Associations
+   DiffViaMappings
+   Disjoints
+   Enrichment
+   LogicalDefinitions
+   Mappings
+   Obsoletes
+   Paths
+   Relationships
+   Rollup
+   Statistics
+   TaxonConstraints
+   TermsetSimilarity
+   ValidateDefinitions
+   ValidateMappings
diff --git a/notebooks/Commands/input/eds-genes-hgnc.tsv → ...xamples/Commands/input/eds-genes-hgnc.tsv b/notebooks/Commands/input/eds-genes-hgnc.tsv → ...xamples/Commands/input/eds-genes-hgnc.tsv
diff --git a/...books/Commands/input/test-create.kgcl.txt → ...mples/Commands/input/test-create.kgcl.txt b/...books/Commands/input/test-create.kgcl.txt → ...mples/Commands/input/test-create.kgcl.txt
diff --git a/notebooks/Commands/input/test.kgcl → docs/examples/Commands/input/test.kgcl b/notebooks/Commands/input/test.kgcl → docs/examples/Commands/input/test.kgcl
diff --git a/...mands/input/validate-definition-conf.yaml → ...mands/input/validate-definition-conf.yaml b/...mands/input/validate-definition-conf.yaml → ...mands/input/validate-definition-conf.yaml
diff --git a/...oks/Commands/input/validate-defs-test.obo → ...les/Commands/input/validate-defs-test.obo b/...oks/Commands/input/validate-defs-test.obo → ...les/Commands/input/validate-defs-test.obo
diff --git a/notebooks/Commands/output/eds.html → docs/examples/Commands/output/eds.html b/notebooks/Commands/output/eds.html → docs/examples/Commands/output/eds.html
diff --git a/notebooks/Commands/output/kgcl-de-novo.obo → ...examples/Commands/output/kgcl-de-novo.obo b/notebooks/Commands/output/kgcl-de-novo.obo → ...examples/Commands/output/kgcl-de-novo.obo
diff --git a/notebooks/Commands/output/kgcl-de-novo.ofn → ...examples/Commands/output/kgcl-de-novo.ofn b/notebooks/Commands/output/kgcl-de-novo.ofn → ...examples/Commands/output/kgcl-de-novo.ofn
diff --git a/notebooks/Commands/output/nerc.png → docs/examples/Commands/output/nerc.png b/notebooks/Commands/output/nerc.png → docs/examples/Commands/output/nerc.png
diff --git a/notebooks/Commands/output/nmbo.png → docs/examples/Commands/output/nmbo.png b/notebooks/Commands/output/nmbo.png → docs/examples/Commands/output/nmbo.png
diff --git a/notebooks/Commands/output/nmbo2.png → docs/examples/Commands/output/nmbo2.png b/notebooks/Commands/output/nmbo2.png → docs/examples/Commands/output/nmbo2.png
diff --git a/...ands/output/trigeminal-ganglion-graph.png → ...ands/output/trigeminal-ganglion-graph.png b/...ands/output/trigeminal-ganglion-graph.png → ...ands/output/trigeminal-ganglion-graph.png
diff --git a/notebooks/Developers-Tutorial.ipynb → docs/examples/Developers-Tutorial.ipynb b/notebooks/Developers-Tutorial.ipynb → docs/examples/Developers-Tutorial.ipynb
@@ -2019,9 +2019,7 @@
    "id": "a3c605ec",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "graph_to_image(graph, seeds=[\"CL:0000540\"], imgfile=\"notebooks/output/neuron-v1.png\")"
-   ]
+   "source": "graph_to_image(graph, seeds=[\"CL:0000540\"], imgfile=\"examples/output/neuron-v1.png\")"
   },
   {
    "cell_type": "markdown",
@@ -2059,9 +2057,7 @@
    "id": "edae4b80",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "graph_to_image(graph, seeds=[\"CL:0000540\"], imgfile=\"notebooks/output/neuron-v2.png\", stylemap=default_stylemap_path())"
-   ]
+   "source": "graph_to_image(graph, seeds=[\"CL:0000540\"], imgfile=\"examples/output/neuron-v2.png\", stylemap=default_stylemap_path())"
   },
   {
    "cell_type": "markdown",
@@ -2329,9 +2325,7 @@
    "id": "a656d404",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "graph_to_image(graph, seeds=terms, imgfile=\"notebooks/output/go-enrichment-from-hp.png\", stylemap=default_stylemap_path())"
-   ]
+   "source": "graph_to_image(graph, seeds=terms, imgfile=\"examples/output/go-enrichment-from-hp.png\", stylemap=default_stylemap_path())"
   },
   {
    "cell_type": "markdown",

diff --git a/notebooks/Draft/enrichment_with_OAK.ipynb → .../examples/Draft/enrichment_with_OAK.ipynb b/notebooks/Draft/enrichment_with_OAK.ipynb → .../examples/Draft/enrichment_with_OAK.ipynb
diff --git a/notebooks/basic-demo.ipynb → ...s/Interfaces/BasicOntologyInterface.ipynb b/notebooks/basic-demo.ipynb → ...s/Interfaces/BasicOntologyInterface.ipynb
diff --git a/...ClassEnrichmentCalculationInterface.ipynb → ...ClassEnrichmentCalculationInterface.ipynb b/...ClassEnrichmentCalculationInterface.ipynb → ...ClassEnrichmentCalculationInterface.ipynb
diff --git a/notebooks/mappings.ipynb → ...Interfaces/MappingProviderInterface.ipynb b/notebooks/mappings.ipynb → ...Interfaces/MappingProviderInterface.ipynb
@@ -1,14 +1,21 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "0846c27a",
    "metadata": {},
+   "cell_type": "markdown",
+   "source": "## MappingProviderInterface Examples",
+   "id": "1ed7c1d66969e87c"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": 1,
    "source": [
+    "\n",
     "%reset -f"
-   ]
+   ],
+   "id": "0846c27a"
   },
   {
    "cell_type": "markdown",

diff --git a/docs/examples/Interfaces/index.rst b/docs/examples/Interfaces/index.rst
@@ -0,0 +1,11 @@
+.. _interfaces_examples:
+
+Interfaces Examples
+===================
+
+.. toctree::
+   :maxdepth: 2
+
+   BasicOntologyInterface
+   ClassEnrichmentCalculationInterface
+   MappingProviderInterface
diff --git a/...essons/Why-predicates-are-important.ipynb → ...s/Ontologies/CHEBI/CHEBI-Predicates.ipynb b/...essons/Why-predicates-are-important.ipynb → ...s/Ontologies/CHEBI/CHEBI-Predicates.ipynb
@@ -5,7 +5,7 @@
    "id": "ef5b9100",
    "metadata": {},
    "source": [
-    "# Why predicates are important\n",
+    "# CHEBI Predicates\n",
     "\n",
     "This notebook is intended as an explanatory guide to the importance of edge types (predicates) in ontologies.\n",
     "\n",

diff --git a/docs/examples/Ontologies/CHEBI/CHEBI-Roles.ipynb b/docs/examples/Ontologies/CHEBI/CHEBI-Roles.ipynb
@@ -0,0 +1,215 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "bf0c4518",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%alias chiro runoak -i sqlite:obo:chiro"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "c726f3db",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "subject\tsubject_label\tpredicate\tpredicate_label\tobject\tobject_label\n",
+      "CHEBI:22180\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003984\tNone\n",
+      "CHEBI:22587\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:10239\tNone\n",
+      "CHEBI:23018\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004089\tNone\n",
+      "CHEBI:23100\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006031\tNone\n",
+      "CHEBI:23529\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009512\tNone\n",
+      "CHEBI:23924\tNone\tobo:chiro#inhibitor_of\tNone\t<http://purl.obolibrary.org/GO_0003824>\tNone\n",
+      "CHEBI:24319\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004356\tNone\n",
+      "CHEBI:25355\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005746\tNone\n",
+      "CHEBI:26087\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009767\tNone\n",
+      "CHEBI:26088\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009522\tNone\n",
+      "CHEBI:26089\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009523\tNone\n",
+      "CHEBI:33282\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:2\tNone\n",
+      "CHEBI:35472\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006954\tNone\n",
+      "CHEBI:35493\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0001660\tNone\n",
+      "CHEBI:35608\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004725\tNone\n",
+      "CHEBI:35634\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004855\tNone\n",
+      "CHEBI:35842\tNone\tobo:chiro#inhibitor_of\tNone\tMP:0003561\tNone\n",
+      "CHEBI:35856\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016165\tNone\n",
+      "CHEBI:36044\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:10239\tNone\n",
+      "CHEBI:36047\tNone\tobo:chiro#inhibitor_of\tNone\t<http://purl.obolibrary.org/NCBITaxon_2>\tNone\n",
+      "CHEBI:37153\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016791\tNone\n",
+      "CHEBI:37416\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0034062\tNone\n",
+      "CHEBI:37670\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004175\tNone\n",
+      "CHEBI:37699\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004672\tNone\n",
+      "CHEBI:37700\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004697\tNone\n",
+      "CHEBI:37733\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004104\tNone\n",
+      "CHEBI:38070\tNone\tobo:chiro#inhibitor_of\tNone\tHP:0011675\tNone\n",
+      "CHEBI:38234\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0034061\tNone\n",
+      "CHEBI:38462\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003990\tNone\n",
+      "CHEBI:38496\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0022900\tNone\n",
+      "CHEBI:38497\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0070469\tNone\n",
+      "CHEBI:38498\tNone\tobo:chiro#inhibitor_of\tNone\t_:riog00000282\tNone\n",
+      "CHEBI:38499\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005750\tNone\n",
+      "CHEBI:38500\tNone\tobo:chiro#inhibitor_of\tNone\t_:riog00000306\tNone\n",
+      "CHEBI:38501\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004129\tNone\n",
+      "CHEBI:38502\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0045275\tNone\n",
+      "CHEBI:38503\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008137\tNone\n",
+      "CHEBI:38637\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004713\tNone\n",
+      "CHEBI:39456\tNone\tobo:chiro#inhibitor_of\tNone\tHP:0000501\tNone\n",
+      "CHEBI:48001\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006412\tNone\n",
+      "CHEBI:48406\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016206\tNone\n",
+      "CHEBI:48422\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0001525\tNone\n",
+      "CHEBI:48550\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004032\tNone\n",
+      "CHEBI:49200\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0022804\tNone\n",
+      "CHEBI:49205\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000005373\tNone\n",
+      "CHEBI:50184\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006811\tNone\n",
+      "CHEBI:50185\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006633\tNone\n",
+      "CHEBI:50380\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003868\tNone\n",
+      "CHEBI:50382\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008120\tNone\n",
+      "CHEBI:50390\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003955\tNone\n",
+      "CHEBI:50427\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0070527\tNone\n",
+      "CHEBI:50445\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004000\tNone\n",
+      "CHEBI:50469\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004623\tNone\n",
+      "CHEBI:50502\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004156\tNone\n",
+      "CHEBI:50627\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004556\tNone\n",
+      "CHEBI:50628\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004558\tNone\n",
+      "CHEBI:50635\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009039\tNone\n",
+      "CHEBI:50643\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004337\tNone\n",
+      "CHEBI:50664\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008237\tNone\n",
+      "CHEBI:50683\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004146\tNone\n",
+      "CHEBI:50750\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003918\tNone\n",
+      "CHEBI:50790\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0070330\tNone\n",
+      "CHEBI:50914\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0035004\tNone\n",
+      "CHEBI:50916\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0001727\tNone\n",
+      "CHEBI:50925\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004674\tNone\n",
+      "CHEBI:50949\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0051610\tNone\n",
+      "CHEBI:51039\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0051583\tNone\n",
+      "CHEBI:52303\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003838\tNone\n",
+      "CHEBI:52425\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004308\tNone\n",
+      "CHEBI:52629\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004523\tNone\n",
+      "CHEBI:52629\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11676\tNone\n",
+      "CHEBI:52726\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0000502\tNone\n",
+      "CHEBI:53659\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0052597\tNone\n",
+      "CHEBI:53746\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003938\tNone\n",
+      "CHEBI:53756\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003964\tNone\n",
+      "CHEBI:53756\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11676\tNone\n",
+      "CHEBI:59105\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016881\tNone\n",
+      "CHEBI:59107\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004222\tNone\n",
+      "CHEBI:5924\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004252\tNone\n",
+      "CHEBI:59285\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004506\tNone\n",
+      "CHEBI:59321\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004058\tNone\n",
+      "CHEBI:59499\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016805\tNone\n",
+      "CHEBI:59517\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0071897\tNone\n",
+      "CHEBI:59647\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004758\tNone\n",
+      "CHEBI:59672\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004100\tNone\n",
+      "CHEBI:59897\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003964\tNone\n",
+      "CHEBI:59997\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004503\tNone\n",
+      "CHEBI:60186\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005388\tNone\n",
+      "CHEBI:60258\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008233\tNone\n",
+      "CHEBI:60280\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004359\tNone\n",
+      "CHEBI:60688\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004834\tNone\n",
+      "CHEBI:60901\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004746\tNone\n",
+      "CHEBI:61115\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004407\tNone\n",
+      "CHEBI:61908\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004517\tNone\n",
+      "CHEBI:62089\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0015930\tNone\n",
+      "CHEBI:62434\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004714\tNone\n",
+      "CHEBI:62530\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0050291\tNone\n",
+      "CHEBI:62608\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003994\tNone\n",
+      "CHEBI:62609\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0033978\tNone\n",
+      "CHEBI:62670\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004721\tNone\n",
+      "CHEBI:62871\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0045548\tNone\n",
+      "CHEBI:62915\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008373\tNone\n",
+      "CHEBI:63090\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004731\tNone\n",
+      "CHEBI:63146\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0030073\tNone\n",
+      "CHEBI:63156\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0047639\tNone\n",
+      "CHEBI:63173\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0042098\tNone\n",
+      "CHEBI:63330\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0044341\tNone\n",
+      "CHEBI:63332\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004035\tNone\n",
+      "CHEBI:63510\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005391\tNone\n",
+      "CHEBI:63674\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003867\tNone\n",
+      "CHEBI:63720\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004799\tNone\n",
+      "CHEBI:63932\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004511\tNone\n",
+      "CHEBI:63958\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0030244\tNone\n",
+      "CHEBI:63962\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000025350\tNone\n",
+      "CHEBI:64133\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004660\tNone\n",
+      "CHEBI:64152\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008234\tNone\n",
+      "CHEBI:64411\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000007961\tNone\n",
+      "CHEBI:64416\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0047794\tNone\n",
+      "CHEBI:64570\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004372\tNone\n",
+      "CHEBI:64670\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000024130\tNone\n",
+      "CHEBI:64696\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008415\tNone\n",
+      "CHEBI:64697\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000015390\tNone\n",
+      "CHEBI:64763\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004435\tNone\n",
+      "CHEBI:64919\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004144\tNone\n",
+      "CHEBI:64920\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000023089\tNone\n",
+      "CHEBI:64924\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008233\tNone\n",
+      "CHEBI:64924\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11103\tNone\n",
+      "CHEBI:64933\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0042438\tNone\n",
+      "CHEBI:64947\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11676\tNone\n",
+      "CHEBI:64955\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0030305\tNone\n",
+      "CHEBI:64964\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004051\tNone\n",
+      "CHEBI:64995\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004052\tNone\n",
+      "CHEBI:64996\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0050473\tNone\n",
+      "CHEBI:65001\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004806\tNone\n",
+      "CHEBI:65053\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008792\tNone\n",
+      "CHEBI:65064\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008825\tNone\n",
+      "CHEBI:65065\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009008\tNone\n",
+      "CHEBI:65232\tNone\tobo:chiro#inhibitor_of\tNone\t<http://purl.obolibrary.org/GO_0003809>\tNone\n",
+      "CHEBI:66921\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004718\tNone\n",
+      "CHEBI:66956\tNone\tobo:chiro#inhibitor_of\tNone\tHP:0100660\tNone\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CHEBI:67079\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006954\tNone\r",
+      "\r\n",
+      "CHEBI:67195\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005243\tNone\r",
+      "\r\n",
+      "CHEBI:67268\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008907\tNone\r",
+      "\r\n",
+      "CHEBI:68494\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006915\tNone\r",
+      "\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "chiro relationships -p obo:chiro#inhibitor_of"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5619e51c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/notebooks/OBO/CHEBI-Slimmer.ipynb → ...ples/Ontologies/CHEBI/CHEBI-Slimmer.ipynb b/notebooks/OBO/CHEBI-Slimmer.ipynb → ...ples/Ontologies/CHEBI/CHEBI-Slimmer.ipynb
diff --git a/docs/examples/Ontologies/CHEBI/index.rst b/docs/examples/Ontologies/CHEBI/index.rst
@@ -0,0 +1,11 @@
+.. _chebi_examples:
+
+CHEBI Examples
+==============
+
+.. toctree::
+   :maxdepth: 2
+
+   CHEBI-Predicates
+   CHEBI-Slimmer
+
diff --git a/notebooks/Neuro/CL-Neuro-Tutorial.ipynb → ...les/Ontologies/CL/CL-Neuro-Tutorial.ipynb b/notebooks/Neuro/CL-Neuro-Tutorial.ipynb → ...les/Ontologies/CL/CL-Neuro-Tutorial.ipynb
diff --git a/notebooks/CellType/LungEpithelialCell.ipynb → ...ogies/CL/Lung-Epithelial-Cell-Types.ipynb b/notebooks/CellType/LungEpithelialCell.ipynb → ...ogies/CL/Lung-Epithelial-Cell-Types.ipynb
@@ -17,7 +17,7 @@
     "\n",
     "An example of a biologist-friendly structure we might want to extract:\n",
     "\n",
-    " ![img](../images/lung-cells-src.png)"
+    " ![img](images/lung-cells-src.png)"
    ],
    "metadata": {
     "collapsed": false

diff --git a/notebooks/images/lung-cells-src.png → ...s/Ontologies/CL/images/lung-cells-src.png b/notebooks/images/lung-cells-src.png → ...s/Ontologies/CL/images/lung-cells-src.png
diff --git a/docs/examples/Ontologies/CL/index.rst b/docs/examples/Ontologies/CL/index.rst
@@ -0,0 +1,12 @@
+.. _cl_examples:
+
+CL Examples
+==============
+
+.. toctree::
+   :maxdepth: 2
+
+   CL-Neuro-Tutorial
+   Lung-Epithelial-Cell-Types
+
+