association graphs (#828)

* Added association-graphs command * format * format
INCATools · Feb 11, 2025 · f9651e9 · f9651e9
1 parent 22ebc5c
commit f9651e9
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diff --git a/docs/examples/AdHoc/Summarizing-with-LLMs.ipynb b/docs/examples/AdHoc/Summarizing-with-LLMs.ipynb
diff --git a/docs/examples/AdHoc/index.rst b/docs/examples/AdHoc/index.rst
@@ -0,0 +1,10 @@
+.. _ad_hoc_examples:
+
+Ad Hoc Examples
+================
+
+.. toctree::
+   :maxdepth: 2
+
+   Summarizing-with-LLMs
+   Text-Content-Analysis
diff --git a/docs/examples/Commands/index.rst b/docs/examples/Commands/index.rst
@@ -8,6 +8,7 @@ Commands
 
    Apply
    Associations
+   Crawl
    DiffViaMappings
    Disjoints
    Enrichment

diff --git a/docs/examples/OntologyEditorsGuide/index.rst b/docs/examples/OntologyEditorsGuide/index.rst
@@ -0,0 +1,9 @@
+.. _ontology_editing_examples:
+
+Ontology Editing Examples
+================
+
+.. toctree::
+   :maxdepth: 2
+
+   Edit-File-Examples
diff --git a/docs/examples/index.rst b/docs/examples/index.rst
@@ -12,3 +12,5 @@ All the examples here are Jupyter notebooks that can be run interactively.
    Ontologies/index
    Adapters/index
    Interfaces/index
+   OntologyEditorsGraph/index
+   AdHoc/index
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,6 +23,7 @@ kgcl-schema = "^0.6.9"
 
 funowl = ">=0.2.0"
 gilda = {version = ">=1.0.0", optional = true}
+bioservices = {version = "*", optional = true}
 semsimian = {version = ">=0.2.18", optional = true}
 kgcl-rdflib = "0.5.0"
 llm = "^0.14"
@@ -77,6 +78,7 @@ boomerang = "oaklib.utilities.mapping.boomer_utils:main"
 [tool.poetry.extras]
 docs = ["Sphinx", "sphinx-rtd-theme", "sphinxcontrib-mermaid", "sphinx-copybutton"]
 gilda = ["scipy", "gilda", "urllib3"]
+bioservices = ["bioservices"]
 llm = ["llm", "aiohttp", "html2text"]
 seaborn = ["seaborn"]
 semsimian = ["semsimian"]