biopragmatics · cthoyt · Jun 12, 2026 · Jun 12, 2026 · Jun 12, 2026 · Jun 12, 2026
diff --git a/docs/source/artifacts.rst b/docs/source/artifacts.rst
@@ -1,45 +1,52 @@
-SeMRA Raw Semantic Mappings Database
-====================================
+######################################
+ SeMRA Raw Semantic Mappings Database
+######################################
 
 .. automodapi:: semra.database
     :no-heading:
 
-Domain-specific Processed Mapping Databases
-===========================================
+#############################################
+ Domain-specific Processed Mapping Databases
+#############################################
 
 .. automodapi:: semra.landscape
     :no-heading:
 
-Disease
--------
+*********
+ Disease
+*********
 
 .. automodapi:: semra.landscape.disease
     :include-all-objects:
     :no-heading:
 
-Cell and Cell Line
-------------------
+********************
+ Cell and Cell Line
+********************
 
 .. automodapi:: semra.landscape.cell
     :include-all-objects:
     :no-heading:
 
-Protein Complex
----------------
+*****************
+ Protein Complex
+*****************
 
 .. automodapi:: semra.landscape.complex
     :include-all-objects:
     :no-heading:
 
-Gene
-----
+******
+ Gene
+******
 
 .. automodapi:: semra.landscape.gene
     :include-all-objects:
     :no-heading:
 
-Anatomy
--------
+*********
+ Anatomy
+*********
 
 .. automodapi:: semra.landscape.anatomy
     :include-all-objects:

diff --git a/docs/source/cli.rst b/docs/source/cli.rst
@@ -1,5 +1,6 @@
-Command Line Interface
-======================
+########################
+ Command Line Interface
+########################
 
 semra automatically installs the command ``semra``. See ``semra --help`` for usage
 details.

diff --git a/docs/source/cypher.rst b/docs/source/cypher.rst
@@ -1,5 +1,6 @@
-Querying with Cypher
-====================
+######################
+ Querying with Cypher
+######################
 
 SeMRA constructs data artifacts and docker configuration for locally deploying a Neo4j
 graph databases and a web application via :func:`semra.io.write_neo4j` (for example
@@ -21,8 +22,9 @@ The contents of the grpah database have the following schema:
 Below, some example Cypher queries are given to show what is possible by direct querying
 of the database.
 
-Lookup by CURIE
----------------
+*****************
+ Lookup by CURIE
+*****************
 
 The following Cypher queries allow for looking up concepts, mappings, evidences, and
 mapping sets.
@@ -79,8 +81,9 @@ the name:
     WHERE n.curie = "cellosaurus:0440"
     RETURN n.name
 
-Traversing Mappings
--------------------
+*********************
+ Traversing Mappings
+*********************
 
 Get all targets for exact match mappings where ``cellosaurus:0440`` is the source:
 
@@ -176,8 +179,9 @@ sets and authors:
         (e)-[:hasAuthor]->(author:concept)
     RETURN source, target, m, e, mset, author
 
-Neo4j Output Reference
-----------------------
+************************
+ Neo4j Output Reference
+************************
 
 .. automodapi:: semra.io.neo4j_io
     :skip: write_neo4j

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,5 +1,6 @@
-SeMRA |release| Documentation
-=============================
+###############################
+ SeMRA |release| Documentation
+###############################
 
 The Semantic Mapping Reasoner and Assembler (SeMRA) assembles semantic mappings to
 support data- and knowledge integration across domains. This Python package can be used
@@ -37,14 +38,21 @@ the digital humanities. Get started by loading external mappings:
         # load mappings from any standardized SSSOM file as a file path or URL
         "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
         license="spdx:CC0-1.0",
-         mapping_set_title="biomappings",
+        mapping_set_title="biomappings",
     )
 
 Or by creating your own mappings:
 
 .. code-block:: python
 
-    from semra import Reference, Mapping, EXACT_MATCH, SimpleEvidence, MappingSet, MANUAL_MAPPING
+    from semra import (
+        Reference,
+        Mapping,
+        EXACT_MATCH,
+        SimpleEvidence,
+        MappingSet,
+        MANUAL_MAPPING,
+    )
 
     r1 = Reference(prefix="chebi", identifier="107635", name="2,3-diacetyloxybenzoic")
     r2 = Reference(prefix="mesh", identifier="C011748", name="tosiben")
@@ -58,17 +66,22 @@ Or by creating your own mappings:
                 justification=MANUAL_MAPPING,
                 confidence=0.99,
                 author=Reference(
-                    prefix="orcid", identifier="0000-0003-4423-4370", name="Charles Tapley Hoyt"
+                    prefix="orcid",
+                    identifier="0000-0003-4423-4370",
+                    name="Charles Tapley Hoyt",
                 ),
                 mapping_set=MappingSet(
-                    name="biomappings", license="CC0", confidence=0.90,
+                    name="biomappings",
+                    license="CC0",
+                    confidence=0.90,
                 ),
             )
-        ]
+        ],
     )
 
-Features
---------
+**********
+ Features
+**********
 
 1. An object model for semantic mappings (based on the `Simple Standard for Sharing
    Ontological Mappings (SSSOM) <https://mapping-commons.github.io/sssom/>`_ and
@@ -82,67 +95,76 @@ Here's a conceptual diagram of SeMRA's architecture:
 
 .. image:: img/architecture.svg
 
-What SeMRA Isn't
-----------------
-SeMRA isn't a tool for predicting semantic mappings like
-`Logmap <https://github.com/ernestojimenezruiz/logmap-matcher>`_,
-`LOOM <https://www.bioontology.org/wiki/LOOM>`_, or `K-Boom <https://www.biorxiv.org/content/10.1101/048843v3>`_.
-Further, it's not a tool for reviewing predicted semantic mappings like
-`MapperGPT <https://arxiv.org/abs/2310.03666>`_. However, any of the outputs
-from these workflows could be used as inputs to SeMRA's assembly and inference
-pipeline.
-
-SeMRA isn't a service that lives on the web, but it does allow you to deploy a local
-web application for your use-case specific mapping database.
-
-SeMRA isn't itself a curation tool, but it has the option to integrate :mod:`biomappings`
-in deployments of its local web application for curation purposes.
-
-SeMRA isn't an tool for merging ontologies like `CoMerger <https://arxiv.org/abs/2005.02659>`_
-or `OntoMerger <https://arxiv.org/abs/2206.02238>`_, but it outputs detailed
-and comprehensive semantic mappings that are critical as input for such tools.
-
-Artifacts Overview
-------------------
-
-SeMRA was used to produce the `SeMRA Raw Semantic Mappings Database <https://doi.org/10.5281/zenodo.11082038>`_,
-a comprehensive raw semantic mappings database, and five domain-specific
-mapping databases (each with a landscape analysis). The results of the
-domain-specific landscape analyses can be found on the SeMRA `GitHub
+******************
+ What SeMRA Isn't
+******************
+
+SeMRA isn't a tool for predicting semantic mappings like `Logmap
+<https://github.com/ernestojimenezruiz/logmap-matcher>`_, `LOOM
+<https://www.bioontology.org/wiki/LOOM>`_, or `K-Boom
+<https://www.biorxiv.org/content/10.1101/048843v3>`_. Further, it's not a tool for
+reviewing predicted semantic mappings like `MapperGPT
+<https://arxiv.org/abs/2310.03666>`_. However, any of the outputs from these workflows
+could be used as inputs to SeMRA's assembly and inference pipeline.
+
+SeMRA isn't a service that lives on the web, but it does allow you to deploy a local web
+application for your use-case specific mapping database.
+
+SeMRA isn't itself a curation tool, but it has the option to integrate
+:mod:`biomappings` in deployments of its local web application for curation purposes.
+
+SeMRA isn't an tool for merging ontologies like `CoMerger
+<https://arxiv.org/abs/2005.02659>`_ or `OntoMerger
+<https://arxiv.org/abs/2206.02238>`_, but it outputs detailed and comprehensive semantic
+mappings that are critical as input for such tools.
+
+********************
+ Artifacts Overview
+********************
+
+SeMRA was used to produce the `SeMRA Raw Semantic Mappings Database
+<https://doi.org/10.5281/zenodo.11082038>`_, a comprehensive raw semantic mappings
+database, and five domain-specific mapping databases (each with a landscape analysis).
+The results of the domain-specific landscape analyses can be found on the SeMRA `GitHub
 repository <https://github.com/biopragmatics/semra/tree/main/landscape>`_.
 
-================== ============================== ================= ===============================================================================================
+================== ============================== ================= =============================================================================
 Domain             Docs and Reproduction          Database Download Analysis
-================== ============================== ================= ===============================================================================================
-Raw                :mod:`semra.database`          |raw|              N/A
-Disease            :mod:`semra.landscape.disease` |disease|         `Disease Analysis <https://github.com/biopragmatics/semra/tree/main/landscape/disease#readme>`_
-Cell and Cell Line :mod:`semra.landscape.cell`    |cell|            `Cell Analysis <https://github.com/biopragmatics/semra/tree/main/landscape/cell#readme>`_
-Anatomy            :mod:`semra.landscape.anatomy` |anatomy|         `Anatomy Analysis <https://github.com/biopragmatics/semra/tree/main/landscape/anatomy#readme>`_
-Protein Complex    :mod:`semra.landscape.complex` |complex|         `Complex Analysis <https://github.com/biopragmatics/semra/tree/main/landscape/complex#readme>`_
-Gene               :mod:`semra.landscape.gene`    |gene|            `Gene Analysis <https://github.com/biopragmatics/semra/tree/main/landscape/gene#readme>`_
-================== ============================== ================= ===============================================================================================
+================== ============================== ================= =============================================================================
+Raw                :mod:`semra.database`          |raw|             N/A
+Disease            :mod:`semra.landscape.disease` |disease|         `Disease Analysis
+                                                                    <https://github.com/biopragmatics/semra/tree/main/landscape/disease#readme>`_
+Cell and Cell Line :mod:`semra.landscape.cell`    |cell|            `Cell Analysis
+                                                                    <https://github.com/biopragmatics/semra/tree/main/landscape/cell#readme>`_
+Anatomy            :mod:`semra.landscape.anatomy` |anatomy|         `Anatomy Analysis
+                                                                    <https://github.com/biopragmatics/semra/tree/main/landscape/anatomy#readme>`_
+Protein Complex    :mod:`semra.landscape.complex` |complex|         `Complex Analysis
+                                                                    <https://github.com/biopragmatics/semra/tree/main/landscape/complex#readme>`_
+Gene               :mod:`semra.landscape.gene`    |gene|            `Gene Analysis
+                                                                    <https://github.com/biopragmatics/semra/tree/main/landscape/gene#readme>`_
+================== ============================== ================= =============================================================================
 
 .. |disease| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091885.svg
-  :target: https://doi.org/10.5281/zenodo.11091885
+    :target: https://doi.org/10.5281/zenodo.11091885
 
 .. |cell| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091580.svg
-  :target: https://doi.org/10.5281/zenodo.11091580
+    :target: https://doi.org/10.5281/zenodo.11091580
 
 .. |anatomy| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091802.svg
-  :target: https://doi.org/10.5281/zenodo.11091802
+    :target: https://doi.org/10.5281/zenodo.11091802
 
 .. |complex| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091421.svg
-  :target: https://doi.org/10.5281/zenodo.11091421
+    :target: https://doi.org/10.5281/zenodo.11091421
 
 .. |gene| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11092012.svg
-  :target: https://doi.org/10.5281/zenodo.11092012
+    :target: https://doi.org/10.5281/zenodo.11092012
 
 .. |raw| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11082038.svg
-  :target: https://doi.org/10.5281/zenodo.11082038
-
+    :target: https://doi.org/10.5281/zenodo.11082038
 
-Table of Contents
------------------
+*******************
+ Table of Contents
+*******************
 
 .. toctree::
     :maxdepth: 2
@@ -159,8 +181,9 @@ Table of Contents
     cli
     cypher
 
-Indices and Tables
-------------------
+********************
+ Indices and Tables
+********************
 
 - :ref:`genindex`
 - :ref:`modindex`

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -1,5 +1,6 @@
-Installation
-============
+##############
+ Installation
+##############
 
 The most recent release can be installed from `PyPI <https://pypi.org/project/semra>`_
 with uv:
@@ -14,8 +15,9 @@ or with pip:
 
     $ python3 -m pip install semra
 
-Installing from git
--------------------
+*********************
+ Installing from git
+*********************
 
 The most recent code and data can be installed directly from GitHub with uv:
 
@@ -29,8 +31,9 @@ or with pip:
 
     $ python3 -m pip install git+https://github.com/biopragmatics/semra.git
 
-Installing for development
---------------------------
+****************************
+ Installing for development
+****************************
 
 To install in development mode with uv:
 

diff --git a/docs/source/io.rst b/docs/source/io.rst
@@ -1,5 +1,6 @@
-Getting and Writing Semantic Mappings
-=====================================
+#######################################
+ Getting and Writing Semantic Mappings
+#######################################
 
 .. automodapi:: semra.io
     :no-heading:
diff --git a/docs/source/pipeline.rst b/docs/source/pipeline.rst
@@ -1,5 +1,6 @@
-Mapping Assembly Pipeline
-=========================
+###########################
+ Mapping Assembly Pipeline
+###########################
 
 .. automodapi:: semra.pipeline
     :no-heading:

diff --git a/docs/source/reference.rst b/docs/source/reference.rst
@@ -1,5 +1,6 @@
-Reference
-=========
+###########
+ Reference
+###########
 
 This contains several SeMRA submodules with low-level functionality. You can use these
 to build your own mapping processing workflows and I/O.

diff --git a/docs/source/struct.rst b/docs/source/struct.rst
@@ -1,5 +1,6 @@
-Data Structure
-==============
+################
+ Data Structure
+################
 
 .. automodapi:: semra.struct
     :skip: Reference,Triple

diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
@@ -1,5 +1,6 @@
-Prioritizing CURIEs in a Dataframe
-==================================
+####################################
+ Prioritizing CURIEs in a Dataframe
+####################################
 
 SeMRA provides tools for data scientists to standardize references using semantic
 mappings.