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mapping-commons · Feb 13, 2024 · 07fa76b · 07fa76b
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diff --git a/docs/technical_docs/cliquesummary.rst b/docs/technical_docs/cliquesummary.rst
@@ -1,4 +1,7 @@
-# sssom-cliquesummary
+.. _clique-summary:
+
+Clique summary
+==============
 
 Data dictionary for clique summary
 
@@ -9,62 +12,62 @@ Slots:
     :header-rows: 1
 
     * - Slot Name
-        - URI
-        - Range
+      - URI
+      - Range
     * - id
-        - http://www.w3.org/2002/07/owl#id
-        - http://www.w3.org/2001/XMLSchema#string
+      - http://www.w3.org/2002/07/owl#id
+      - http://www.w3.org/2001/XMLSchema#string
     * - members
-        - http://w3id.org/sssom/schema/cliquesummary/members
-        - http://www.w3.org/2001/XMLSchema#string
+      - http://w3id.org/sssom/schema/cliquesummary/members
+      - http://www.w3.org/2001/XMLSchema#string
     * - members_labels
-        - http://w3id.org/sssom/schema/cliquesummary/members_labels
-        - http://www.w3.org/2001/XMLSchema#string
+      - http://w3id.org/sssom/schema/cliquesummary/members_labels
+      - http://www.w3.org/2001/XMLSchema#string
     * - num_members
-        - http://w3id.org/sssom/schema/cliquesummary/num_members
-        - http://www.w3.org/2001/XMLSchema#integer
+      - http://w3id.org/sssom/schema/cliquesummary/num_members
+      - http://www.w3.org/2001/XMLSchema#integer
     * - sources
-        - http://w3id.org/sssom/schema/cliquesummary/sources
-        - http://www.w3.org/2001/XMLSchema#string
+      - http://w3id.org/sssom/schema/cliquesummary/sources
+      - http://www.w3.org/2001/XMLSchema#string
     * - num_sources
-        - http://w3id.org/sssom/schema/cliquesummary/num_sources
-        - http://www.w3.org/2001/XMLSchema#integer
+      - http://w3id.org/sssom/schema/cliquesummary/num_sources
+      - http://www.w3.org/2001/XMLSchema#integer
     * - max_confidence
-        - http://w3id.org/sssom/schema/cliquesummary/max_confidence
-        - http://www.w3.org/2001/XMLSchema#double
+      - http://w3id.org/sssom/schema/cliquesummary/max_confidence
+      - http://www.w3.org/2001/XMLSchema#double
     * - min_confidence
-        - http://w3id.org/sssom/schema/cliquesummary/min_confidence
-        - http://www.w3.org/2001/XMLSchema#double
+      - http://w3id.org/sssom/schema/cliquesummary/min_confidence
+      - http://www.w3.org/2001/XMLSchema#double
     * - avg_confidence
-        - http://w3id.org/sssom/schema/cliquesummary/avg_confidence
-        - http://www.w3.org/2001/XMLSchema#double
+      - http://w3id.org/sssom/schema/cliquesummary/avg_confidence
+      - http://www.w3.org/2001/XMLSchema#double
     * - is_conflated
-        - http://w3id.org/sssom/schema/cliquesummary/is_conflated
-        - http://www.w3.org/2001/XMLSchema#boolean
+      - http://w3id.org/sssom/schema/cliquesummary/is_conflated
+      - http://www.w3.org/2001/XMLSchema#boolean
     * - is_all_conflated
-        - http://w3id.org/sssom/schema/cliquesummary/is_all_conflated
-        - http://www.w3.org/2001/XMLSchema#boolean
+      - http://w3id.org/sssom/schema/cliquesummary/is_all_conflated
+      - http://www.w3.org/2001/XMLSchema#boolean
     * - total_conflated
-        - http://w3id.org/sssom/schema/cliquesummary/total_conflated
-        - http://www.w3.org/2001/XMLSchema#integer
+      - http://w3id.org/sssom/schema/cliquesummary/total_conflated
+      - http://www.w3.org/2001/XMLSchema#integer
     * - proportion_conflated
-        - http://w3id.org/sssom/schema/cliquesummary/proportion_conflated
-        - http://www.w3.org/2001/XMLSchema#double
+      - http://w3id.org/sssom/schema/cliquesummary/proportion_conflated
+      - http://www.w3.org/2001/XMLSchema#double
     * - conflation_score
-        - http://w3id.org/sssom/schema/cliquesummary/conflation_score
-        - http://www.w3.org/2001/XMLSchema#double
+      - http://w3id.org/sssom/schema/cliquesummary/conflation_score
+      - http://www.w3.org/2001/XMLSchema#double
     * - members_count
-        - http://w3id.org/sssom/schema/cliquesummary/members_count
-        - http://www.w3.org/2001/XMLSchema#integer
+      - http://w3id.org/sssom/schema/cliquesummary/members_count
+      - http://www.w3.org/2001/XMLSchema#integer
     * - min_count_by_source
-        - http://w3id.org/sssom/schema/cliquesummary/min_count_by_source
-        - http://www.w3.org/2001/XMLSchema#integer
+      - http://w3id.org/sssom/schema/cliquesummary/min_count_by_source
+      - http://www.w3.org/2001/XMLSchema#integer
     * - max_count_by_source
-        - http://w3id.org/sssom/schema/cliquesummary/max_count_by_source
-        - http://www.w3.org/2001/XMLSchema#integer
+      - http://w3id.org/sssom/schema/cliquesummary/max_count_by_source
+      - http://www.w3.org/2001/XMLSchema#integer
     * - avg_count_by_source
-        - http://w3id.org/sssom/schema/cliquesummary/avg_count_by_source
-        - http://www.w3.org/2001/XMLSchema#double
+      - http://w3id.org/sssom/schema/cliquesummary/avg_count_by_source
+      - http://www.w3.org/2001/XMLSchema#double
     * - harmonic_mean_count_by_source
-        - http://w3id.org/sssom/schema/cliquesummary/harmonic_mean_count_by_source
-        - http://www.w3.org/2001/XMLSchema#double
+      - http://w3id.org/sssom/schema/cliquesummary/harmonic_mean_count_by_source
+      - http://www.w3.org/2001/XMLSchema#double
diff --git a/docs/technical_docs/context.rst b/docs/technical_docs/context.rst
@@ -1,11 +1,10 @@
-Utilities for loading JSON-LD contexts
-======================================
+.. _context:
 
-This module provides utility functions for loading JSON-LD contexts.
+JSON-LD context-loading utilities.
+==================================
 
+This module provides utility functions for loading JSON-LD contexts.
 
-Functions
----------
 
 **get_converter**
 

diff --git a/docs/technical_docs/writers.rst b/docs/technical_docs/writers.rst
@@ -1,4 +1,7 @@
-## Serialization Functions for SSSOM
+.. _writers:
+
+Serialization Functions for SSSOM
+=================================
 
 This module contains functions for serializing SSSOM mapping set dataframes to various formats, including TSV, OWL, JSON, FHIR JSON, and RDF.
 
@@ -9,26 +12,26 @@ This module contains functions for serializing SSSOM mapping set dataframes to v
     :header-rows: 1
 
     * - Writer Function
-        - Output Format
-        - Description
+      - Output Format
+      - Description
     * - `write_table`
-        - TSV
-        - This function writes a `MappingSetDataFrame` object to a file as a table.
+      - TSV
+      - This function writes a `MappingSetDataFrame` object to a file as a table.
     * - `write_owl`
-        - OWL
-        - This function writes a `MappingSetDataFrame` object to a file as OWL.
+      - OWL
+      - This function writes a `MappingSetDataFrame` object to a file as OWL.
     * - `write_ontoportal_json`
-        - Ontoportal JSON
-        - This function writes a `MappingSetDataFrame` object to a file as the ontoportal mapping JSON model.
+      - Ontoportal JSON
+      - This function writes a `MappingSetDataFrame` object to a file as the ontoportal mapping JSON model.
     * - `write_fhir_json`
-        - FHIR JSON
-        - This function writes a `MappingSetDataFrame` object to a file as FHIR ConceptMap JSON.
+      - FHIR JSON
+      - This function writes a `MappingSetDataFrame` object to a file as FHIR ConceptMap JSON.
     * - `write_json`
-        - JSON
-        - This function writes a `MappingSetDataFrame` object to a file as JSON.
+      - JSON
+      - This function writes a `MappingSetDataFrame` object to a file as JSON.
     * - `write_rdf`
-        - RDF
-        - This function writes a `MappingSetDataFrame` object to a file as RDF.
+      - RDF
+      - This function writes a `MappingSetDataFrame` object to a file as RDF.
 
 The `get_writer_function()` function can be used to obtain the appropriate writer function based on the desired output format.
 
@@ -39,23 +42,23 @@ The `get_writer_function()` function can be used to obtain the appropriate write
     :header-rows: 1
 
     * - Converter Function
-        - Output Format
-        - Description
+      - Output Format
+      - Description
     * - `to_owl_graph`
-        - OWL graph
-        - This function converts a `MappingSetDataFrame` object to OWL in an RDF graph.
+      - OWL graph
+      - This function converts a `MappingSetDataFrame` object to OWL in an RDF graph.
     * - `to_rdf_graph`
-        - RDF graph
-        - This function converts a `MappingSetDataFrame` object to an RDF graph.
+      - RDF graph
+      - This function converts a `MappingSetDataFrame` object to an RDF graph.
     * - `to_fhir_json`
-        - FHIR JSON
-        - This function converts a `MappingSetDataFrame` object to a JSON object.
+      - FHIR JSON
+      - This function converts a `MappingSetDataFrame` object to a JSON object.
     * - `to_json`
-        - JSON
-        - This function converts a `MappingSetDataFrame` object to a JSON object.
+      - JSON
+      - This function converts a `MappingSetDataFrame` object to a JSON object.
     * - `to_ontoportal_json`
-        - Ontoportal JSON
-        - This function converts a `MappingSetDataFrame` object to a list of ontoportal mapping JSON objects.
+      - Ontoportal JSON
+      - This function converts a `MappingSetDataFrame` object to a list of ontoportal mapping JSON objects.
 
 ### Support Methods
 
@@ -64,11 +67,11 @@ The `get_writer_function()` function can be used to obtain the appropriate write
     :header-rows: 1
 
     * - Method
-        - Description
+      - Description
     * - `_get_separator`
-        - Returns the appropriate separator character for the specified table format.
+      - Returns the appropriate separator character for the specified table format.
     * - `_inject_annotation_properties`
-        - Injects annotation properties into an RDF graph.
+      - Injects annotation properties into an RDF graph.
 
 ### Writing Tables