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diff --git a/_modules/oaklib/interfaces/association_provider_interface.html b/_modules/oaklib/interfaces/association_provider_interface.html
diff --git a/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt b/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt
@@ -61,7 +61,7 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl
 | [class_id](class_id.md) | 1..1 <br/> [Uriorcurie](Uriorcurie.md) | The class id | direct |
 | [class_label](class_label.md) | 0..1 <br/> [String](String.md) | The class label | direct |
 | [rank](rank.md) | 0..1 <br/> [Integer](Integer.md) | The rank of this result | direct |
-| [p_value](p_value.md) | 1..1 <br/> [Float](Float.md) | The p-value | direct |
+| [p_value](p_value.md) | 0..1 <br/> [Float](Float.md) | The p-value | direct |
 | [p_value_adjusted](p_value_adjusted.md) | 0..1 <br/> [Float](Float.md) | The adjusted p-value | direct |
 | [false_discovery_rate](false_discovery_rate.md) | 0..1 <br/> [Float](Float.md) | The false discovery rate | direct |
 | [fold_enrichment](fold_enrichment.md) | 0..1 <br/> [Float](Float.md) | The fold enrichment | direct |
@@ -163,7 +163,6 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: float
-    required: true
   p_value_adjusted:
     name: p_value_adjusted
     description: The adjusted p-value
@@ -308,7 +307,6 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: float
-    required: true
   p_value_adjusted:
     name: p_value_adjusted
     description: The adjusted p-value

diff --git a/_sources/datamodels/class-enrichment/p_value.md.txt b/_sources/datamodels/class-enrichment/p_value.md.txt
@@ -30,8 +30,6 @@ URI: [OBI:0000175](http://purl.obolibrary.org/obo/OBI_0000175)
 
 * Range: [Float](Float.md)
 
-* Required: True
-
 
 
 
@@ -66,7 +64,6 @@ owner: ClassEnrichmentResult
 domain_of:
 - ClassEnrichmentResult
 range: float
-required: true
 
 ```
 </details>
diff --git a/_sources/howtos/use-llms.rst.txt b/_sources/howtos/use-llms.rst.txt
@@ -1,3 +1,5 @@
+.. _use_llms
+
 How to use Large Language Models (LLMs) with OAK
 ===============================================
 

diff --git a/_sources/packages/implementations/llm.rst.txt b/_sources/packages/implementations/llm.rst.txt
@@ -3,6 +3,8 @@
 LLM Adapter
 =============
 
+See also :ref:`use_llms`
+
 Command Line Examples
 ----------------------
 
@@ -14,12 +16,25 @@ Use the :code:`llm` selector, wrapping an existing source
 
 Annotation
 ^^^^^^^^^^
+
 .. code:: shell
 
    runoak -i llm:sqlite:obo:hp annotate "abnormalities were found in the eye and the liver"
 
+Validation of Mappings
+^^^^^^^^^^^^^^^^^^^^^^
+
+.. code:: shell
+
+   runoak -i llm:sqlite:obo:go validate-mappings .desc//p=i "molecular_function"
+
+See:
+
+ - `MapperGPT <https://arxiv.org/abs/2310.03666>`_
+ - `GO RHEA Analysis <https://github.com/cmungall/rhea-go-llm-analysis>`_
+
 Code
 ----
-.. currentmodule:: oaklib.implementations.llm
+.. currentmodule:: oaklib.implementations.llm.llm_implementation
 
 .. autoclass:: LLMImplementation
diff --git a/class-enrichment/ClassEnrichmentResult.md b/class-enrichment/ClassEnrichmentResult.md
@@ -61,7 +61,7 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl
 | [class_id](class_id.md) | 1..1 <br/> [Uriorcurie](Uriorcurie.md) | The class id | direct |
 | [class_label](class_label.md) | 0..1 <br/> [String](String.md) | The class label | direct |
 | [rank](rank.md) | 0..1 <br/> [Integer](Integer.md) | The rank of this result | direct |
-| [p_value](p_value.md) | 1..1 <br/> [Float](Float.md) | The p-value | direct |
+| [p_value](p_value.md) | 0..1 <br/> [Float](Float.md) | The p-value | direct |
 | [p_value_adjusted](p_value_adjusted.md) | 0..1 <br/> [Float](Float.md) | The adjusted p-value | direct |
 | [false_discovery_rate](false_discovery_rate.md) | 0..1 <br/> [Float](Float.md) | The false discovery rate | direct |
 | [fold_enrichment](fold_enrichment.md) | 0..1 <br/> [Float](Float.md) | The fold enrichment | direct |
@@ -163,7 +163,6 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: float
-    required: true
   p_value_adjusted:
     name: p_value_adjusted
     description: The adjusted p-value
@@ -308,7 +307,6 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: float
-    required: true
   p_value_adjusted:
     name: p_value_adjusted
     description: The adjusted p-value

diff --git a/class-enrichment/p_value.md b/class-enrichment/p_value.md
@@ -30,8 +30,6 @@ URI: [OBI:0000175](http://purl.obolibrary.org/obo/OBI_0000175)
 
 * Range: [Float](Float.md)
 
-* Required: True
-
 
 
 
@@ -66,7 +64,6 @@ owner: ClassEnrichmentResult
 domain_of:
 - ClassEnrichmentResult
 range: float
-required: true
 
 ```
 </details>
diff --git a/cli.html b/cli.html
@@ -69,6 +69,7 @@
 <li class="toctree-l4"><a class="reference internal" href="#runoak-apply-obsolete">apply-obsolete</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#runoak-apply-taxon-constraints">apply-taxon-constraints</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#runoak-associations">associations</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#runoak-associations-counts">associations-counts</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#runoak-associations-matrix">associations-matrix</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#runoak-axioms">axioms</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#runoak-cache-clear">cache-clear</a></li>
@@ -1032,6 +1033,157 @@ <h4>associations<a class="headerlink" href="#runoak-associations" title="Link to
 <dd><p>Optional argument(s)</p>
 </dd></dl>
 
+</section>
+<section id="runoak-associations-counts">
+<h4>associations-counts<a class="headerlink" href="#runoak-associations-counts" title="Link to this heading"></a></h4>
+<p>Count associations, grouped by subject or object</p>
+<p>Example:</p>
+<blockquote>
+<div><p>runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations-counts</p>
+</div></blockquote>
+<p>This will default to summarzing by objects (HPO term), showing the number
+of associations for each term.</p>
+<p>This will be direct counts only. To include is-a closure, specify
+the closure predicate(s), e.g.</p>
+<p>Example:</p>
+<blockquote>
+<div><p>runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations -p i</p>
+</div></blockquote>
+<p>You can also group by other fields</p>
+<p>Example:</p>
+<blockquote>
+<div><p>runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations-counts –group-by subject</p>
+</div></blockquote>
+<p>This will show the number of associations for each disease.</p>
+<p>OAK also includes a number of specialized adapters that implement this method
+for particular databases.</p>
+<p>For example, to get the number of IEA associations for each GO term:</p>
+<blockquote>
+<div><p>runoak -i amigo: associations-counts  –limit -1 -F evidence_type=IEA –no-autolabel</p>
+</div></blockquote>
+<p>This can be constrained by species:</p>
+<blockquote>
+<div><p>runoak -i amigo:NCBITaxon:9606 associations-counts  –limit -1 -F evidence_type=IEA –no-autolabel</p>
+</div></blockquote>
+<p>Other options:</p>
+<p>This command accepts many of the same options as the associations command, see
+the docs for this command for details.</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>runoak<span class="w"> </span>associations-counts<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>TERMS<span class="o">]</span>...
+</pre></div>
+</div>
+<p class="rubric">Options</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-o">
+<span id="cmdoption-runoak-associations-counts-output"></span><span class="sig-name descname"><span class="pre">-o</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--output</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;output&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-o" title="Link to this definition"></a></dt>
+<dd><p>Output file, e.g. obo file</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-p">
+<span id="cmdoption-runoak-associations-counts-predicates"></span><span class="sig-name descname"><span class="pre">-p</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--predicates</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;predicates&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-p" title="Link to this definition"></a></dt>
+<dd><p>A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-autolabel">
+<span id="cmdoption-runoak-associations-counts-no-autolabel"></span><span class="sig-name descname"><span class="pre">--autolabel</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--no-autolabel</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-autolabel" title="Link to this definition"></a></dt>
+<dd><p>If set, results will automatically have labels assigned</p>
+<dl class="field-list simple">
+<dt class="field-odd">Default<span class="colon">:</span></dt>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">True</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-O">
+<span id="cmdoption-runoak-associations-counts-output-type"></span><span class="sig-name descname"><span class="pre">-O</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--output-type</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;output_type&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-O" title="Link to this definition"></a></dt>
+<dd><p>Desired output type</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-0">
+<span id="cmdoption-runoak-associations-counts-1"></span><span class="sig-name descname"><span class="pre">-o</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--output</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;output&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-0" title="Link to this definition"></a></dt>
+<dd><p>Output file, e.g. obo file</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-add-closure-fields">
+<span id="cmdoption-runoak-associations-counts-no-add-closure-fields"></span><span class="sig-name descname"><span class="pre">--add-closure-fields</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--no-add-closure-fields</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-add-closure-fields" title="Link to this definition"></a></dt>
+<dd><p>Add closure fields to the output</p>
+<dl class="field-list simple">
+<dt class="field-odd">Default<span class="colon">:</span></dt>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">False</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-association-predicates">
+<span class="sig-name descname"><span class="pre">--association-predicates</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;association_predicates&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-association-predicates" title="Link to this definition"></a></dt>
+<dd><p>A comma-separated list of predicates for the association relation</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-Q">
+<span id="cmdoption-runoak-associations-counts-terms-role"></span><span class="sig-name descname"><span class="pre">-Q</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--terms-role</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;terms_role&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-Q" title="Link to this definition"></a></dt>
+<dd><p>How to interpret query terms.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Default<span class="colon">:</span></dt>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">object</span></code></p>
+</dd>
+<dt class="field-even">Options<span class="colon">:</span></dt>
+<dd class="field-even"><p>subject | object | both</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-L">
+<span id="cmdoption-runoak-associations-counts-limit"></span><span class="sig-name descname"><span class="pre">-L</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--limit</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;limit&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-L" title="Link to this definition"></a></dt>
+<dd><p>Limit the number of results</p>
+<dl class="field-list simple">
+<dt class="field-odd">Default<span class="colon">:</span></dt>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">10</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-F">
+<span id="cmdoption-runoak-associations-counts-filter"></span><span class="sig-name descname"><span class="pre">-F</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--filter</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;filter&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-F" title="Link to this definition"></a></dt>
+<dd><p>Additional filters in K=V format</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-min-facet-count">
+<span class="sig-name descname"><span class="pre">--min-facet-count</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;min_facet_count&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-min-facet-count" title="Link to this definition"></a></dt>
+<dd><p>Minimum count for a facet to be included</p>
+<dl class="field-list simple">
+<dt class="field-odd">Default<span class="colon">:</span></dt>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">1</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-group-by">
+<span class="sig-name descname"><span class="pre">--group-by</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;group_by&gt;</span></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-group-by" title="Link to this definition"></a></dt>
+<dd><p>Group by subject or object</p>
+<dl class="field-list simple">
+<dt class="field-odd">Default<span class="colon">:</span></dt>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">object</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Arguments</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-associations-counts-arg-TERMS">
+<span class="sig-name descname"><span class="pre">TERMS</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-runoak-associations-counts-arg-TERMS" title="Link to this definition"></a></dt>
+<dd><p>Optional argument(s)</p>
+</dd></dl>
+
 </section>
 <section id="runoak-associations-matrix">
 <h4>associations-matrix<a class="headerlink" href="#runoak-associations-matrix" title="Link to this heading"></a></h4>
@@ -1979,6 +2131,12 @@ <h4>enrichment<a class="headerlink" href="#runoak-enrichment" title="Link to thi
 <dd><p>If true, filter out redundant terms</p>
 </dd></dl>
 
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-runoak-enrichment-allow-labels">
+<span id="cmdoption-runoak-enrichment-no-allow-labels"></span><span class="sig-name descname"><span class="pre">--allow-labels</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--no-allow-labels</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-runoak-enrichment-allow-labels" title="Link to this definition"></a></dt>
+<dd><p>If true, allow labels as well as CURIEs in the input files</p>
+</dd></dl>
+
 <p class="rubric">Arguments</p>
 <dl class="std option">
 <dt class="sig sig-object std" id="cmdoption-runoak-enrichment-arg-TERMS">
@@ -5460,16 +5618,25 @@ <h4>validate-mappings<a class="headerlink" href="#runoak-validate-mappings" titl
 <div><p>runoak validate-mappings -i db/uberon.db -o bad-mappings.sssom.tsv</p>
 </div></blockquote>
 <p>By default this will attempt to download and connect to
-sqlite versions of different ontologies.</p>
-<p>You can customize this:</p>
+sqlite versions of different ontologies, when attempting to resolve a foreign
+subject or object id.</p>
+<p>You can customize this mapping:</p>
 <blockquote>
 <div><p>runoak validate-mappings -i db/uberon.db –adapter-mapping uberon=db/uberon.db             –adapter-mapping zfa=db/zfa.db</p>
 </div></blockquote>
+<p>This will use a local sqlite file for ZFA:nnnnnnn IDs.</p>
 <p>You can use “*” as a wildcard, in the case where you have an application ontology
 with many mapped entities merged in:</p>
 <blockquote>
 <div><p>runoak validate-mappings -i db/uberon.db –adapter-mapping “*”=db/merged.db”</p>
 </div></blockquote>
+<p>The default behavior for this command is to perform deterministic rule-based
+checks; for example, the mapped IDs should not be obsolete, and if the mapping
+is skos:exactMatch, then the cardinality is expected to be 1:1.</p>
+<p>Other adapters may choose to implement bespoke behaviors. In future there
+might be a boomer adapter that will perform probabilistic reasoning on the
+mappings. The experimental LLM backend will use an LLM to qualitatively
+validate mappings (see the LLM how-to guide for more details).</p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>runoak<span class="w"> </span>validate-mappings<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>TERMS<span class="o">]</span>...
 </pre></div>
 </div>