Deploying to gh-pages from @ 10ccb21 🚀

_modules/index.html

@@ -95,6 +95,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="oaklib/implementations/ols/ols_implementation.html">oaklib.implementations.ols.ols_implementation</a></li>
 <li><a href="oaklib/implementations/ontobee/ontobee_implementation.html">oaklib.implementations.ontobee.ontobee_implementation</a></li>
 <li><a href="oaklib/implementations/owlery/owlery_implementation.html">oaklib.implementations.owlery.owlery_implementation</a></li>
+<li><a href="oaklib/implementations/pantherdb/pantherdb_implementation.html">oaklib.implementations.pantherdb.pantherdb_implementation</a></li>
 <li><a href="oaklib/implementations/pronto/pronto_implementation.html">oaklib.implementations.pronto.pronto_implementation</a></li>
 <li><a href="oaklib/implementations/simpleobo/simple_obo_implementation.html">oaklib.implementations.simpleobo.simple_obo_implementation</a></li>
 <li><a href="oaklib/implementations/sparql/sparql_implementation.html">oaklib.implementations.sparql.sparql_implementation</a></li>

_modules/oaklib/interfaces/class_enrichment_calculation_interface.html

@@ -88,6 +88,8 @@ <h1>Source code for oaklib.interfaces.class_enrichment_calculation_interface</h1
 <span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Iterable</span><span class="p">,</span> <span class="n">Iterator</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span>
 
+<span class="kn">from</span> <span class="nn">typing_extensions</span> <span class="kn">import</span> <span class="n">ClassVar</span>
+
 <span class="kn">from</span> <span class="nn">oaklib.datamodels.association</span> <span class="kn">import</span> <span class="n">Association</span>
 <span class="kn">from</span> <span class="nn">oaklib.datamodels.class_enrichment</span> <span class="kn">import</span> <span class="n">ClassEnrichmentResult</span>
 <span class="kn">from</span> <span class="nn">oaklib.datamodels.item_list</span> <span class="kn">import</span> <span class="n">ItemList</span>
@@ -113,6 +115,8 @@ <h1>Source code for oaklib.interfaces.class_enrichment_calculation_interface</h1
 <span class="sd">    test for over representation of a disease in a set of genes.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
+    <span class="n">requires_associations</span><span class="p">:</span> <span class="n">ClassVar</span><span class="p">[</span><span class="nb">bool</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+
 <div class="viewcode-block" id="ClassEnrichmentCalculationInterface.enriched_classes">
 <a class="viewcode-back" href="../../../packages/interfaces/class-enrichment.html#oaklib.interfaces.class_enrichment_calculation_interface.ClassEnrichmentCalculationInterface.enriched_classes">[docs]</a>
     <span class="k">def</span> <span class="nf">enriched_classes</span><span class="p">(</span>

_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt

@@ -27,6 +27,8 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl
 
       ClassEnrichmentResult : descendant_of_more_informative_result
 
+      ClassEnrichmentResult : direction
+
       ClassEnrichmentResult : false_discovery_rate
 
       ClassEnrichmentResult : fold_enrichment
@@ -70,6 +72,7 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl
 | [background_total](background_total.md) | 0..1 <br/> [Integer](Integer.md) | The background total | direct |
 | [ancestor_of_more_informative_result](ancestor_of_more_informative_result.md) | 0..1 <br/> [Boolean](Boolean.md) | This term is more general than a previously reported result | direct |
 | [descendant_of_more_informative_result](descendant_of_more_informative_result.md) | 0..1 <br/> [Boolean](Boolean.md) | This term is more specific than a previously reported result | direct |
+| [direction](direction.md) | 0..1 <br/> [Integer](Integer.md) | The direction of the enrichment | direct |
 
 
 
@@ -243,6 +246,14 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: boolean
+  direction:
+    name: direction
+    description: The direction of the enrichment
+    from_schema: https://w3id.org/oak/class-enrichment
+    rank: 1000
+    domain_of:
+    - ClassEnrichmentResult
+    range: integer
 
 ```
 </details>
@@ -400,6 +411,16 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: boolean
+  direction:
+    name: direction
+    description: The direction of the enrichment
+    from_schema: https://w3id.org/oak/class-enrichment
+    rank: 1000
+    alias: direction
+    owner: ClassEnrichmentResult
+    domain_of:
+    - ClassEnrichmentResult
+    range: integer
 
 ```
 </details>

_sources/datamodels/class-enrichment/direction.md.txt

@@ -0,0 +1,68 @@
+# Slot: direction
+
+
+_The direction of the enrichment_
+
+
+
+URI: [ontoenrich:direction](https://w3id.org/oak/class-enrichment/direction)
+
+
+
+<!-- no inheritance hierarchy -->
+
+
+
+
+## Applicable Classes
+
+| Name | Description | Modifies Slot |
+| --- | --- | --- |
+[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result |  no  |
+
+
+
+
+
+
+
+## Properties
+
+* Range: [Integer](Integer.md)
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/oak/class-enrichment
+
+
+
+
+## LinkML Source
+
+<details>
+```yaml
+name: direction
+description: The direction of the enrichment
+from_schema: https://w3id.org/oak/class-enrichment
+rank: 1000
+alias: direction
+owner: ClassEnrichmentResult
+domain_of:
+- ClassEnrichmentResult
+range: integer
+
+```
+</details>

_sources/datamodels/class-enrichment/index.md.txt

@@ -28,6 +28,7 @@ Name: class-enrichment
 | [class_id](class_id.md) | The class id |
 | [class_label](class_label.md) | The class label |
 | [descendant_of_more_informative_result](descendant_of_more_informative_result.md) | This term is more specific than a previously reported result |
+| [direction](direction.md) | The direction of the enrichment |
 | [false_discovery_rate](false_discovery_rate.md) | The false discovery rate |
 | [fold_enrichment](fold_enrichment.md) | The fold enrichment |
 | [p_value](p_value.md) | The p-value |

_sources/packages/implementations/index.rst.txt

@@ -22,4 +22,5 @@ Implementations (also known as *adapters*) implement one or more :ref:`interface
    ols
    gilda
    aggregator
+   pantherdb
    llm

_sources/packages/implementations/pantherdb.rst.txt

@@ -0,0 +1,36 @@
+.. _pantherdb_implementation:
+
+PantherDB Adapter
+=============
+
+Command Line Examples
+----------------------
+
+Use the :code:`pantherdb` selector, with an optional NCBI Taxon local ID.
+
+Annotation
+^^^^^^^^^^
+
+.. code:: shell
+
+    runoak -i pantherdb:9606 associations -Q subject UniProtKB:P04217 --no-autolabel
+
+Enrichment
+^^^^^^^^^^
+
+.. code:: shell
+
+   runoak -i pantherdb:9606 enrichment -U my-gene-ids.txt
+
+Mapping
+^^^^^^^^^^
+
+.. code:: shell
+
+   runoak -i pantherdb:9606 mappings UniProtKB:P04217
+
+Code
+----
+.. currentmodule:: oaklib.implementations.pantherdb.pantherdb_implementation
+
+.. autoclass:: PantherDBImplementation

class-enrichment/ClassEnrichmentResult.md

@@ -27,6 +27,8 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl
         
       ClassEnrichmentResult : descendant_of_more_informative_result
         
+      ClassEnrichmentResult : direction
+        
       ClassEnrichmentResult : false_discovery_rate
         
       ClassEnrichmentResult : fold_enrichment
@@ -70,6 +72,7 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl
 | [background_total](background_total.md) | 0..1 <br/> [Integer](Integer.md) | The background total | direct |
 | [ancestor_of_more_informative_result](ancestor_of_more_informative_result.md) | 0..1 <br/> [Boolean](Boolean.md) | This term is more general than a previously reported result | direct |
 | [descendant_of_more_informative_result](descendant_of_more_informative_result.md) | 0..1 <br/> [Boolean](Boolean.md) | This term is more specific than a previously reported result | direct |
+| [direction](direction.md) | 0..1 <br/> [Integer](Integer.md) | The direction of the enrichment | direct |
 
 
 
@@ -243,6 +246,14 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: boolean
+  direction:
+    name: direction
+    description: The direction of the enrichment
+    from_schema: https://w3id.org/oak/class-enrichment
+    rank: 1000
+    domain_of:
+    - ClassEnrichmentResult
+    range: integer
 
 ```
 </details>
@@ -400,6 +411,16 @@ attributes:
     domain_of:
     - ClassEnrichmentResult
     range: boolean
+  direction:
+    name: direction
+    description: The direction of the enrichment
+    from_schema: https://w3id.org/oak/class-enrichment
+    rank: 1000
+    alias: direction
+    owner: ClassEnrichmentResult
+    domain_of:
+    - ClassEnrichmentResult
+    range: integer
 
 ```
 </details>

class-enrichment/direction.md

@@ -0,0 +1,68 @@
+# Slot: direction
+
+
+_The direction of the enrichment_
+
+
+
+URI: [ontoenrich:direction](https://w3id.org/oak/class-enrichment/direction)
+
+
+
+<!-- no inheritance hierarchy -->
+
+
+
+
+## Applicable Classes
+
+| Name | Description | Modifies Slot |
+| --- | --- | --- |
+[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result |  no  |
+
+
+
+
+
+
+
+## Properties
+
+* Range: [Integer](Integer.md)
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/oak/class-enrichment
+
+
+
+
+## LinkML Source
+
+<details>
+```yaml
+name: direction
+description: The direction of the enrichment
+from_schema: https://w3id.org/oak/class-enrichment
+rank: 1000
+alias: direction
+owner: ClassEnrichmentResult
+domain_of:
+- ClassEnrichmentResult
+range: integer
+
+```
+</details>

class-enrichment/index.md

@@ -28,6 +28,7 @@ Name: class-enrichment
 | [class_id](class_id.md) | The class id |
 | [class_label](class_label.md) | The class label |
 | [descendant_of_more_informative_result](descendant_of_more_informative_result.md) | This term is more specific than a previously reported result |
+| [direction](direction.md) | The direction of the enrichment |
 | [false_discovery_rate](false_discovery_rate.md) | The false discovery rate |
 | [fold_enrichment](fold_enrichment.md) | The fold enrichment |
 | [p_value](p_value.md) | The p-value |

datamodels/class-enrichment/ClassEnrichmentResult.html

@@ -102,6 +102,8 @@ <h1>Class: ClassEnrichmentResult<a class="headerlink" href="#class-classenrichme
 
       ClassEnrichmentResult : descendant_of_more_informative_result
 
+      ClassEnrichmentResult : direction
+
       ClassEnrichmentResult : false_discovery_rate
 
       ClassEnrichmentResult : fold_enrichment
@@ -201,6 +203,11 @@ <h2>Slots<a class="headerlink" href="#slots" title="Link to this heading"></a
 <td><p>This term is more specific than a previously reported result</p></td>
 <td><p>direct</p></td>
 </tr>
+<tr class="row-even"><td><p><a class="reference internal" href="direction.html"><span class="std std-doc">direction</span></a></p></td>
+<td><p>0..1 <br/> <a class="reference internal" href="Integer.html"><span class="std std-doc">Integer</span></a></p></td>
+<td><p>The direction of the enrichment</p></td>
+<td><p>direct</p></td>
+</tr>
 </tbody>
 </table>
 </section>
@@ -378,6 +385,14 @@ <h3>Direct<a class="headerlink" href="#direct" title="Link to this heading"><
     domain_of:
     - ClassEnrichmentResult
     range: boolean
+  direction:
+    name: direction
+    description: The direction of the enrichment
+    from_schema: https://w3id.org/oak/class-enrichment
+    rank: 1000
+    domain_of:
+    - ClassEnrichmentResult
+    range: integer
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>&lt;/details&gt;
 
 ### Induced
@@ -533,6 +548,16 @@ <h3>Direct<a class="headerlink" href="#direct" title="Link to this heading"><
     domain_of:
     - ClassEnrichmentResult
     range: boolean
+  direction:
+    name: direction
+    description: The direction of the enrichment
+    from_schema: https://w3id.org/oak/class-enrichment
+    rank: 1000
+    alias: direction
+    owner: ClassEnrichmentResult
+    domain_of:
+    - ClassEnrichmentResult
+    range: integer
 
 </pre></div>
 </div>