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dev/assets/coremeta4cat_vocabulary.xlsx

@@ -816,7 +816,7 @@ <h2 id="slots">Slots</h2>
 <td><a href="../../slots/type/">type</a></td>
 <td>* <br/> <a href="../DefinedTerm/">DefinedTerm</a></td>
 <td>A type of the Dataset.</td>
-<td><a href="../Dataset/">Dataset</a>, <a href="../ClassifierMixin/">ClassifierMixin</a></td>
+<td><a href="../ClassifierMixin/">ClassifierMixin</a>, <a href="../Dataset/">Dataset</a></td>
 </tr>
 <tr>
 <td><a href="../../slots/rdf_type/">rdf_type</a></td>

dev/assets/metadata_characterization_hierarchy.html

@@ -841,13 +841,13 @@ <h2 id="applicable-classes">Applicable Classes</h2>
 </thead>
 <tbody>
 <tr>
-<td><a href="../../classes/ElectronMicroscopyMixin/">ElectronMicroscopyMixin</a></td>
-<td>Mixin providing electron gun and image parameters shared by electron<br>microscopy techniques (TransmissionElectronMicroscopy,<br>ScanningElectronMicroscopy).</td>
+<td><a href="../../classes/TransmissionElectronMicroscopy/">TransmissionElectronMicroscopy</a></td>
+<td>TEM for atomic-resolution imaging and diffraction of catalyst particles.</td>
 <td>no</td>
 </tr>
 <tr>
-<td><a href="../../classes/TransmissionElectronMicroscopy/">TransmissionElectronMicroscopy</a></td>
-<td>TEM for atomic-resolution imaging and diffraction of catalyst particles.</td>
+<td><a href="../../classes/ElectronMicroscopyMixin/">ElectronMicroscopyMixin</a></td>
+<td>Mixin providing electron gun and image parameters shared by electron<br>microscopy techniques (TransmissionElectronMicroscopy,<br>ScanningElectronMicroscopy).</td>
 <td>no</td>
 </tr>
 <tr>

dev/assets/metadata_coremeta4cat_overview.html

@@ -822,14 +822,24 @@ <h2 id="applicable-classes">Applicable Classes</h2>
 </thead>
 <tbody>
 <tr>
+<td><a href="../../classes/CatalysisDataset/">CatalysisDataset</a></td>
+<td>A dcat:Dataset that contains research data in the field of catalysis.<br><br>The catalysis research field is expressed via rdf_type using a voc4cat<br>term from CatalysisResearchFieldEnum (following DCAT-AP-PLUS Pattern 3).<br>For example, a dataset from heterogeneous catalysis research would carry:<br>  rdf_type:<br>    id: VOC4CAT:0007001<br>    title: "heterogeneous catalysis"<br><br>The four CoreMeta4Cat minimum information pillars are linked via the slots<br>below, each pointing to the corresponding DataGeneratingActivity or<br>EvaluatedActivity subclass defined in the CoreMeta4Cat subprofile modules.</td>
+<td>no</td>
+</tr>
+<tr>
+<td><a href="../../classes/AnalysisDataset/">AnalysisDataset</a></td>
+<td>A Dataset that was generated by an analysis of some previously generated data. For example, a dataset that contains the data of an assignment of a chemical structure to a sample based on the spectral data obtained from the sample is an AnalyticalDataset.</td>
+<td>no</td>
+</tr>
+<tr>
 <td><a href="../../classes/SubstanceSampleCharacterizationDataset/">SubstanceSampleCharacterizationDataset</a></td>
 <td>A Dataset about a SubstanceSample that was produced by a SubstanceSampleCharacterization activity. This is a coarse-grained convenience shape that conflates measurement and analysis into a single data-generating activity. Domain-specific sub-profiles that need to distinguish raw measurement from post-processing or structure assignment should define their own Dataset subclasses, potentially using the DCAT-AP+ DataAnalysis/AnalysisDataset chain instead of reusing this class.</td>
 <td>no</td>
 </tr>
 <tr>
-<td><a href="../../classes/CatalysisDataset/">CatalysisDataset</a></td>
-<td>A dcat:Dataset that contains research data in the field of catalysis.<br><br>The catalysis research field is expressed via rdf_type using a voc4cat<br>term from CatalysisResearchFieldEnum (following DCAT-AP-PLUS Pattern 3).<br>For example, a dataset from heterogeneous catalysis research would carry:<br>  rdf_type:<br>    id: VOC4CAT:0007001<br>    title: "heterogeneous catalysis"<br><br>The four CoreMeta4Cat minimum information pillars are linked via the slots<br>below, each pointing to the corresponding DataGeneratingActivity or<br>EvaluatedActivity subclass defined in the CoreMeta4Cat subprofile modules.</td>
-<td>no</td>
+<td><a href="../../classes/Dataset/">Dataset</a></td>
+<td>A collection of data, published or curated by a single agent, and available for access or download in one or more representations.</td>
+<td>yes</td>
 </tr>
 <tr>
 <td><a href="../../classes/DataService/">DataService</a></td>
@@ -841,16 +851,6 @@ <h2 id="applicable-classes">Applicable Classes</h2>
 <td>A Dataset about a ChemicalReaction that was produced by a ReactionMonitoring activity. This is a coarse-grained convenience shape that conflates experimental documentation and analysis into a single data-generating activity. Domain-specific sub-profiles that need to distinguish reaction monitoring from subsequent data evaluation should define their own Dataset subclasses, potentially using the DCAT-AP+ DataAnalysis/AnalysisDataset chain instead of reusing this class.</td>
 <td>no</td>
 </tr>
-<tr>
-<td><a href="../../classes/AnalysisDataset/">AnalysisDataset</a></td>
-<td>A Dataset that was generated by an analysis of some previously generated data. For example, a dataset that contains the data of an assignment of a chemical structure to a sample based on the spectral data obtained from the sample is an AnalyticalDataset.</td>
-<td>no</td>
-</tr>
-<tr>
-<td><a href="../../classes/Dataset/">Dataset</a></td>
-<td>A collection of data, published or curated by a single agent, and available for access or download in one or more representations.</td>
-<td>yes</td>
-</tr>
 </tbody>
 </table>
 <h2 id="properties">Properties</h2>

dev/assets/metadata_reaction_hierarchy.html

@@ -836,13 +836,13 @@ <h2 id="applicable-classes">Applicable Classes</h2>
 <td>no</td>
 </tr>
 <tr>
-<td><a href="../../classes/Synthesis/">Synthesis</a></td>
-<td>A DataGeneratingActivity in which a catalyst is prepared.<br><br>The preparation protocol is linked via realized_plan using a<br>PreparationMethod instance. Input materials (Precursors) are linked via<br>had_input_entity. The resulting catalyst (CatalystSample) is linked via<br>had_output_entity.<br><br>The type of synthesis is further specified via rdf_type using an ontology<br>term (e.g. a VOC4CAT preparation method term), following DCAT-AP-PLUS<br>Pattern 3.</td>
+<td><a href="../../classes/CatalysisDataGeneratingActivity/">CatalysisDataGeneratingActivity</a></td>
+<td>A CoreMeta4Cat specialization of DCAT-AP-PLUS's DataGeneratingActivity<br>that adds a type designator (activity_designator). Synthesis,<br>Characterization, and Simulation all specialize this class instead of<br>DataGeneratingActivity directly, so that when one of them is nested<br>inside CatalysisDataset.was_generated_by, the LinkML Python loader can<br>tell which concrete subclass a given entry is meant to be and keep its<br>subclass-specific fields (e.g. Characterization.realized_plan) rather<br>than falling back to DataGeneratingActivity's own generic slot<br>definitions.<br><br>activity_designator is filled in automatically by LinkML when a class<br>is instantiated directly (e.g. loading a standalone Synthesis-NNN.yaml<br>file) -- it does not need to be set by hand there. It only needs to be<br>set explicitly in the source data when a Synthesis/Characterization/<br>Simulation instance is nested inside another object's was_generated_by<br>list (e.g. in a combined CatalysisDataset file), so the loader knows<br>which of the three to construct.</td>
 <td>no</td>
 </tr>
 <tr>
-<td><a href="../../classes/CatalysisDataGeneratingActivity/">CatalysisDataGeneratingActivity</a></td>
-<td>A CoreMeta4Cat specialization of DCAT-AP-PLUS's DataGeneratingActivity<br>that adds a type designator (activity_designator). Synthesis,<br>Characterization, and Simulation all specialize this class instead of<br>DataGeneratingActivity directly, so that when one of them is nested<br>inside CatalysisDataset.was_generated_by, the LinkML Python loader can<br>tell which concrete subclass a given entry is meant to be and keep its<br>subclass-specific fields (e.g. Characterization.realized_plan) rather<br>than falling back to DataGeneratingActivity's own generic slot<br>definitions.<br><br>activity_designator is filled in automatically by LinkML when a class<br>is instantiated directly (e.g. loading a standalone Synthesis-NNN.yaml<br>file) -- it does not need to be set by hand there. It only needs to be<br>set explicitly in the source data when a Synthesis/Characterization/<br>Simulation instance is nested inside another object's was_generated_by<br>list (e.g. in a combined CatalysisDataset file), so the loader knows<br>which of the three to construct.</td>
+<td><a href="../../classes/Synthesis/">Synthesis</a></td>
+<td>A DataGeneratingActivity in which a catalyst is prepared.<br><br>The preparation protocol is linked via realized_plan using a<br>PreparationMethod instance. Input materials (Precursors) are linked via<br>had_input_entity. The resulting catalyst (CatalystSample) is linked via<br>had_output_entity.<br><br>The type of synthesis is further specified via rdf_type using an ontology<br>term (e.g. a VOC4CAT preparation method term), following DCAT-AP-PLUS<br>Pattern 3.</td>
 <td>no</td>
 </tr>
 </tbody>