update examples

emmo-repo · Jan 28, 2024 · c66d950 · c66d950
1 parent 4732457
commit c66d950
Show file tree

Hide file tree

Showing 6 changed files with 147 additions and 25 deletions.
diff --git a/sphinx/example_alkaline_electrochemical_cell.rst b/sphinx/example_alkaline_electrochemical_cell.rst
@@ -0,0 +1,39 @@
+Alkaline Electrochemical Cell
+=============================
+
+This example, let's describe an instance of a simple alkaline electrochemical cell. 
+
+.. hint::
+
+   In this ontology, an ``ElectrochemicalCell`` is simply a combination of components in a holistic arrangement (i.e. two electrodes in contact with an electrolyte). Adding a case and terminals to make it a functional device makes it a ``BatteryCell`` described in the battery domain ontology.
+
+The JSON-LD description of the material is given below:
+
+.. tab-set::
+
+   .. tab-item:: JSON
+
+      .. code-block:: json
+         :linenos:
+
+         {
+            "@context": "https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/context.json",
+            "@type": "ElectrochemicalCell",
+            "hasNegativeElectrode": {
+               "@type": "ZincElectrode"
+            },
+            "hasPositiveElectrode": {
+               "@type": "ManganeseDioxideElectrode"
+            },
+            "hasElectrolyte": {
+               "@type": "AlkalineElectrolyte"
+            }
+         }
+
+   .. tab-item:: JSON-LD Playground
+
+      .. raw:: html
+
+         <div style="position: relative; padding-top: 56.25%; height: 0;">
+            <iframe src="https://json-ld.org/playground/#startTab=tab-table&json-ld=%7B%22%40context%22%3A%22https%3A%2F%2Fraw.githubusercontent.com%2Femmo-repo%2Fdomain-electrochemistry%2Fmaster%2Fcontext.json%22%2C%22%40type%22%3A%22ElectrochemicalCell%22%2C%22hasNegativeElectrode%22%3A%7B%22%40type%22%3A%22ZincElectrode%22%7D%2C%22hasPositiveElectrode%22%3A%7B%22%40type%22%3A%22ManganeseDioxideElectrode%22%7D%2C%22hasElectrolyte%22%3A%7B%22%40type%22%3A%22AlkalineElectrolyte%22%7D%7D" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;" frameborder="0" allowfullscreen></iframe>
+         </div>
diff --git a/sphinx/example_aqueous_electrolyte_KOH.rst b/sphinx/example_aqueous_electrolyte_KOH.rst
@@ -0,0 +1,65 @@
+Aqueous KOH Electrolyte
+=======================
+
+This example, let's describe an instance of some aqueous potassium hydroxide (KOH) electrolyte with some properties. The JSON-LD description of the material is given below:
+
+.. tab-set::
+
+   .. tab-item:: JSON
+
+      .. code-block:: json
+         :linenos:
+
+         {
+            "@context": "https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/context.json",
+            "@type": "Electrolyte",
+            "hasSolvent": {
+               "@type": "Water"
+            },
+            "hasSolute": {
+               "@type": "PotassiumHydroxide",
+               "hasProperty": {
+                     "@type": ["AmountConcentration", "ModelledProperty"],
+                     "hasNumericalPart": {
+                        "@type": "Real",
+                        "hasNumericalValue": 7
+                     },
+                     "hasMeasurementUnit": "emmo:MolePerLitre"
+               }
+            },
+            "hasProperty": [
+               {
+                     "@type": ["Density", "MeasuredProperty"],
+                     "hasNumericalPart": {
+                        "@type": "Real",
+                        "hasNumericalValue": 1.289
+                     },
+                     "hasMeasurementUnit": "emmo:KilogramPerLitre"
+               },
+               {
+                     "@type": ["IonicConductivity", "MeasuredProperty"],
+                     "hasNumericalPart": {
+                        "@type": "Real",
+                        "hasNumericalValue": 65
+                     },
+                     "hasMeasurementUnit": "emmo:SiemensPerCentiMetre"
+               }
+            ]
+         }
+
+   .. tab-item:: JSON-LD Playground
+
+      .. raw:: html
+
+         <div style="position: relative; padding-top: 56.25%; height: 0;">
+            <iframe src="https://json-ld.org/playground/#startTab=tab-table&json-ld=%7B%22%40context%22%3A%22https%3A%2F%2Fraw.githubusercontent.com%2Femmo-repo%2Fdomain-electrochemistry%2Fmaster%2Fcontext.json%22%2C%22%40type%22%3A%22Electrolyte%22%2C%22hasSolvent%22%3A%7B%22%40type%22%3A%22Water%22%7D%2C%22hasSolute%22%3A%7B%22%40type%22%3A%22PotassiumHydroxide%22%2C%22hasProperty%22%3A%7B%22%40type%22%3A%5B%22AmountConcentration%22%2C%22ModelledProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A7%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3AMolePerLitre%22%7D%7D%2C%22hasProperty%22%3A%5B%7B%22%40type%22%3A%5B%22Density%22%2C%22MeasuredProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A1.289%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3AKilogramPerLitre%22%7D%2C%7B%22%40type%22%3A%5B%22IonicConductivity%22%2C%22MeasuredProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A65%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3ASiemensPerCentiMetre%22%7D%5D%7D" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;" frameborder="0" allowfullscreen></iframe>
+         </div>
+
+This example highlights a few things:
+
+#. **EMMO distinguishes properties according to how they were determined.** In this example, a ``ConventionalProperty`` is a property whose value is assigned by convention (e.g. from a technical specification sheet, handbook, etc.). EMMO also provides terms for ``MeasuredProperty`` for properties which were actually determined by some measurement and ``ModelledProperty`` for properties that were obtained from some model. 
+
+#. **EMMO has a specific way of expressing quantitative properties.** As shown in the example, a quantitative property has a ``@type`` that describes what kind of property it is, ``hasNumericalPart`` describes the value, and ``hasMeasurementUnit`` defines the unit. Please adhere to this format when expressing quantities in your linked data. 
+
+#. **We can re-use terms from common vocabularies like schema.org.** One of the core principles of linked data is to re-use existing vocabularies when possible. The schema.org vocabulary was developed to support internet search engines and contains terms for things that people often search for (e.g. people, organizations, products, etc.) In this case, we can re-use schema.org terms to describe the manufacturer and product.  
+
diff --git a/sphinx/example_zinc_electrode.rst b/sphinx/example_zinc_electrode.rst
@@ -1,15 +1,7 @@
 Zinc Electrode
 ==============
 
-This example, let's describe an instance of some zinc powder with a set of properties defined in the specification sheet from the manufacturer. This example highlights a few things:
-
-#. **EMMO distinguishes properties according to how they were determined.** In this example, a ``ConventionalProperty`` is a property whose value is assigned by convention (e.g. from a technical specification sheet, handbook, etc.). EMMO also provides terms for ``MeasuredProperty`` for properties which were actually determined by some measurement and ``ModelledProperty`` for properties that were obtained from some model. 
-
-#. **EMMO has a specific way of expressing quantitative properties.** As shown in the example, a quantitative property has a ``@type`` that describes what kind of property it is, ``hasNumericalPart`` describes the value, and ``hasMeasurementUnit`` defines the unit. Please adhere to this format when expressing quantities in your linked data. 
-
-#. **We can re-use terms from common vocabularies like schema.org.** One of the core principles of linked data is to re-use existing vocabularies when possible. The schema.org vocabulary was developed to support internet search engines and contains terms for things that people often search for (e.g. people, organizations, products, etc.) In this case, we can re-use schema.org terms to describe the manufacturer and product.  
-
-The JSON-LD description of the material is given below:
+This example, let's describe an instance of some electrode made by a specific person at a research institute using zinc foil. The electrode has properties that were determined from a combination of a specification sheet and actual measurements. The JSON-LD description of the material is given below:
 
 .. tab-set::
 
@@ -76,3 +68,11 @@ The JSON-LD description of the material is given below:
             <iframe src="https://json-ld.org/playground/#startTab=tab-canonized&json-ld=%7B%22%40context%22%3A%22https%3A%2F%2Fraw.githubusercontent.com%2Femmo-repo%2Fdomain-electrochemistry%2Fmaster%2Fcontext.json%22%2C%22%40type%22%3A%22Electrode%22%2C%22schema%3Amanufacturer%22%3A%7B%22%40id%22%3A%22https%3A%2F%2Fwww.wikidata.org%2Fwiki%2FQ3041255%22%2C%22schema%3Aname%22%3A%22SINTEF%22%7D%2C%22schema%3Acreator%22%3A%7B%22%40id%22%3A%22https%3A%2F%2Forcid.org%2F0000-0002-8758-6109%22%2C%22schema%3Aname%22%3A%22Simon%20Clark%22%7D%2C%22hasActiveMaterial%22%3A%7B%22%40type%22%3A%5B%22Zinc%22%2C%22Foil%22%5D%7D%2C%22hasProperty%22%3A%5B%7B%22%40type%22%3A%5B%22SpecificCapacity%22%2C%22MeasuredProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A800%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3AMilliAmpereHourPerGram%22%7D%2C%7B%22%40type%22%3A%5B%22Thickness%22%2C%22ConventionalProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A250%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3AMicroMetre%22%7D%2C%7B%22%40type%22%3A%5B%22Diameter%22%2C%22MeasuredProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A2%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3ACentiMetre%22%7D%2C%7B%22%40type%22%3A%5B%22Mass%22%2C%22MeasuredProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A2.5%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3AGram%22%7D%5D%7D" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;" frameborder="0" allowfullscreen></iframe>
          </div>
 
+This example highlights a few things:
+
+#. **EMMO distinguishes properties according to how they were determined.** In this example, a ``ConventionalProperty`` is a property whose value is assigned by convention (e.g. from a technical specification sheet, handbook, etc.). EMMO also provides terms for ``MeasuredProperty`` for properties which were actually determined by some measurement and ``ModelledProperty`` for properties that were obtained from some model. 
+
+#. **EMMO has a specific way of expressing quantitative properties.** As shown in the example, a quantitative property has a ``@type`` that describes what kind of property it is, ``hasNumericalPart`` describes the value, and ``hasMeasurementUnit`` defines the unit. Please adhere to this format when expressing quantities in your linked data. 
+
+#. **We can re-use terms from common vocabularies like schema.org.** One of the core principles of linked data is to re-use existing vocabularies when possible. The schema.org vocabulary was developed to support internet search engines and contains terms for things that people often search for (e.g. people, organizations, products, etc.) In this case, we can re-use schema.org terms to describe the manufacturer and product.  
+
diff --git a/sphinx/example_zinc_powder.rst b/sphinx/example_zinc_powder.rst
@@ -1,15 +1,7 @@
 Zinc Powder
 ===========
 
-This example, let's describe an instance of some zinc powder with a set of properties defined in the specification sheet from the manufacturer. This example highlights a few things:
-
-#. **EMMO distinguishes properties according to how they were determined.** In this example, a ``ConventionalProperty`` is a property whose value is assigned by convention (e.g. from a technical specification sheet, handbook, etc.). EMMO also provides terms for ``MeasuredProperty`` for properties which were actually determined by some measurement and ``ModelledProperty`` for properties that were obtained from some model. 
-
-#. **EMMO has a specific way of expressing quantitative properties.** As shown in the example, a quantitative property has a ``@type`` that describes what kind of property it is, ``hasNumericalPart`` describes the value, and ``hasMeasurementUnit`` defines the unit. Please adhere to this format when expressing quantities in your linked data. 
-
-#. **We can re-use terms from common vocabularies like schema.org.** One of the core principles of linked data is to re-use existing vocabularies when possible. The schema.org vocabulary was developed to support internet search engines and contains terms for things that people often search for (e.g. people, organizations, products, etc.) In this case, we can re-use schema.org terms to describe the manufacturer and product.  
-
-The JSON-LD description of the material is given below:
+This example, let's describe an instance of some zinc powder with a set of properties defined in the specification sheet from the manufacturer. The JSON-LD description of the material is given below:
 
 .. tab-set::
 
@@ -48,3 +40,10 @@ The JSON-LD description of the material is given below:
             <iframe src="https://json-ld.org/playground/#startTab=tab-table&json-ld=%7B%22%40context%22%3A%22https%3A%2F%2Fraw.githubusercontent.com%2Femmo-repo%2Fdomain-electrochemistry%2Fmaster%2Fcontext.json%22%2C%22%40type%22%3A%5B%22Zinc%22%2C%22Powder%22%5D%2C%22schema%3Amanufacturer%22%3A%7B%22%40id%22%3A%22https%3A%2F%2Fwww.wikidata.org%2Fwiki%2FQ680841%22%2C%22schema%3Aname%22%3A%22Sigma-Aldrich%22%7D%2C%22schema%3AproductID%22%3A%22324930%22%2C%22schema%3Aurl%22%3A%22https%3A%2F%2Fwww.sigmaaldrich.com%2FNO%2Fen%2Fproduct%2Faldrich%2F324930%22%2C%22hasProperty%22%3A%5B%7B%22%40type%22%3A%5B%22D95ParticleSize%22%2C%22ConventionalProperty%22%5D%2C%22hasNumericalPart%22%3A%7B%22%40type%22%3A%22Real%22%2C%22hasNumericalValue%22%3A150%7D%2C%22hasMeasurementUnit%22%3A%22emmo%3AMicroMetre%22%2C%22dc%3Asource%22%3A%22https%3A%2F%2Fwww.sigmaaldrich.com%2FNO%2Fen%2Fproduct%2Faldrich%2F324930%22%7D%5D%7D" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;" frameborder="0" allowfullscreen></iframe>
          </div>
 
+This example highlights a few things:
+
+#. **EMMO distinguishes properties according to how they were determined.** In this example, a ``ConventionalProperty`` is a property whose value is assigned by convention (e.g. from a technical specification sheet, handbook, etc.). EMMO also provides terms for ``MeasuredProperty`` for properties which were actually determined by some measurement and ``ModelledProperty`` for properties that were obtained from some model. 
+
+#. **EMMO has a specific way of expressing quantitative properties.** As shown in the example, a quantitative property has a ``@type`` that describes what kind of property it is, ``hasNumericalPart`` describes the value, and ``hasMeasurementUnit`` defines the unit. Please adhere to this format when expressing quantities in your linked data. 
+
+#. **We can re-use terms from common vocabularies like schema.org.** One of the core principles of linked data is to re-use existing vocabularies when possible. The schema.org vocabulary was developed to support internet search engines and contains terms for things that people often search for (e.g. people, organizations, products, etc.) In this case, we can re-use schema.org terms to describe the manufacturer and product.  
diff --git a/sphinx/examples.rst b/sphinx/examples.rst
@@ -13,25 +13,25 @@ Examples
     .. grid-item-card::
         :link: example_zinc_electrode.html
 
-        :octicon:`book;1em;sd-text-info`  Zinc Electrode
+        :octicon:`plus;1em;sd-text-info`  Zinc Electrode
         ^^^^^^^^^^^
         A zinc foil electrode manufactured by a person at a research institute with a mix of properties from a specification sheet and measured.
 
 .. grid::
 
     .. grid-item-card::
-        :link: examples.html
+        :link: example_aqueous_electrolyte_KOH.html
 
-        :octicon:`pencil;1em;sd-text-info`  Examples
+        :octicon:`plus-circle;1em;sd-text-info`  Aqueous KOH Electrolyte
         ^^^^^^^^
-        Here are some examples that demonstrate basic usage of the ontology
+        An aqueous potassium hydroxide electrolyte with some properties. 
 
     .. grid-item-card::
-        :link: contribute.html
+        :link: example_alkaline_electrochemical_cell.html
 
-        :octicon:`thumbsup;1em;sd-text-info`  Contribute
+        :octicon:`thumbsup;1em;sd-text-info`  Alkaline Electrochemical Cell
         ^^^^^^^^^^
-        Help us develop the ontology by following these guidelines
+        An alkaline electrochemical cell.
 
 
 Electrochemical Cell

diff --git a/sphinx/index.rst b/sphinx/index.rst
@@ -24,6 +24,25 @@ a foundational resource for harmonizing electrochemical knowledge
 representation, enhancing data interoperability, and accelerating
 progress in electrochemical research and development.
 
+A Simple Example
+~~~~~~~~~~~~~~~~
+.. code-block:: json
+         :linenos:
+
+         {
+            "@context": "https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/context.json",
+            "@type": "ElectrochemicalCell",
+            "hasNegativeElectrode": {
+               "@type": "ZincElectrode"
+            },
+            "hasPositiveElectrode": {
+               "@type": "ManganeseDioxideElectrode"
+            },
+            "hasElectrolyte": {
+               "@type": "AlkalineElectrolyte"
+            }
+         }
+
 .. grid::
 
     .. grid-item-card::