update docs

sphinx/about.rst

@@ -1,29 +1,187 @@
-About Battery Domain Ontology
-=============================
+Electrochemistry Domain Ontology
+================================
 
-Contributors
+.. raw:: html
+
+   <!-- [![CI tests](https://github.com/emmo-repo/domain-electrochemistry/workflows/CI%20tests/badge.svg)](https://github.com/emmo-repo/domain-electrochemistry/actions/) -->
+
+The Electrochemistry Domain Ontology is a specialized domain within the
+Elementary Multiperspective Materials Ontology
+`(EMMO) <https://github.com/emmo-repo/EMMO>`__, that encompasses
+essential terms and relationships for electrochemical systems,
+materials, methods, and data. Its primary objective is to enable the
+creation of linked and FAIR (Findable, Accessible, Interoperable, and
+Reusable) data, thereby fostering advancements in research and
+innovation within the realm of electrochemistry. This ontology serves as
+a foundational resource for harmonizing electrochemical knowledge
+representation, enhancing data interoperability, and accelerating
+progress in electrochemical research and development.
+
+A reference documentation is available in
+`html <https://emmo-repo.github.io/domain-electrochemistry/index.html>`__
+and
+`pdf <https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.pdf>`__
+formats.
+
+Persistent Identifiers
+~~~~~~~~~~~~~~~~~~~~~~
+
+This ontology assigns persistent machine-readable identifiers to
+concepts from the electrochemistry domain. These identifiers facilitate
+data exchange and interoperability among various tools and systems. It
+includes annotations to other sources of information including
+`DBPedia <https://www.dbpedia.org/>`__ and
+`Wikidata <https://www.wikidata.org/>`__.
+
+Standardized Nomenclature
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The ontology builds on standardized nomenclature for electrochemistry,
+relying on recognized authorities including
+`IUPAC <https://iupac.org/what-we-do/nomenclature/>`__ and the
+`IEC <https://www.electropedia.org/>`__. IUPAC is the
+universally-recognized authority on chemical nomenclature and
+terminology, and IEC is the the world’s leading organization that
+prepares and publishes International Standards for all electrical,
+electronic and related technologies. This consistency in naming
+conventions enhances collaboration and data sharing.
+
+Key Features
 ------------
 
--  Simon Clark, SINTEF, Norway
--  Eibar Flores, SINTEF, Norway
--  Francesca Lønstad Bleken, SINTEF, Norway
--  Jesper Friis, SINTEF, Norway
--  Casper Welzel Andersen, SINTEF, Norway
--  Martin Uhrin, EPFL, Switzerland
--  Simon Stier, Fraunhofer, Germany
--  Marek Marcinek, Warsaw University of Technology, Poland
--  Anna Szczesna, Warsaw University of Technology, Poland
--  Miran Gaberscek, National Institute of Chemistry, Slovenia
--  Deyana Stoytcheva, ICMAB, Spain
--  Rosa Palacin, ICMAB, Spain
--  Ingeborg-Helene Svenum, SINTEF, Norway
--  Inga Gudem Ringdalen, SINTEF, Norway
--  Emanuele Farhi, SOLEIL synchrotron, France
-
-Projects
---------
-
--  `BIG-MAP <http://www.big-map.eu/>`__; Grant Agreement No: 957189
+-  Seamless integration with the EMMO ontology.
+-  Provides persistent machine-readable identifiers for electorchemical
+   systems, devices, methods, datasets, and quantities.
+-  Standardized nomenclature for electrochemical entities.
+-  Facilitates data exchange and interoperability within the EMMO
+   ecosystem.
+
+Usage
+-----
+
+Researchers, domain experts, and developers within the electrochemical
+communities can utilize the ontology for various purposes, including:
+
+-  Incorporating consistent and standardized information into their
+   modeling and simulation activities.
+-  Enhancing data interoperability between modeling tools, databases,
+   and platforms.
+-  Supporting research projects that require precise and standardized
+   electrochemical knowledge representation.
+-  Building applications, databases, or knowledge graphs that leverage
+   EMMO and require electrochemical information.
+-  Generating linked data in the semantic web.
+-  Complying with FAIR data mandates (FAIR Guidelines available
+   `here <FAIR.md>`__)
+
+Structure and Integration with EMMO
+-----------------------------------
+
+The Electrochemistry Domain Ontology is an official domain on the EMMO.
+The asserted source consists of two files: - ``electrochemistry.ttl``:
+describes terms and object properties for the electrochemistry domain. -
+``electrochemicalquantities.ttl``: describes the physical quantities
+related to the electrochemistry domain. It is encapsulated to allow it
+to be imported by other EMMO domains without needing to import the
+entire ontology.
+
+The electrochemistry domain also imports other EMMO domains: - `Chemical
+Substance Domain
+Ontology <https://github.com/emmo-repo/domain-chemical-substance>`__:
+provides material annotations for electrochemical (meta)data.
+
+The import structure is summarized in the following table:
+
+.. list-table::
+   :header-rows: 1
+
+   * - **Imported Ontologies**
+     - **Version**
+   * - EMMO
+     - 1.0.0-beta5
+   * - chemical-substance
+     - 0.2.0-alpha 
+
+For simplicity, we complie the source files and other imports into a
+`pre-inferred
+ontology <inferred_version/electrochemistry-inferred.ttl>`__. This is
+the result of running the asserted source files through a semantic
+reasoner and includes both asserted and inferred properties in a clear
+graph.
+
+Getting Started
+---------------
+
+Prerequisites
+~~~~~~~~~~~~~
+
+Before you begin, we recommend that you install the following tools.
+They are not all required, but greatly simplify the process of working
+with ontologies:
+
+-  `Protégé <https://protege.stanford.edu/>`__ (a graphical ontology
+   editor)
+
+   -  Installation instructions are available
+      `here <https://protege.stanford.edu/software.php#desktop-protege>`__.
+
+-  `EMMOntoPy <https://github.com/emmo-repo/EMMOntoPy>`__ (python
+   package for working with EMMO ontologies)
+
+   -  Installation instructions are available
+      `here <https://github.com/emmo-repo/EMMOntoPy#installation>`__.
+
+-  `RDFLib <https://rdflib.readthedocs.io/en/stable/>`__ (optional,
+   python package for working with RDF graphs)
+
+   -  Installation instructions are available
+      `here <https://rdflib.readthedocs.io/en/stable/gettingstarted.html>`__.
+
+-  `VS Studio Code <https://code.visualstudio.com/>`__ (optional, a code
+   editor with extensions for RDF formats like TTL and JSON-LD)
+
+   -  Installation instructions are available
+      `here <https://code.visualstudio.com/download>`__.
+
+Quick Start
+~~~~~~~~~~~
+
+To quickly explore and make use of the ontology, first download the
+pre-inferred version `pre-inferred
+ontology <inferred_version/electrochemistry-inferred.ttl>`__. You can
+then simply open the file in Protégé and explore its content or load the
+ontology into python using EMMOntoPy.
+
+In `EMMOntoPy <https://github.com/emmo-repo/EMMOntoPy>`__, you can
+choose to import the ontology from your local downloaded copy or
+directly from the web. Commands for both options are given below:
+
+.. code:: python
+
+   from ontopy import get_ontology
+
+   # Loading from local repository
+   electrochemistry = get_ontology('/path/to/domain-electrochemistry/electrochemistry-inferred.ttl').load(url_from_catalog=True)
+
+   # Loading from web
+   electrochemistry = get_ontology('https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/inferred_version/electrochemistry-inferred.ttl').load()
+
+Contributing
+------------
+
+We welcome contributions from the community to enhance and expand the
+ontology. If you have suggestions, improvements, or additional chemical
+substance information to contribute, please refer to our `Contribution
+Guidelines <CONTRIBUTING.md>`__.
+
+
+Acknowledgements
+~~~~~~~~~~~~~~~~
+
+This project has received support from European Union research and
+innovation programs, under grant agreement numbers:
+
+-  957189 - `BIG-MAP <http://www.big-map.eu/>`__
 
 License
 -------
@@ -32,3 +190,6 @@ The Battery Interface Domain Ontology is released under the `Creative
 Commons Attribution 4.0
 International <https://creativecommons.org/licenses/by/4.0/legalcode>`__
 license (CC BY 4.0).
+
+.. |DOI| image:: https://zenodo.org/badge/570454941.svg
+   :target: https://zenodo.org/badge/latestdoi/570454941

sphinx/examples.rst

@@ -115,5 +115,3 @@ This example can be explored using the JSON-LD playground:
    <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%5B%22Electrode%22%2C%22Foil%22%5D%2C%22hasActiveMaterial%22%3A%7B%22%40type%22%3A%22Zinc%22%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>
-
-