From 191b7dbb1bb491ca1550e26f4167718e274188f9 Mon Sep 17 00:00:00 2001 From: Simon Clark Date: Fri, 26 Jan 2024 16:28:18 +0100 Subject: [PATCH] update docs --- sphinx/about.rst | 207 ++++++++++++++++++++++++++++++++++++++----- sphinx/examples.rst | 2 - sphinx/index.rst | 210 +++++--------------------------------------- 3 files changed, 205 insertions(+), 214 deletions(-) diff --git a/sphinx/about.rst b/sphinx/about.rst index 858e66f..0779e0d 100644 --- a/sphinx/about.rst +++ b/sphinx/about.rst @@ -1,29 +1,187 @@ -About Battery Domain Ontology -============================= +Electrochemistry Domain Ontology +================================ -Contributors +.. raw:: html + + + +The Electrochemistry Domain Ontology is a specialized domain within the +Elementary Multiperspective Materials Ontology +`(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 `__ +and +`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 `__ and +`Wikidata `__. + +Standardized Nomenclature +~~~~~~~~~~~~~~~~~~~~~~~~~ + +The ontology builds on standardized nomenclature for electrochemistry, +relying on recognized authorities including +`IUPAC `__ and the +`IEC `__. 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 `__; 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 `__) + +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 `__: +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 `__. 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 `__ (a graphical ontology + editor) + + - Installation instructions are available + `here `__. + +- `EMMOntoPy `__ (python + package for working with EMMO ontologies) + + - Installation instructions are available + `here `__. + +- `RDFLib `__ (optional, + python package for working with RDF graphs) + + - Installation instructions are available + `here `__. + +- `VS Studio Code `__ (optional, a code + editor with extensions for RDF formats like TTL and JSON-LD) + + - Installation instructions are available + `here `__. + +Quick Start +~~~~~~~~~~~ + +To quickly explore and make use of the ontology, first download the +pre-inferred version `pre-inferred +ontology `__. You can +then simply open the file in Protégé and explore its content or load the +ontology into python using EMMOntoPy. + +In `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 `__. + + +Acknowledgements +~~~~~~~~~~~~~~~~ + +This project has received support from European Union research and +innovation programs, under grant agreement numbers: + +- 957189 - `BIG-MAP `__ License ------- @@ -32,3 +190,6 @@ The Battery Interface Domain Ontology is released under the `Creative Commons Attribution 4.0 International `__ license (CC BY 4.0). + +.. |DOI| image:: https://zenodo.org/badge/570454941.svg + :target: https://zenodo.org/badge/latestdoi/570454941 diff --git a/sphinx/examples.rst b/sphinx/examples.rst index 2aa12ce..11fe3a5 100644 --- a/sphinx/examples.rst +++ b/sphinx/examples.rst @@ -115,5 +115,3 @@ This example can be explored using the JSON-LD playground:
- - diff --git a/sphinx/index.rst b/sphinx/index.rst index 93e5c77..d8f928d 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -4,207 +4,39 @@ :hidden: About - self Class Index Examples Resources Contribute -Electrochemistry Domain Ontology -================================ +.. grid:: -.. raw:: html + .. grid-item-card:: - - -The Electrochemistry Domain Ontology is a specialized domain within the -Elementary Multiperspective Materials Ontology -`(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 `__ -and -`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 `__ and -`Wikidata `__. - -Standardized Nomenclature -~~~~~~~~~~~~~~~~~~~~~~~~~ - -The ontology builds on standardized nomenclature for electrochemistry, -relying on recognized authorities including -`IUPAC `__ and the -`IEC `__. 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 ------------- - -- 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 `__) - -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 `__: -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 `__. 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 -~~~~~~~~~~~~~ + Quick Start + ^^^^^^^^^^^ + panel 1 content + more content -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: + .. grid-item-card:: -- `Protégé `__ (a graphical ontology - editor) + Class Index + ^^^^^^^^^^^ + panel 2 content - - Installation instructions are available - `here `__. +.. grid:: -- `EMMOntoPy `__ (python - package for working with EMMO ontologies) + .. grid-item-card:: + :link: - - Installation instructions are available - `here `__. + Examples + ^^^^^^^^ + panel 1 content + more content -- `RDFLib `__ (optional, - python package for working with RDF graphs) + .. grid-item-card:: - - Installation instructions are available - `here `__. - -- `VS Studio Code `__ (optional, a code - editor with extensions for RDF formats like TTL and JSON-LD) - - - Installation instructions are available - `here `__. - -Quick Start -~~~~~~~~~~~ - -To quickly explore and make use of the ontology, first download the -pre-inferred version `pre-inferred -ontology `__. You can -then simply open the file in Protégé and explore its content or load the -ontology into python using EMMOntoPy. - -In `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 `__. - - -Acknowledgements -~~~~~~~~~~~~~~~~ - -This project has received support from European Union research and -innovation programs, under grant agreement numbers: - -- 957189 - `BIG-MAP `__ - -License -------- - -The Battery Interface Domain Ontology is released under the `Creative -Commons Attribution 4.0 -International `__ -license (CC BY 4.0). - -.. |DOI| image:: https://zenodo.org/badge/570454941.svg - :target: https://zenodo.org/badge/latestdoi/570454941 - - + Contribute + ^^^^^^^^^^ + panel 2 content \ No newline at end of file