deploy: c84d5e1

.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 090a261bc36f9ff8186470012185ad5d
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/index.rst.txt

@@ -0,0 +1,205 @@
+
+.. toctree::
+   :includehidden:
+   :hidden:
+
+   self
+   electrochemistry
+
+
+Electrochemistry Domain Ontology
+================================
+
+.. 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
+------------
+
+-  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
+-------
+
+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
+
+

_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,134 @@
+/*
+ * _sphinx_javascript_frameworks_compat.js
+ * ~~~~~~~~~~
+ *
+ * Compatability shim for jQuery and underscores.js.
+ *
+ * WILL BE REMOVED IN Sphinx 6.0
+ * xref RemovedInSphinx60Warning
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}