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Merge pull request #62 from emmo-repo/dev
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Upgrade to v0.7.0-alpha
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@jsimonclark
jsimonclark authored Dec 5, 2023
2 parents cde0e40 + 5a7fbd1 commit 623f197
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23 changes: 0 additions & 23 deletions .github/workflows/ci_tests.yml
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Expand Up @@ -38,26 +38,3 @@ jobs:
--configfile=.github/utils/emmocheck_config.yml \
electrochemicalquantities.ttl
- name: Run EMMO Check - emmo-concepts
run: |
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
emmo-concepts.ttl
- name: Run EMMO Check - isq_bigmap
run: |
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
isq_bigmap.ttl
- name: Run EMMO Check - material_bigmap_temp
run: |
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
material_bigmap_temp.ttl
35 changes: 35 additions & 0 deletions CONTRIBUTING.md
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# Contributing to the ontology

There are two ways you can contribute to the ontology:
- Suggesting minor changes to the developers by reporting issues. This is the best option for most people.
- Editing the ontology files directly and submitting a pull request. This requires a more detailed knowledge of ontology development and EMMO guidelines.

These two options are described below.

## Suggest minor changes on existing elements

[Create a feature request](https://github.com/emmo-repo/domain-electrochemistry/issues/new) in a [Github Issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue) to suggest edits to names, defintions, references on existing classes and properties.

## Propose additions/deletion of elements

We recommend using the [forking workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow) to contribute additions/deletions.
Fork this repository, clone the fork on your local PC, create your branch based on the existing `dev` branch (e.g. `dev_john_doe`) and work on the editions in you local copy.

### Editing the ontology programmatically in python
One is programmatically, using for instance [EMMOntoPy](https://github.com/emmo-repo/EMMOntoPy).

### Editing the ontology in a graphical user interface (GUI)
[Protégé](https://protege.stanford.edu/) is a widely used graphical development environment for ontologies and knowledge graphs. It is open-source software that is maintained by Stanford University in the United States.

Before adding elements, ensure Prot´égé is configured to create IRIs in the right format:

* Open Protégé
* Go to File/Open and load the ontology file you wish to modify
* Go to File/Preferences and there go to the New Entities Tab
* Ensure you have configured the preferences as shown below:

![Protege config.](docs/images/protege_config_contribute.png)
Here is the "Specified IRI" for you to copy: ```https://w3id.org/emmo/domain/electrochemistry#```

Once you have made your changes, commit them to your fork and [create a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
* We will assess the request and submit feedback if necessary. If the pull request meets the requirements for inclusion, we will merge it.
69 changes: 13 additions & 56 deletions README.md
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# Electrochemistry Domain Ontology

<!-- [![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, a specialized domain within the Elementary Multiperspective Materials Ontology [(EMMO)][1], 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.

An electrochemistry domain ontology developed in the [BIG-MAP][2] project.
The ontology is a part of the [Battery Interface Domain Ontology (BattINFO)](https://github.com/BIG-MAP/BattINFO).
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.

The ontology is based on [EMMO][1].
## Integration with EMMO

A reference documentation of the individual classes 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.
The Electrochemistry Domain Ontology is an official domain on the EMMO. It 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:
- the [Chemical Substance Domain Ontology](https://github.com/emmo-repo/domain-chemical-substance): provides material annotations for electrochemical (meta)data.

## Obtaining the ontology

Expand All @@ -37,61 +42,13 @@ electrochemistry = get_ontology('/path/to/domain-electrochemistry/electrochemist
electrochemistry = get_ontology('https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry.ttl').load()
```

## Contributing to the ontology

There are two ways you can contribute to the ontology.

### Suggest minor changes on existing elements

[Create a feature request](https://github.com/emmo-repo/domain-electrochemistry/issues/new) in a [Github Issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue) to suggest edits to names, defintions, references on existing classes and properties.

### Propose additions/deletion of elements

> **_NOTE:_** We recommend contacting some of [BattINFO](https://github.com/BIG-MAP/BattINFO) contributors in advance to discuss which additions deletions you wish to make.
We recommend using the [forking workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow) to contribute additions/deletions.
Fork this repository, clone the fork on your local PC, create your branch based on the existing `dev` branch (e.g. `dev_john_doe`) and work on the editions in you local copy.

You can edit ontologes in two main ways.
One is programmatically, using for instance [EMMOntoPy](https://github.com/emmo-repo/EMMOntoPy).
The second and more common is using the interface provided by the Protégé software.
In case of the latter, [install Protégé](https://protege.stanford.edu/) and use it to open the ontology file you wish to edit.
Before adding elements, ensure Prot´égé is configured to create IRIs in the right format:

* Open Protégé
* Go to File/Open and load the ontology file you wish to modify
* Go to File/Preferences and there go to the New Entities Tab
* Ensure you have configured the preferences as shown below:

![Protege config.](doc/img/protege_config_contribute.png)
Here is the "Specified IRI" for you to copy: ```https://emmo.info/electrochemistry#```

* Once you have made your changes, commit them to your fork and [create a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
* We will merge the request after assessing it.

## Attributions and credits

### Contributors
### Acknowledgements

* 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
<img src="documentation/images/flag_of_europe.png" alt="EU-Flag" width="100">

### Projects
This project has received support from European Union research and innovation programs, under grant agreement numbers:

* [BIG-MAP](http://www.big-map.eu/); Grant Agreement No: 957189 <img src="bigmap.png" alt="BIG-MAP" width="30">
* 957189 - [BIG-MAP](http://www.big-map.eu/)

## License

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12 changes: 8 additions & 4 deletions catalog-v001.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri id="Imports Wizard Entry" name="https://w3id.org/emmo/domain/chemicalsubstance/0.2.0/chemicalsubstance" uri="https://raw.githubusercontent.com/emmo-repo/domain-chemical-substance/main/chemicalsubstance.ttl"/>
<uri id="Imports Wizard Entry" name="http://emmo.info/emmo/domain/chameo/chameo/1.0.0-beta5" uri="https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/1.0.0-beta3/chameo.ttl"/>
<uri id="Imports Wizard Entry" name="http://emmo.info/emmo/1.0.0-beta5" uri="https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/emmo.ttl"/>
<uri id="Imports Wizard Entry" name="http://emmo.info/emmo/1.0.0-beta5/disciplines/units/unclassifiedunits" uri="https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/units/unclassifiedunits.ttl"/>
<group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
<uri name="http://emmo.info/electrochemistry/0.6.0/electrochemistry" uri="./electrochemistry.ttl"/>
<uri name="http://emmo.info/electrochemistry/0.6.0/electrochemicalquantities" uri="./electrochemicalquantities.ttl"/>
<uri name="http://emmo.info/material/0.1.0/material" uri="./material.ttl"/>
<uri name="http://emmo.info/1.0.0-beta5/emmo-inferred" uri="https://emmo-repo.github.io/versions/1.0.0-beta5/emmo-inferred.ttl"/>
<uri name="https://w3id.org/emmo/domain/electrochemistry/0.7.0-alpha/electrochemistry" uri="./electrochemistry.ttl"/>
<uri name="https://w3id.org/emmo/domain/electrochemistry/0.7.0-alpha/electrochemicalquantities" uri="./electrochemicalquantities.ttl"/>
<uri name="https://w3id.org/emmo/domain/chemicalsubstance/0.2.0/chemicalsubstance" uri="./chemicalsubstance.ttl"/>
<uri name="http://emmo.info/emmo/1.0.0-beta5-inferred" uri="./emmo-inferred.ttl"/>
</group>
</catalog>
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