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66 changes: 17 additions & 49 deletions README.md
Original file line number Diff line number Diff line change
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# CIF Ontology

[![CI tests](https://github.com/emmo-repo/CIF-ontology/workflows/CI/badge.svg)](https://github.com/emmo-repo/CIF-ontology/actions/)
[![DOI](https://zenodo.org/badge/272473769.svg)](https://zenodo.org/badge/latestdoi/272473769)

This repository provides an ontologisation of the CIF Dictionary Definition Language ([DDLm](https://www.iucr.org/resources/cif/ddl/ddlm)) and the [CIF core dictionary](https://www.iucr.org/resources/cif/dictionaries/cif_core) by IUCr.
The development version of these dictionaries can be found in the [COMCIFS/cif_core](https://github.com/COMCIFS/cif_core) GitHub repository.

# CIF ontology

A crystallography domain ontology based on [EMMO][1] and the [CIF core][2] dictionary.
It is implemented as a formal language.

## Status

- [ ] Proposal
- [X] Accepted, under development
- [ ] Official

This ontology is work-in-progress (WIP).
It is part of the overall process of developing a domain ontology for crystallography.

## Imported Ontologies

This ontology builds on top of EMMO.
See the following table for version compatibilies:

| Imported Ontologies | Version |
| ------------------- | ----------------- |
| emmo-inferred | 1.0.0-beta |

## Generator tool (`dic2owl`)
The CIF Ontology has no dependencies to any upper ontology.
But the EMMC crystallography task group is providing an EMMO-based [Crystallography Domain Ontology](https://github.com/emmo-repo/domain-crystallography), which is based on both the CIF Ontology and [EMMO](https://github.com/emmo-repo/EMMO).

This repository contains both ontologies (under [`/ontology`](ontology)) and the `dic2owl` generator tool (under [`/dic2owl`](dic2owl)), written in Python.
## Obtaining CIF-ontology

Go to the [README](dic2owl/README.md) of `dic2owl` to read more about the generator tool.
A table with available releases can be found in [the documentation](https://emmo-repo.github.io/CIF-ontology/).

## Obtaining CIF-ontology
### Manually generating the cif core ontology

This ontology build on EMMO-1.0.0-beta.
The correct path to the inferred verion 'emmo-inferred' is specified in the catalog file, [`catalog-v001.xml`](ontology/catalog-v001.xml).
It is also possible to clone this repository and generate the CIF ontology.

The domain ontology is obtained with:
First clone this repository with

```console
git clone https://github.com/emmo-repo/CIF-ontology.git
```

When opening [cif.ttl](https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif.ttl) in Protégé, the correct version of emmo-inferred will be downloaded and imported.

In EMMO-python correct import is obtained with

```python
from emmo import get_ontology

# Loading crystallography from local repository
cif_onto = get_ontology('/path/to/cif.ttl').load(url_from_catalog=True)

# Loading crystallography from web
cif_onto = get_ontology('https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif.ttl').load()
```
and then run the `dic2owl` tool following the instructions in the [dic2owl/README.md](dic2owl/README.md) file.

## Attributions and credits

Expand All @@ -70,24 +39,23 @@ cif_onto = get_ontology('https://raw.githubusercontent.com/emmo-repo/CIF-ontolog
- Joana Morgado, Fraunhofer IWM
- Stuart Chalk

### Projects
### Contributing projects

- Demystify ontologies - Internal project at [SINTEF](www.sintef.no)
- [MarketPlace](https://www.the-marketplace-project.eu/);
Grant Agreement No: 760173
<!-- markdownlint-disable-next-line MD033 -->
<img src="https://www.the-marketplace-project.eu/content/dam/iwm/the-marketplace-project/images/MARKETPLACE_LOGO_300dpi.png" width="120">
- [OntoTrans](https://ontotrans.eu/);
Grant Agreement No: 862136
<!-- markdownlint-disable-next-line MD033 -->
<img src="https://ontotrans.eu/wp-content/uploads/2020/05/ot_logo_rosa_gro%C3%9F.svg" height="50">
- [BIG-MAP](https://www.big-map.eu/);
Grant Agreement No: 957189
<!-- markdownlint-disable-next-line MD033 -->
<img src="https://avatars1.githubusercontent.com/u/72801303?s=200&v=4" height="50">

License
-------
## License

The CIF ontology is released under the [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/legalcode) license (CC BY 4.0).
See also the [LICENSE](LICENSE) file.

[1]: https://github.com/emmo-repo/EMMO
[2]: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/index.html