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78 changes: 35 additions & 43 deletions README.md
Original file line number Diff line number Diff line change
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[![CI tests](https://github.com/emmo-repo/CIF-ontology/workflows/CI/badge.svg)](https://github.com/emmo-repo/CIF-ontology/actions/)

# CIF ontology
CIF Ontology
============
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This repository provides an ontologisation of the CIF Dictionary
Definition Language ([DDLm]) and the [CIF core dictionary] by IUCr.
The development version of these dictionaries can be found in the
[COMCIFS/cif_core] GitHub repository.
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A crystallography domain ontology based on [EMMO][1] and the [CIF core][2] dictionary.
It is implemented as a formal language.
The CIF Ontology has no dependencies to any upper ontology. But the
EMMC crystallography task group is providing an EMMO-based
[Crystallography Domain Ontology] which is based on both the CIF
Ontology and [EMMO].
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## Status

- [ ] Proposal
- [X] Accepted, under development
- [ ] Official
Obtaining CIF-ontology
-----------------------
A table with available releases can be found on
https://emmo-repo.github.io/CIF-ontology/
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This ontology is work-in-progress (WIP).
It is part of the overall process of developing a domain ontology for crystallography.

## Imported Ontologies
### Manually generating the cif core ontology

This ontology builds on top of EMMO.
See the following table for version compatibilies:
It is also possible to clone this repository and generate the CIF
ontology yourselves.
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| Imported Ontologies | Version |
| ------------------- | ----------------- |
| emmo-inferred | 1.0.0-beta |

## Generator tool (`dic2owl`)

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

Go to the [README](dic2owl/README.md) of `dic2owl` to read more about the generator tool.

## Obtaining CIF-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).

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
and then run the `dic2owl` tool following the instructions in the
[dic2owl/README.md] file.
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```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()
```

## Attributions and credits
Attributions and credits
------------------------
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### Contributors

Expand All @@ -68,7 +50,8 @@ 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/);
Expand All @@ -87,5 +70,14 @@ 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




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[DDLm]: https://www.iucr.org/resources/cif/ddl/ddlm
[CIF core dictionary]: https://www.iucr.org/resources/cif/dictionaries/cif_core
[COMCIFS/cif_core]: https://github.com/COMCIFS/cif_core
[Crystallography Domain Ontology]: https://github.com/emmo-repo/domain-crystallography
[EMMO]: https://github.com/emmo-repo/EMMO
[cif_core.ttl]: https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif-core.ttl
[dic2owl/README.md]: https://github.com/emmo-repo/CIF-ontology/blob/main/dic2owl/README.md
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