From da3f1a536d028973398f5f7938c292adf87ff858 Mon Sep 17 00:00:00 2001 From: Jesper Friis Date: Thu, 27 Oct 2022 20:06:16 +0200 Subject: [PATCH 1/3] Improve readme file --- README.md | 78 +++++++++++++++++++++++++------------------------------ 1 file changed, 35 insertions(+), 43 deletions(-) diff --git a/README.md b/README.md index 26b8786..17ded3f 100644 --- a/README.md +++ b/README.md @@ -1,60 +1,42 @@ [![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 +============ +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. -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]. -## 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/ -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. -| 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. -```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 +------------------------ ### Contributors @@ -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/); @@ -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 + + + + +[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 From a63df306fc36a0f892c51505e4f94bee6b8f51dc Mon Sep 17 00:00:00 2001 From: Jesper Friis Date: Mon, 10 Apr 2023 14:39:51 +0200 Subject: [PATCH 2/3] Changed to relative links so that they points to the current branch. --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 17ded3f..ce563c1 100644 --- a/README.md +++ b/README.md @@ -73,11 +73,10 @@ See also the [LICENSE](LICENSE) file. - [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 +[cif_core.ttl]: ontology/cif-core.ttl +[dic2owl/README.md]: dic2owl/README.md From 4ecaa98ee2d3f4e2a03a9525baa210049e6cf9ba Mon Sep 17 00:00:00 2001 From: Casper Welzel Andersen Date: Mon, 30 Oct 2023 13:32:34 +0100 Subject: [PATCH 3/3] Make README.md comply with markdownlint --- README.md | 53 +++++++++++++++-------------------------------------- 1 file changed, 15 insertions(+), 38 deletions(-) diff --git a/README.md b/README.md index eabab55..dea64b8 100644 --- a/README.md +++ b/README.md @@ -1,30 +1,21 @@ +# 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 -============ -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. - -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]. - +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). -Obtaining CIF-ontology ------------------------ -A table with available releases can be found on -https://emmo-repo.github.io/CIF-ontology/ +## Obtaining CIF-ontology +A table with available releases can be found in [the documentation](https://emmo-repo.github.io/CIF-ontology/). ### Manually generating the cif core ontology -It is also possible to clone this repository and generate the CIF -ontology yourselves. +It is also possible to clone this repository and generate the CIF ontology. First clone this repository with @@ -32,13 +23,9 @@ First clone this repository with git clone https://github.com/emmo-repo/CIF-ontology.git ``` -and then run the `dic2owl` tool following the instructions in the -[dic2owl/README.md] file. - - +and then run the `dic2owl` tool following the instructions in the [dic2owl/README.md](dic2owl/README.md) file. -Attributions and credits ------------------------- +## Attributions and credits ### Contributors @@ -52,33 +39,23 @@ Attributions and credits - Joana Morgado, Fraunhofer IWM - Stuart Chalk - ### Contributing projects - Demystify ontologies - Internal project at [SINTEF](www.sintef.no) - [MarketPlace](https://www.the-marketplace-project.eu/); Grant Agreement No: 760173 + - [OntoTrans](https://ontotrans.eu/); Grant Agreement No: 862136 + - [BIG-MAP](https://www.big-map.eu/); Grant Agreement No: 957189 + -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. - - - - -[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]: ontology/cif-core.ttl -[dic2owl/README.md]: dic2owl/README.md