diff --git a/README.md b/README.md index fe697fc..bf148b8 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,7 @@ An EMMO-based ontology for magnetic materials. Status ------ + - [X] Proposal - [ ] Accepted, under development - [ ] Official @@ -18,8 +19,9 @@ This ontology is work-in-progress (WIP). Imported ontologies ------------------- + This ontology builds on top of [EMMO](https://github.com/emmo-repo/EMMO) [^1]. See the following table for version -compatibilies: +compatibilities: | Imported Ontologies | Version | | | -------------------- | --------------------| --------- | @@ -29,14 +31,14 @@ compatibilies: Using ----- -You may view the ontology by browsing through the [html documentation](https://mammos-project.github.io/MagneticMaterialsOntology/doc/magnetic_material_mammos.html) +You may view the ontology by browsing through the [html documentation](https://mammos-project.github.io/MagneticMaterialsOntology/doc/magnetic_material_mammos.html). -Alternatively you can use [Protégé](https://protege.stanford.edu/) +Alternatively you can use [Protégé](https://protege.stanford.edu/): * Install Protégé * Download the file `magnetic_material_mammos.ttl` Click on the file Select the icon for `Downloading raw file` -* Start Protégé and open the magnetic materials ontololgy +* Start Protégé and open the magnetic materials ontology File --> Open magnetic_material_mammos.ttl * Run the Reasoner Reasoner --> select HermiT @@ -54,13 +56,20 @@ Alternatively you can use [Protégé](https://protege.stanford.edu/) Building -------- -MagneticMaterialsOntology is built using tools provided by EMMO. For more details see the [src directory](https://github.com/MaMMoS-project/MagneticMaterialsOntology/tree/main/src) +MagneticMaterialsOntology is built using tools provided by EMMO. For more details see the [src directory](https://github.com/MaMMoS-project/MagneticMaterialsOntology/tree/main/src). -Installation of required software is also explained in [src/README.md](https://github.com/MaMMoS-project/MagneticMaterialsOntology/tree/main/src/README.md) +Installation of required software is also explained in [src/README.md](https://github.com/MaMMoS-project/MagneticMaterialsOntology/tree/main/src/README.md). + + +Build Status +------------ + +[![build](https://github.com/MaMMoS-project/MagneticMaterialsOntology/actions/workflows/build.yaml/badge.svg)](https://github.com/MaMMoS-project/MagneticMaterialsOntology/actions/workflows/build.yaml) Attributions and credits ------------------------ + ### Authors - Thomas Schrefl, DISS-UWK - Wilfried Hortschitz, DISS-UWK @@ -76,16 +85,13 @@ Funded by the European Union. Views and opinions expressed are however those of ![image info](img/euflag.png) -## License +License +------- + This project is licensed under the [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/). -## References +References +---------- [^1]: https://github.com/emmo-repo/EMMO -[^2]: https://mammos-project.github.io/ - -Status ------- - -[![build](https://github.com/MaMMoS-project/MagneticMaterialsOntology/actions/workflows/build.yaml/badge.svg)](https://github.com/MaMMoS-project/MagneticMaterialsOntology/actions/workflows/build.yaml) - +[^2]: https://mammos-project.github.io/ \ No newline at end of file diff --git a/doc/README.md b/doc/README.md index a25e1f6..780cd13 100644 --- a/doc/README.md +++ b/doc/README.md @@ -1,6 +1,6 @@ ## Create documentation -### Generation html documentation +### Generating html documentation We use `mammosdoc` which is a modified version of `ontodoc` from EMMOntoPy as follows @@ -15,7 +15,7 @@ for creating the html file. ### Documentation The created documentation can be viewed here -[view html file](https://mammos-project.github.io/MagneticMaterialsOntology/doc/magnetic_material_mammos.html) +[view html file](https://mammos-project.github.io/MagneticMaterialsOntology/doc/magnetic_material_mammos.html) . ### Change the content of the html file @@ -23,19 +23,22 @@ You may change the content of the html file by editing the following files #### mammos.md, specify graphs to be shown -Gives the content of the html file. It is an markdown file that will be converted to an html file. -With preprocessing command, which start with %, content from the ontology can be included. +Gives the content of the html file. It is a markdown file that will be converted to an html file. +With preprocessing commands, which start with %, content from the ontology can be included. +Examples are: +``` %HEADER "header text" level=2 creates a header that is included in the table of content %BRANCHFIG name addnodes=1 parents=0 rankdir='LR' relations=isA,hasSpatialPart,hasSpatialTile edgelabels=1 adds a plot of the ontology branch `name` +``` You may use the following parameters: |parameter and default value | task | |----------------------------|------| -|caption='' | will give "Granular Microstructure branch.| +|caption='' | will add a caption below the graph| |terminated=1 | whether the graph should be terminated at leaf nodes| |strict_leaves=1 | whether to strictly exclude leave descendants| |width=0px | optional figure width| @@ -45,7 +48,7 @@ You may use the following parameters: |rankdir='BT' | graph direction (BT, TB, RL, LR: bottom-top, top-bottom, right-left, left-right)| |legend=1 | whether to add legend| |namespaces='' | sequence of names of namespaces to be included| -|ontologies='' | sequence of names of ontologies to be included +|ontologies='' | sequence of names of ontologies to be included| |addnodes=1 | whether to add missing target nodes in relations (1: True, 0: False)| |parents=1 | Adds n levels of parents to graph| @@ -55,20 +58,20 @@ You may use the following parameters: Provide pandoc arguments/options via this file. These include the name of the input file for the meta data, the depth of the table of content, and the filename of the files for logo and EU flag. -#### pandoc-html-options.yaml. +#### pandoc-html-options.yaml Provide pandoc arguments for html output via this file. These include the html style file and the html template. #### pandoc-template.html, pandoc-html.css -The html template file and html style file +The html template file and html style file. ### Create a plot of a concept Here is an example for plotting branches. To create on or more plots you can use `mammosdoc`. -* Add multiple BRANCHFIG preprocessing directives to themarkdown template file `plots.md` -* Change to the directiory `MagneticMaterialsOntology/doc` +* Add multiple BRANCHFIG preprocessing directives to the markdown template file `plots.md` +* Change to the directory `MagneticMaterialsOntology/doc` * Run mammosdoc: ``` @@ -80,9 +83,9 @@ The parameters after the preprocessor directive `%BRANCHFIG` in the file `plots. | problem | solution | parameter setting | |---------|----------|-------------------| -| no childs are displayes | add missing target nodes in relations | `addnodes=1` | +| no children are displayes | add missing target nodes in relations | `addnodes=1` | | plot has too many nodes | reduce level of shown parents | `parents=0` | -| plot has too many connetion | select only a few realations | `relations=isA,hasSpatialPart` | +| plot has too many connection | select only a few relations | `relations=isA,hasSpatialPart` | | bubbles and fonts are very small | change graph direction | `rankdir='LR'` | For readability it is recommended to switch on edge labels with `edgelabels=1` and to add a caption with `caption='Explain what we see.'` diff --git a/doc/magnetic_material_mammos.html b/doc/magnetic_material_mammos.html index 2655559..1a6a034 100644 --- a/doc/magnetic_material_mammos.html +++ b/doc/magnetic_material_mammos.html @@ -9,7 +9,7 @@ - + Magnetic Material Ontology