Fix typos and formatting.

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/

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
 
@@ -15,27 +15,30 @@ 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
 
 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.'`

doc/mammos.md

@@ -2,7 +2,7 @@
 
 %HEADER Overview 
 
-The MaMMoS magnetic materials ontology is a domain ontology which uses [EMMO](https://github.com/emmo-repo/EMMO) as top level ontology. The magnetic material ontology reflects the hierarchical structure of the magnet. It reveals its physical parts at different length scales.
+The MaMMoS magnetic materials ontology is a domain ontology which uses [EMMO](https://github.com/emmo-repo/EMMO) as top and middle level ontology. The magnetic material ontology reflects the hierarchical structure of the magnet. It reveals its physical parts at different length scales.
 
 %HEADER "Magnet" level=2  
 
@@ -16,7 +16,7 @@ A magnet may have a *granular microstructure*.
 The spatial parts of the granular microstructure are
 the *main magnetic phase*, the *grain boundary phase*, and *secondary phase*.
 
-The granular microstructure constists of a *main magnetic phase*, possible *grain boundary phases* and *secondary phases*.  
+The granular microstructure consists of a *main magnetic phase*, possible *grain boundary phases*, and *secondary phases*.  
 
 %BRANCHFIG GranularMicrostructure addnodes=1 parents=1 rankdir='LR' relations=isA,hasSpatialPart,hasSpatialTile edgelabels=1 caption='The granular microstructure of a magnet.'
 
@@ -45,11 +45,11 @@ The *intrinsic magnetic properties* depend on the chemical composition and the c
 Whereas the intrinsic magnetic properties are a property of a magnetic material, the *extrinsic magnetic properties* depend on the microstructure and shape of the magnet. They are a property of the magnet. An important subset of the extrinsic magnetic properties are the *magnetic hysteresis properties*.
 
 %BRANCHFIG BulkMagnet addnodes=1 parents=1 rankdir='LR' relations=all edgelabels=1 caption='A bulk magnet and its properties.'
-%BRANCHFIG ExtrinsicMagneticProperties addnodes=1 parents=1 rankdir='LR' relations=hasProperty edgelabels=1 caption='The exterinsic magnetic properties.'
+%BRANCHFIG ExtrinsicMagneticProperties addnodes=1 parents=1 rankdir='LR' relations=hasProperty edgelabels=1 caption='The extrinsic magnetic properties.'
 
 %% you may add options to the documentation of a branch:  
 %% (default values are listed below)  
-%% 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  

doc/mammosdoc-meta.yaml

@@ -12,11 +12,16 @@ institute: 'Magnetic Multiscale Modelling Suite (MaMMoS)'
 keywords: [EMMO, 'materials science', modelling, characterisation, materials, ontology]
 abstract: |
   An EMMO-based ontology for magnetic materials.
-  Created within the EU project Magnetic Multiscale Mdelling Suite (MaMMoS), Grant number 101135546 (HORIZON-CL4-2023-DIGITAL-EMERGING-01)
+  
+  Created within the EU project Magnetic Multiscale Mdelling Suite (MaMMoS), 
+  Grant number 101135546 (HORIZON-CL4-2023-DIGITAL-EMERGING-01).
   MagneticMaterial is released under the Creative Commons Attribution 4.0
   International license (CC BY 4.0).  
   
-  Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the
-  European Union or European Health and Digital Executive Agency (HADEA). Neither the European Union nor the granting authority can be held
+  
+  Funded by the European Union. Views and opinions expressed are however those
+  of the author(s) only and do not necessarily reflect those of the
+  European Union or European Health and Digital Executive Agency (HADEA).
+  Neither the European Union nor the granting authority can be held
   responsible for them.
 ...

doc/plots.md

@@ -12,7 +12,7 @@
 
 %% you may add options to the documentation of a branch:  
 %% (default values are listed below)  
-%% 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