Merge pull request #28 from MetabolicAtlas/develop

standard-GEM 0.5

.standard-GEM.md

@@ -1,10 +1,10 @@
-standard-GEM v0.4
+standard-GEM 0.5
 =================
 
 For details about the [aims](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#aims), [scope](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#scope), and [use case](https://github.com/MetabolicAtlas/standard-GEM/wiki/Use-case) of this standard see the [wiki pages of the `standard-GEM` repository](https://github.com/MetabolicAtlas/standard-GEM/wiki).
 
 ### Terminology
-To facilitate understading, the definitions used throughout this guide are copied below  [from the wiki](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#terminology). For easier differentiation, we have associated colors to each of them.
+To facilitate understanding, the definitions used throughout this guide are copied below  [from the wiki](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#terminology). For easier differentiation, we have associated colors to each of them.
 ```
 Based on the ISO guidelines, tweaked for easy understanding.
 🟥 Requirements: must, must not
@@ -37,7 +37,7 @@ The topic `standard-GEM` must be added. Other topics like `genome-scale-models`,
 Topics are not copied from `standard-GEM`, so they need to be added manually.
 
 - [ ] 🟨 Add a repository URL  
-The URL can be the _doi_.
+The URL can be the link to the publication/pre-print/website where the model is introduced, for example via an identifier system (doi/EuropePMC/PubMed).
 
 
 Repository workflow
@@ -46,7 +46,7 @@ Repository workflow
 The GEM repository must have at least two branches: _master_ and _develop_.
 
 - [ ] 🟥 Releases  
-Releases must use the tag format `X.X.X` where X are numbers, according to [semantic versioning principles](https://semver.org/). The last field (“patch”) can also be used to indicate changes to the repository that do not actually change the GEM itself. The use of a `v` before the version number (`v1.0`) is [discouraged](https://semver.org/#is-v123-a-semantic-version).
+Releases must use the tag format `X.X.X` where X are numbers, according to [semantic versioning principles](https://semver.org/). The last field, also called “patch”, can also be used to indicate changes to the repository that do not actually change the GEM itself. The use of a `v` before the version number (`v1.0`) [is discouraged](https://semver.org/#is-v123-a-semantic-version). For more information about releases see the [documentation at GitHub](https://docs.github.com/en/github/administering-a-repository/managing-releases-in-a-repository).  
 
 - [ ] 🟨 Commits  
 Commit messages can follow the style of semantic commits.
@@ -96,7 +96,7 @@ The repository must contain a license file. The default license is [CC-BY 4.0 In
 - [ ] 🟥 `/README.md`  
 The repository must contain a `README.md` file. A default file is provided, and the adequate contents must be filled in.  
 The `/README.md` file must include a version badge. A default is provided in the file.  
-Additionally, the `/README.md` file	should contain [Zenodo](https://zenodo.org) badge. As soon as the first public release is in made, the repository must be archived via Zenodo, and the corresponding badge be updated. A default is provided in the file.  
+Additionally, the `/README.md` file should contain the [Zenodo](https://zenodo.org) badge. As soon as the first public release is in made, the repository [should be archived via Zenodo](https://github.com/MetabolicAtlas/standard-GEM/wiki/FAQ#zenodo), and the corresponding badge be updated. A default is provided in the file.  
 The `/README.md` can contain a contact badge, for example [Gitter](https://gitter.io). When setting up the Gitter chat room, the GitHub activity should be synced with Gitter in order to see the latest updates of the repository in the chat room. A default for this badge is provided in the file.
 
 - [x] 🟥 `/version.txt`  

README.md

@@ -30,14 +30,16 @@ If you find this template does not fit your needs, we would appreciate if you co
 #### Keywords
 
 > Keywords are be separated by semicolons.
-> The `Model source` field contains the source(s) of the current model, eg existing GEMs. If possible, use the Markdown format to add the URL with the DOI.
+> The `Model source` field contains the source(s) of the current model, eg existing GEMs. If possible, use the Markdown format to add the URL with the DOI. The (NCBI) taxonomy ID should be provided in the [format from identifiers.org](https://registry.identifiers.org/registry/taxonomy). For the genome identifier, please provide the ENA/GenBank/RefSeq identifier via *identifiers.org*, or from other sources such as PATRIC or KBase.  
 
 **Utilisation:** {{ experimental data reconstruction; multi-omics integrative analysis;, _in silico_ strain design; model template }}  
 **Field:** {{ metabolic-network reconstruction }}  
 **Type of model:** {{ reconstruction; curated }}  
 **Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }}  
 **Omic source:** {{ genomics; metabolomics }}  
-**Taxonomy:** {{ _Saccharomyces cerevisiae_ }}  
+**Taxonomic name:** {{ _Saccharomyces cerevisiae_ }}  
+**Taxonomy ID:** {{ [taxonomy:559292](https://identifiers.org/taxonomy:559292) }}  
+**Genome ID:** {{ [insdc.gca:GCA_000146045.2](https://identifiers.org/insdc.gca:GCA_000146045.2)  }}  
 **Metabolic system:** {{ general metabolism }}  
 **Tissue:**  
 **Bioreactor:**