From 2aac30fc3fba029b2062763e7e79ec7ff073ee14 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Tue, 8 Sep 2020 15:54:04 +0300 Subject: [PATCH 01/11] feat: add field for genome id to readme resolves #17 --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4325d31..1b279a8 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,8 @@ If you find this template does not fit your needs, we would appreciate if you co **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_ }} +**Genome ID:** {{ provide identifier from PATRIC or GenBank }} **Metabolic system:** {{ general metabolism }} **Tissue:** **Bioreactor:** From 3a480d70511be3c581aa3e5ddab25c7609a7c10c Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Tue, 8 Sep 2020 17:04:52 +0300 Subject: [PATCH 02/11] fix: clarify usage of Zenodo resolves #14 --- .standard-GEM.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.standard-GEM.md b/.standard-GEM.md index a74fdb1..d25efcf 100644 --- a/.standard-GEM.md +++ b/.standard-GEM.md @@ -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` From 9b32df2f3002d88a2bf5685e92f04041f236ca1f Mon Sep 17 00:00:00 2001 From: Hao-Chalmers Date: Tue, 8 Sep 2020 19:05:48 +0200 Subject: [PATCH 03/11] fix: allow Genome ID from any sources - A wide range databases provide genome IDs that should be allowed as well --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1b279a8..9552585 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ If you find this template does not fit your needs, we would appreciate if you co **Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }} **Omic source:** {{ genomics; metabolomics }} **Taxonomic name:** {{ _Saccharomyces cerevisiae_ }} -**Genome ID:** {{ provide identifier from PATRIC or GenBank }} +**Genome ID:** {{ provide identifier from PATRIC，GenBank, or other sources }} **Metabolic system:** {{ general metabolism }} **Tissue:** **Bioreactor:** From 6050e32c435df3b42316b27ffc3be0af563412b7 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Wed, 9 Sep 2020 12:38:18 +0300 Subject: [PATCH 04/11] refactor: clearer guidelines for the genome id --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1b279a8..81d0540 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ 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. For the genome identifier, please provide the ENA/GenBank/RefSeq identifier via *identifiers.org*. **Utilisation:** {{ experimental data reconstruction; multi-omics integrative analysis;, _in silico_ strain design; model template }} **Field:** {{ metabolic-network reconstruction }} @@ -38,7 +38,7 @@ If you find this template does not fit your needs, we would appreciate if you co **Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }} **Omic source:** {{ genomics; metabolomics }} **Taxonomic name:** {{ _Saccharomyces cerevisiae_ }} -**Genome ID:** {{ provide identifier from PATRIC or GenBank }} +**Genome ID:** {{ [insdc.gca:GCA_000146045.2](https://identifiers.org/insdc.gca:GCA_000146045.2) }} **Metabolic system:** {{ general metabolism }} **Tissue:** **Bioreactor:** From bf274aba430948e04f8144ff5411a3b55d127196 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Thu, 10 Sep 2020 15:09:25 +0300 Subject: [PATCH 05/11] feat: add taxonomy id resolves #13 --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4325d31..4a855aa 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ 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). **Utilisation:** {{ experimental data reconstruction; multi-omics integrative analysis;, _in silico_ strain design; model template }} **Field:** {{ metabolic-network reconstruction }} @@ -38,6 +38,7 @@ If you find this template does not fit your needs, we would appreciate if you co **Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }} **Omic source:** {{ genomics; metabolomics }} **Taxonomy:** {{ _Saccharomyces cerevisiae_ }} +**Taxonomy ID:** {{ [taxonomy:559292](https://identifiers.org/taxonomy:559292) }} **Metabolic system:** {{ general metabolism }} **Tissue:** **Bioreactor:** From 0ac317ef69232a48c265e7fd5582dd4854c6373d Mon Sep 17 00:00:00 2001 From: Hao-Chalmers Date: Thu, 10 Sep 2020 18:35:28 +0200 Subject: [PATCH 06/11] doc: add description for genome id The Genbank/Refseq ids are recommended, while the others (e.g. PATRIC, KBase) are also allowed. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9552585..0e4dd14 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ If you find this template does not fit your needs, we would appreciate if you co **Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }} **Omic source:** {{ genomics; metabolomics }} **Taxonomic name:** {{ _Saccharomyces cerevisiae_ }} -**Genome ID:** {{ provide identifier from PATRIC，GenBank, or other sources }} +**Genome ID:** {{ provide identifier from GenBank or other sources such as PATRIC, KBase}} **Metabolic system:** {{ general metabolism }} **Tissue:** **Bioreactor:** From 8b195123e0a2df2e62a5d0258f866cdb1ab4072d Mon Sep 17 00:00:00 2001 From: Ulf Liebal Date: Tue, 15 Sep 2020 08:14:28 +0300 Subject: [PATCH 07/11] fix: typo --- .standard-GEM.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.standard-GEM.md b/.standard-GEM.md index d25efcf..b2930b8 100644 --- a/.standard-GEM.md +++ b/.standard-GEM.md @@ -4,7 +4,7 @@ standard-GEM v0.4 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 From 1a4a02b828ebf0640ee1297964f9ec1db7b0dce6 Mon Sep 17 00:00:00 2001 From: Ulf Liebal Date: Tue, 15 Sep 2020 08:22:17 +0300 Subject: [PATCH 08/11] feat: add link to documentation for git releases --- .standard-GEM.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.standard-GEM.md b/.standard-GEM.md index b2930b8..9d76dd7 100644 --- a/.standard-GEM.md +++ b/.standard-GEM.md @@ -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. From 39c6a950c4f64d7d6a2555f4cd21ede193a99ebd Mon Sep 17 00:00:00 2001 From: Ulf Liebal Date: Tue, 15 Sep 2020 08:29:16 +0300 Subject: [PATCH 09/11] feat: improved description of the repository url --- .standard-GEM.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.standard-GEM.md b/.standard-GEM.md index 9d76dd7..0d8dcb6 100644 --- a/.standard-GEM.md +++ b/.standard-GEM.md @@ -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 paper, for example via an identifier system like the doi, EuropePMC or PubMed. Repository workflow From 60448c5202aa22f85f51745689c10039a80f0007 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Wed, 30 Sep 2020 20:30:50 +0300 Subject: [PATCH 10/11] fix: clarify the role of the url when setting up a standard-GEM --- .standard-GEM.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.standard-GEM.md b/.standard-GEM.md index 0d8dcb6..418d8d3 100644 --- a/.standard-GEM.md +++ b/.standard-GEM.md @@ -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 link to the paper, for example via an identifier system like the doi, EuropePMC or PubMed. +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 From 8992c82ea3fc7e58fa3193f641bc678d6ea15854 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Thu, 1 Oct 2020 14:10:34 +0300 Subject: [PATCH 11/11] chore: version bump --- .standard-GEM.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.standard-GEM.md b/.standard-GEM.md index 418d8d3..154a857 100644 --- a/.standard-GEM.md +++ b/.standard-GEM.md @@ -1,4 +1,4 @@ -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).