diff --git a/README.md b/README.md index c62cc89..f491e9d 100644 --- a/README.md +++ b/README.md @@ -1,55 +1,77 @@ -> Please read the paragraph below and delete it: -This is the `README.md` template provided by [standard-GEM](https://github.com/SysBioChalmers/standard-GEM). -Blanks are indicated by `{{ }}`. Below are examples of blanks used throughout this file: -`{{organization or username}}` is the organization name or username for this GitHub repository, eg. `SysBioChalmers` -`{{repository name}}` is the name of this GitHub repository, eg. `yeast-GEM` +# Rat-GEM: The generic genome-scale metabolic model of _Rattus norvegicus_ -## {{repository name}}: {{repository description}} -[![Version](https://badge.fury.io/gh/{{organization or username}}%2F{{repository name}}.svg)](https://badge.fury.io/gh/sysbiochalmers/yeast-gem) -[![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}}) -[![Gitter chat](https://badges.gitter.im/{{organization or username}}/{{repository name}}.svg)](https://gitter.im/{{organization or username}}/{{repository name}}) +[![Version](https://badge.fury.io/gh/{{organization or username}}%2F{{repository name}}.svg)](https://badge.fury.io/gh/sysbiochalmers/rat-gem) +[![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}}) #### Brief Model Description -{{ fill in a short description or the paper abstract }} - +This repository contains the latest version of Rat-GEM, a rat genome-scale metabolic model. #### Citation -{{ provide the citation once available, for example: - > Lu, H., Li, F., Sánchez, B.J. et al (2019). A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun 10, 3586 [doi:10.1038/s41467-019-11581-3](https://doi.org/10.1038/s41467-019-11581-3) - -}} - +Manuscript under preparation #### Model Keywords -**Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template +**Utilisation:** multi-omics integrative analysis, predictive simulation **Field:** metabolic-network reconstruction **Type of Model:** reconstruction, curated -**Model Source:** YeastMetabolicNetwork -**Omic Source:** genomics, metabolomics -**Taxonomy:** _Saccharomyces cerevisiae_ +**Model source:** [Human-GEM](https://doi.org/10.1126/scisignal.aaz1482) +**Omic source:** genomics; metabolomics +**Taxonomic name:** _Rattus norvegicus_ +**Taxonomy ID:** [10116](https://identifiers.org/taxonomy:10116) +**Genome ID:** [GCF_000001895.5](https://identifiers.org/insdc.gca:GCF_000001895.5) **Metabolic System:** general metabolism **Tissue:** **Bioreactor:** **Cell type:** **Cell line:** -**Strain:** S288C -**Condition:** aerobic, glucose-limited, defined media +**Condition:** generic metabolism + + +### Model Overview + +|Taxonomy | Template Model | Reactions | Metabolites| Genes | +| ------------- |:-------------:|:-------------:|:-------------:|:-----:| +|_Rattus norvegicus_ | Human-GEM | | | | + + +## Installation + +### Required Software +* A functional MATLAB installation (MATLAB 7.3 and higher). +* The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN). +* The [COBRA toolbox](https://github.com/opencobra/cobratoolbox) (not necessary for most functionality). + + +### Dependencies - Recommended Software +* The libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended). +* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations. + + +### Installation Instructions +* Clone the [master branch](https://github.com/SysBioChalmers/Rat-GEM/tree/master) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Rat-GEM/releases/latest). +* Add the directory to your MATLAB path (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)). + + +## Usage +#### Loading/saving the model -### Installation +`Rat-GEM.mat` (Recommended if on `master` branch) +* Load and save using the built-in MATLAB `load()` and `save()` functions. -{{ Be mindful of users who do not have a typical background - provide a clear overview of the required software. Also, there might be different requirements for users and collaborators. }} +`Rat-GEM.xml` (SBML format) +* Load using the `importModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) +* Save using the `exportModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) -### Usage +## Websites -{{ Describe how to load and save the model. }} +- [Metabolic Atlas](https://metabolicatlas.org/) enables visualization and exploration of Rat-GEM content. ### Contributing diff --git a/code/README.md b/code/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/code/masterScriptRatGEM.m b/code/masterScriptRatGEM.m new file mode 100644 index 0000000..acf8605 --- /dev/null +++ b/code/masterScriptRatGEM.m @@ -0,0 +1,77 @@ +% +% FILE NAME: masterScriptRatGEM.m +% +% PURPOSE: This script is for reconstruction of the Rat-GEM, by using +% the Human-GEM as template and taking in account mouse-specific +% pathways/reactions. +% +% + + +%% Load Human-GEM as template +load('Human-GEM.mat'); + + +% convert gene identifiers from Ensembl ids to gene symbols +[grRules,genes,rxnGeneMat] = translateGrRules(ihuman.grRules,'Name','ENSG'); +ihuman.grRules = grRules; +ihuman.genes = genes; +ihuman.rxnGeneMat = rxnGeneMat; + + + +%% Use MA reactions identifiers + +% load reaction annotaiton files +rxnAssoc = jsondecode(fileread('humanGEMRxnAssoc.JSON')); + +%replace reaction identifiers with MA ids if available +ind = getNonEmptyList(rxnAssoc.rxnMAID); +ihuman.rxns(ind) = rxnAssoc.rxnMAID(ind); + + + +%% Generate Rat-GEM using Human-GEM as template + +% get ortholog pairs from human to rat +ratOrthologPairs = extractAllianceGenomeOrthologs('human2RatOrthologs.json'); +ratGEM = getModelFromOrthology(ihuman, ratOrthologPairs); +ratGEM.id = 'Rat-GEM'; + + + +%% Incorporate rat-specific reactions + +% get metabolic networks based on the KEGG annoation using function getKEGGModelForOrganism +KEGG_human=getKEGGModelForOrganism('hsa'); +KEGG_rat=getKEGGModelForOrganism('rno'); + +% remove shared human reactions +RatSpecificRxns=setdiff(KEGG_rat.rxns,KEGG_human.rxns); + +% remove reactions included in Human-GEM +RatSpecificRxns=setdiff(RatSpecificRxns,rxnAssoc.rxnKEGGID); + +% get species-specific network for manual inspection +ratSpecificNetwork=removeReactions(KEGG_rat, setdiff(KEGG_rat.rxns,RatSpecificRxns), true, true, true); + +% organize species-specific pathways into two tsv files: +% "ratSpecificMets.tsv" contains new metabolites +metsToAdd = importTsvFile('ratSpecificMets.tsv'); + +% "ratSpecificRxns.tsv" contains new reactions +rxnsToAdd = importTsvFile('ratSpecificRxns.tsv'); +rxnsToAdd.subSystems = cellfun(@(s) {{s}}, rxnsToAdd.subSystems); + +% integrate rat-specific metabolic network +[ratGEM, modelChanges] = addMetabolicNetwork(ratGEM, rxnsToAdd, metsToAdd); + + + +%% Save the generated model into Matlab, Yaml and SBML formats + +save('../model/Rat-GEM.mat', 'ratGEM'); +writeHumanYaml(ratGEM, '../model/Rat-GEM.yml'); +exportModel(ratGEM, '../model/Rat-GEM.xml'); + + diff --git a/data/README.md b/data/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/data/human2RatOrthologs.json b/data/human2RatOrthologs.json new file mode 100644 index 0000000..8d49a82 --- /dev/null +++ b/data/human2RatOrthologs.json @@ -0,0 +1,1067044 @@ +{ + "apiVersion": "0.91", + "errorMessage": "", + "note": "", + "request": { + "parameterMap": { + "filter.stringency": [ + "stringent" + ], + "limit": [ + "50000" + ], + "page": [ + "1" + ] + }, + "uri": "/api/homologs/9606/10116" + }, + "requestDate": "2020/09/07 15:01:19", + "requestDuration": "00:00:00", + "results": [ + { + "best": "Yes", + "bestReverse": "Yes", + "gene": { + "id": "HGNC:5", + "species": { + "commonNames": "['human']", + "dataProviderFullName": "Rat Genome Database", + "dataProviderShortName": "RGD", + "name": "Homo sapiens", + "shortName": "Hsa", + "taxonId": "NCBITaxon:9606" + }, + "symbol": "A1BG", + "taxonId": 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+1,10 @@ +mets metNames metFormulas metCharges compartments metKEGGID metPubChemID metChEBIID metMetaCycID metMetaNetXID +"m20001g" "N-Acetyllactosamine" "C14H25NO11" 0 "g" "C00611" "3885" "CHEBI:16153" "BETA-D-GALACTOSYL-ETCETERA-GLUCOSAMINE" "MNXM729847" +"m20002g" "alpha-D-Galactosyl-1,3-beta-D-galactosyl-1,4-N-acetyl-D-glucosamine" "C20H35NO16" 0 "g" "C04847" "7404" "CHEBI:18217;CHEBI:62327" "ALPHA-D-GALACTOSYL-13-BETA-D-GALACTOS" "MNXM735633" +"m20003c" "L-Allothreonine" "C4H9NO3" 0 "c" "C05519" "7864" "CHEBI:58585" "L-ALLO-THREONINE" "MNXM2125" +"m20005p" "1,3,7-Trimethyluric acid" "C8H10N4O3" 0 "p" "C16361" "47205669" "CHEBI:691622" "CPD-12480" "MNXM2761" +"m20006p" "3,6,8-Trimethylallantoin" "C7H12N4O3" 0 "p" "C16362" "47205670" "CHEBI:80471" "CPD-12485" "MNXM6778" +"m20007r" "L-xylo-Hexulonolactone" "C6H8O6" 0 "r" "C03289" "6146" "CHEBI:73681" "" "MNXM731654" +"m01368r" "ascorbate" "C6H7O6" -1 "r" "C00072" "" "CHEBI:38290" "ASCORBATE" "MNXM727871" +"m01104p" "5-hydroxyisourate" "C5H4N4O4" 0 "p" "C11821" "" "CHEBI:250388" "5-HYDROXYISOURATE" "MNXM1137" +"m10018p" "5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate" "C5H5N4O5" -1 "p" "C12248" "" "CHEBI:58639" "CPD-5821" "MNXM1805" diff --git a/data/ratSpecificRxns.tsv b/data/ratSpecificRxns.tsv new file mode 100644 index 0000000..b1f32d2 --- /dev/null +++ b/data/ratSpecificRxns.tsv @@ -0,0 +1,10 @@ +rxns equations ub lb eccodes subSystems grRules rxnReferences rxnConfidenceScores rxnKEGGID rxnMetaCycID rxnREACTOMEID rxnMetaNetXID +"MA_20001" "NAD+[m] + threonine[m] => NADH[m] + H+[m] + L-2-amino-3-oxobutanoic acid[m]" 1000 0 "1.1.1.103" "Glycine, serine and threonine metabolism" "Tdh" "" 2 "R01465" "THREODEHYD-RXN" "R-HSA-6798667" "MNXR103402" +"MA_20002" "N-Acetyllactosamine[g] + UDP-galactose[g] => alpha-D-Galactosyl-1,3-beta-D-galactosyl-1,4-N-acetyl-D-glucosamine[g] + UDP[g] + H+[g]" 1000 0 "2.4.1.87" "Glycosphingolipid biosynthesis" "Ggta1" "PMID:12626403" 4 "R04531" "2.4.1.124-RXN" "" "MNXR115091" +"MA_20003" "L-Allothreonine[c] <=> glycine[c] + acetaldehyde[c]" 1000 -1000 "4.1.2.48;4.1.2.49" "Glycine, serine and threonine metabolism" "LOC688286" "" 2 "R06171" "LTAA-RXN" "" "MNXR104834" +"MA_20004" "H2O[p] + 5-hydroxyisourate[p] => 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[p] + H+[p]" 1000 0 "3.5.2.17" "Purine metabolism" "RGD1309350" "" 2 "R06601" "3.5.2.17-RXN" "" "MNXR100652" +"MA_20005" "5-hydroxyisourate[p] <=> 5-hydroxyisourate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" "" +"MA_20006" "5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[p] <=> 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" "" +"MA_20007" "2 H2O[p] + O2[p] + 1,3,7-Trimethyluric acid[p] <=> CO2[p] + H2O2[p] + 3,6,8-Trimethylallantoin[p]" 1000 -1000 "1.7.3.3" "Caffeine metabolism" "Uox" "" 2 "R07981" "" "" "MNXR111564" +"MA_20008" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + ascorbate[r] + H+[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "" 2 "R10053" "RXN-13689" "" "MNXR116004" +"MA_20009" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + L-xylo-Hexulonolactone[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "" 2 "R03184" "L-GULONOLACTONE-OXIDASE-RXN" "" "MNXR140097" diff --git a/docs/_config.yml b/docs/_config.yml deleted file mode 100644 index a45c832..0000000 --- a/docs/_config.yml +++ /dev/null @@ -1,4 +0,0 @@ - -theme: jekyll-theme-minimal -logo: docs/icon.png -show_downloads: "true" diff --git a/modelFiles/.keep b/model/.keep similarity index 100% rename from modelFiles/.keep rename to model/.keep