Integration

adaptDraftModelID(modelIDIn)

This function adapts the name of the draft reconstruction entered into the pipeline into a suitable curated reconstruction ID.

USAGE:

microbeID = adaptDraftModelID (modelIDIn)

INPUT:

modelIDIn – name of the KBase draft reconstruction file to refine

OUTPUT:

microbeID – name of the resulting refined reconstruction

checkInputData(inputData, strainInformation)

Part of the DEMETER pipeline. This function checks for duplicate and removed strains in the input data files and removes them. Also adds strains in the reconstruction resource that were not yet present in the input file.

USAGE:

[checkedData, addedStrains, removedStrains, duplicateStrains] = checkInputData (inputData, strainInformation)

INPUTS:

• inputData – Table with experimental data to check

• strainInformation – Table with list on all strains to reconstruct

OUTPUTS:

• checkedData – Corrected table with experimental data to check

• addedStrains – Strains that were missing from inputData

• removedStrains – Strains that were in inputData but are not present in strainInformation

• duplicateStrains – Strains that were in inputData more than once

createInfoFileDEMETER(taxIDs, strainNames)

Creates a taxonomy table that can be used as input for DEMETER from a list of NCBI Taxonomy IDs. The taxonomy IDs can be on any taxonomical level but should be on the strain level to generate a unique model ID. If this is not the case, a list of unique and custom gene names each corresponding to each taxonomy ID can be provided to serve as strain identifiers.

USAGE:

infoFile = createInfoFileDEMETER (taxIDs, strainNames)

INPUTS:

taxIDs – Vector or cell array of numerics that represent valid NCBI Taxonomy IDs.

OPTIONAL INPUTS:

strainNames – List of custom gene names to be used a model IDs

OUTPUT:

infoFile – Table with taxonomic information, gram staining, and oxygen requirement for each strain

createRBioNetDBFromVMHDB(varargin)

This function creates an input fit for rBioNet from the VMH metabolite and reaction database and builds a new database settings file. It enables using the VMH database to modify or build reconstructions.

USAGE:

createRBioNetDBFromVMHDB (‘rBioNetDBFolder’,rBioNetDBFolder)

OPTIONAL INPUT:

rBioNetDBFolder Path where to save the created database and – database settings file. Default: current path

gapfillRefinedGenomeReactions(genomeAnnotation)

Part of the DEMETER pipelinbe. Adds reactions needed to connect pathways introduced based on comparative genomic analyses.comparative genomics.

USAGE:

gapfilledGenomeAnnotation = gapfillRefinedGenomeReactions (genomeAnnotation)

INPUT:

genomeAnnotation – Text file with genome annotations that had been retrieved through the function writeReactionsFromPubSeedSpreadsheets

OUTPUT:

gapfilledGenomeAnnotation – Text file with genome annotations that have been gap-filled to enable flux through reactions added based on genome annotations

getCurationStatus(infoFilePath, inputDataFolder, getComparativeGenomics)

This function retrieves for each organism in a reconstruction resource whether the strain was refined based on experimental data and/or comparative genomic data. For experimental data, 2 indicates that the reconstruction was refined against available experimental data for the strain, 1 indicates that published studied were available for the strain but no suitable data was found or all findings were negative, and 0 indicates that no experimental data was available. For comparative genomic data, 2 indicates that genome annotations were refined for all subsystems, 1 indicates that certain subsystems were refined, and 0 indicates that no comparative genomic refinement was performed. the file with curation status information will be saved as a file called curationStatus.txt in the inputDataFolder.

USAGE:

curationStatus = getCurationStatus (infoFilePath, inputDataFolder, getComparativeGenomics)

INPUTS:

• infoFilePath – File with information on reconstructions to refine

• inputDataFolder – Folder with experimental data and database files to

• getComparativeGenomics – Boolean indicating whether PubSEED spreadsheets with information on the reconstructed strains are available

OUTPUT:

curationStatus – Table with curation status of each model

getUnannotatedReactionsFromPubSeedSpreadsheets(infoFilePath, inputDataFolder, spreadsheetFolder)

Part of the DEMETER pipeline. Prepares input file for the refinement based on comparative genomics analyses. Gets all the reactions that were not found in the respective organism through comparative genomics to remove them from the draft reconstructions.

USAGE:

unannotatedRxns = getUnannotatedReactionsFromPubSeedSpreadsheets (infoFilePath, inputDataFolder, spreadsheetFolder)

INPUTS:

• infoFilePath – File with information on reconstructions to refine

• inputDataFolder – Folder to save propagated data to (default: folder in current path called “InputData”)

• spreadsheetFolder – Folder with comparative genomics data retrieved from PubSEED in spreadsheet format if available. For an example of the required format, see cobratoolbox/papers/2021_demeter/exampleSpreadsheets.

OUTPUT:

unannotatedRxns – Cell array of organism ID, reaction ID pairs for reactions not found through comparative genomics that are removed from the draft reconstructions

loadVMHDatabase()

This function loads the database with reactions and metabolites in Virtual Metabolic Human (https://www.vmh.life/) nomenclature.

USAGE:

database = loadVMHDatabase()

OUTPUT:

database – Structure with reaction and metabolite database

• .metabolites - Cell array, the VMH metabolite database

• .reactions - Cell array, the VMH reaction database

mapKBaseToVMHReactions(translatedRxns)

Part of the DEMETER pipeline. This functions aids in translating reactions from KBase to VMH nomenclature. Requires running the function propagateKBaseMetTranslationToRxns beforehand to translate metabolite IDs, which will then allow matching translated reactions to reactions that already exist in the VMH (Virtual Metabolic Human) database.

USAGE:

[sameReactions, similarReactions] = mapKBaseToVMHReactions (translatedRxns)

INPUTS:

translatedRxns – Table with untranslated KBase reactions but translated metabolite IDs

OUTPUTS:

• sameReactions – Table with translated KBase reactions that already exist in the VMH database with corresponding IDs

• similarReactions – Table with translated KBase reactions for which a reaction with the same formula but irreversible in VMH and reversible in KBase (or vice versa) exists

mapMediumData2AGORA(strainGrowth, inputMedia)

This function extracts experimentally determined growth of species on multiple media and converts the in silico minimal medium the strain can grow on into an input fit for DEMETER. The input data was retrieved from Tramontano et al., Nat Microbiol 2019 (PMID: 29556107).

USAGE:

mappedMedia = mapMediumData2AGORA (strainGrowth, inputMedia)

INPUTS:

• strainGrowth – Growth of strains on the different media reported by Tramontano et al.

• inputMedia – Growth media tested by Tramontano et al. converted into a computationally readable format

OUTPUT:

mappedMedia – Data from Tramontano et al. converted into a format that can be added to GrowthRequirementsTable

parseNCBItaxonomy(NCBI)

Grabs taxonomic lineage from NCBI using the NCBI ID

USAGE:

taxonomy = parseNCBItaxonomy (NCBI)

INPUT:

NCBI – NCBI ID (e.g., 511145)

OUTPUT:

taxonomy – Structure containing the taxonomic lineage

• .superkingdom - Superkingdom of the organism

• .kingdom - Kingdom of the organism

• .phylum - Phylum of the organism

• .class - Class of the organism

• .order - Order of the organism

• .family - Family of the organism

• .genus - Genus of the organism

• .species - Species of the organism

• .strain - Strain identifier parsed from the NCBI taxonomy browser page title

prepareInputData(infoFilePath, varargin)

This function propagates available experimental data that was collected for AGORA2 (https://www.biorxiv.org/content/10.1101/2020.11.09.375451v1) to newly reconstructed strains and reads information from comparative genomic data in PubSEED spreadsheet format if available. It is recommended to check the propagated data manually afterwards.

USAGE:

[adaptedInfoFilePath, inputDataFolder] = prepareInputData (infoFilePath, varargin)

INPUT:

infoFilePath – File with information on reconstructions to refine

OPTIONAL INPUTS:

• inputDataFolder – Folder to save propagated data to (default: folder in current path called “InputData”)

• spreadsheetFolder – Folder with comparative genomics data retrieved from PubSEED in spreadsheet format if available. For an example of the required format, see cobratoolbox/papers/2021_demeter/exampleSpreadsheets.

OUTPUTS:

• adaptedInfoFilePath – Path to file with taxonomic information adapted with gram staining information

• inputDataFolder – Folder to save propagated data to (default: folder in current path called “InputData”)

printRefinedModelIDs(draftFolder)

This function prints the adapted names of the draft reconstruction entered into DEMETER. The adapted names need to be present in the MicrobeID column of the file with taxonomic information exactly as written in the output draftModelIDs.

USAGE:

draftModelIDs = printRefinedModelIDs (draftFolder)

INPUT:

draftFolder – Folder with draft COBRA models generated by KBase pipeline to analyze

OUTPUT:

draftModelIDs – Names of the refined models generated by DEMETER

propagateKBaseMetTranslationToRxns(toTranslatePath)

This functions replaced already translated metabolites in reactions with KBase/Model SEED nomenclature that are not yet translated. The function creates an output fit for the ReconstructionTool interface in rBioNet that can be used to check if the reactions already exist in the VMH database.

USAGE:

[translatedRxns] = propagateKBaseMetTranslationToRxns (toTranslatePath)

INPUT:

toTranslatePath – String containing the path to xlsx, csv, or txt file with reaction IDs in KBase/ModelSEED nomenclature to translate (e.g., rxn00001)

OUTPUTS:

translatedRxns – Table with reactions with already translated metabolite IDs replaced that can serve as input for rBioNet to check if the reactions already exist in the VMH database.

readInputTableForPipeline(tablePath)

Reads tables, such as text files, that are needed as input data for DEMETER in a format fit for the pipeline. The necessary inputs depend on the version of MATLAB.

USAGE:

formattedTable = readInputTableForPipeline (tablePath)

INPUT:

tablePath – Path to file with the table to read in text or table format

OUTPUT:

formattedTable – Table in cell array format

translateKBaseToVMHMets(toTranslatePath)

This functions translates metabolites inKBase/Model SEED nomenclature that are not yet translated to VMH nomenclature based on names/InCHi keys. It is recommended the resulting translated is verified through manual inspection.

USAGE:

[translatedMets] = translateKBaseToVMHMets (toTranslatePath)

INPUT:

toTranslatePath – String containing the path to xlsx, csv, or txt file with metabolite IDs in KBase/ModelSEED nomenclature to translate (e.g., cpd00001)

OUTPUTS:

translatedMets – Table with KBase metabolite IDs that could be matched to VMH metabolite IDs

updateAGORATaxonomyFile(version)

Retrieved up to date taxonomic information for AGORA strains from NCBI and saves an updated table with the most recent taxonomic assignments.

USAGE:

infoFile = updateAGORATaxonomyFile (version)

INPUT:

version – Version of AGORA for which the information table should be updated (allowed inputs: ‘AGORA’,’AGORA2’)

OUTPUT:

infoFile – Updated table with up to date taxonomic information

writeReactionsFromPubSeedSpreadsheets(infoFilePath, inputDataFolder, spreadsheetFolder)

Prepares input file for the comparative genomics part Write reaction spreadsheets from InReactions and PubSEED spreadsheets.

USAGE:

writeReactionsFromPubSeedSpreadsheets (infoFilePath, inputDataFolder, spreadsheetFolder)

INPUTS:

• infoFilePath – File with information on reconstructions to refine

• inputDataFolder – Folder to save propagated data to (default: folder in current path called “InputData”)

• spreadsheetFolder – Folder with comparative genomics data retrieved from PubSEED in spreadsheet format if available. For an example of the required format, see cobratoolbox/papers/2021_demeter/exampleSpreadsheets.