Download databases#

MATLAB functions in GECKO/src/download_databases of the GECKO toolbox.

Functions#

Function	Summary
`downloadKEGG`	Download a KEGG organism's gene data and write a CSV.
`downloadUniProt`	Download UniProt protein data for an organism and write a TSV.
`fetchBrendaAsset`	Download (once) GECKO's BRENDA files and return their folder.
`loadBRENDAdata`	Load kcat and specific activity data from BRENDA files.
`loadDatabases`	Load the organism-specific KEGG and UniProt databases.
`resolveKcatAggregation`	Settle which BRENDA aggregate to read.

Reference#

downloadKEGG#

function downloadKEGG(keggID, filePath, keggGeneID)

Download a KEGG organism's gene data and write a CSV.

Downloads gene information for every gene of a KEGG organism code, and writes the result to a CSV file. Used by loadDatabases when its expected kegg.tsv is missing; can also be called directly to refresh one organism's KEGG snapshot without re-running loadDatabases for everything else.

Parameters

keggID : char: KEGG organism code, e.g. 'sce' for Saccharomyces cerevisiae.
filePath : char: destination CSV path (overwritten if it exists).
keggGeneID : char: which KEGG gene identifier field becomes the output's gene-name column. 'kegg' (or empty, the default) uses the bare KEGG gene id; any other value is looked up as a cross-reference identifier on each KEGG entry (e.g. 'UniProt').

Examples

downloadKEGG('sce', 'kegg.tsv', 'UniProt');

See also

loadDatabases, downloadUniProt

downloadUniProt#

function downloadUniProt(uniprotID, filePath, geneIDfield, type, reviewed)

Download UniProt protein data for an organism and write a TSV.

Downloads accession, gene name, EC number, mass and sequence for every protein matching the given organism identifier, and writes the result to a TSV file. Used by loadDatabases when its expected uniprot.tsv is missing; can also be called directly to refresh one organism's UniProt snapshot without re-running loadDatabases for everything else.

Parameters

uniprotID : char: UniProt-side identifier whose meaning depends on type, e.g. an NCBI taxonomy ID such as 559292 for Saccharomyces cerevisiae S288C.
filePath : char: destination TSV path (overwritten if it exists).
geneIDfield : char: UniProt field that becomes the second column (the gene matching key) (optional, default 'gene_oln', Ordered Locus Names, which works for most prokaryotes and budding yeast).
type : char: UniProt query field for uniprotID (optional, default 'taxonomy_id'). 'taxonomy' is accepted as an alias.
reviewed : logical: whether to restrict the query to reviewed (Swiss-Prot) entries (optional, default true).

Examples

downloadUniProt(559292, 'uniprot.tsv');
downloadUniProt(559292, 'uniprot.tsv', 'gene_oln', 'taxonomy_id', true);

See also

loadDatabases, downloadKEGG

fetchBrendaAsset#

function folder = fetchBrendaAsset(files)

Download (once) GECKO's BRENDA files and return their folder.

GECKO does not ship BRENDA data. The files of the toolbox-assets release brenda-2026.1-1 (BRENDA 2026.1, CC BY 4.0) are downloaded on first use with RAVEN's fetchToolboxAsset, which checks them against the checksums of the toolbox-assets manifest, and are unpacked into databases/brenda-2026.1-1 in the GECKO folder. geckopy reads the same release (fetch_brenda_asset). A project can use its own BRENDA files instead, in data/brenda (see ModelAdapter.getBrendaDBFolder).

Parameters

files : cell: file names (default: kcat.tsv, sa.tsv, mw.tsv and measurements.tsv); the release also has sequences.fasta, substrates.tsv and kcatCombineParams.tsv.

Returns

folder : char: the folder with the files, unpacked.

Examples

folder = fetchBrendaAsset();
folder = fetchBrendaAsset({'kcatCombineParams.tsv'});

See also

loadBRENDAdata, loadBrendaMeasurements, ModelAdapter

loadBRENDAdata#

function [KCATcell, SAcell] = loadBRENDAdata(varargin)

Load kcat and specific activity data from BRENDA files.

Reads the BRENDA data files (kcat.tsv, sa.tsv and mw.tsv) from the BRENDA database folder defined by the model adapter, and returns the kcat values and specific activities (the latter converted to kcat values using the molecular weights).

kcat.tsv and sa.tsv each carry both a max and a median aggregate per (EC, substrate, organism) triple; kcatAggregation selects which of the two is read. Each file starts with a #-prefixed release-version line followed by a tab-delimited column header, both skipped on read.

Name-Value Arguments

modelAdapter : ModelAdapter: a loaded model adapter (default: the current default model adapter).
kcatAggregation : char: which aggregate to read from kcat.tsv and sa.tsv, 'max' or 'median' (default: params.kcatAggregation from the model adapter, or 'max' if the adapter does not set it). A triple's max is the highest turnover reported for it; its median is the middle one.

Returns

KCATcell : cell: kcat data extracted from BRENDA.
SAcell : cell: specific activity data extracted from BRENDA.

Examples

% optional arguments may be given positionally or as name-value pairs:
[KCATcell, SAcell] = loadBRENDAdata();
[KCATcell, SAcell] = loadBRENDAdata('modelAdapter', adapter);
[KCATcell, SAcell] = loadBRENDAdata('kcatAggregation', 'median');

See also

loadDatabases, getECfromDatabase

loadDatabases#

function databases = loadDatabases(varargin)

Load the organism-specific KEGG and UniProt databases.

Loads (and downloads if necessary) the organism-specific KEGG and UniProt databases that are required to extract protein information. The uniprot.ID and kegg.ID are taken from the ModelAdapter.

Name-Value Arguments

selectDatabase : char: which databases should be loaded, either 'uniprot', 'kegg' or 'both' (default 'both').
modelAdapter : ModelAdapter: a loaded model adapter (default: the current default model adapter; send in [] for default).

Returns

databases : struct: contains .uniprot and .kegg structures, dependent on which databases were selected.

Examples

% optional arguments may be given positionally or as name-value pairs:
databases = loadDatabases('both', adapter);
databases = loadDatabases('selectDatabase', 'both');

See also

getECfromDatabase, loadBRENDAdata, downloadKEGG, downloadUniProt

resolveKcatAggregation#

function kcatAggregation = resolveKcatAggregation(kcatAggregation, modelAdapter)

Settle which BRENDA aggregate to read.

The BRENDA snapshot records both a maximum and a median per (EC, substrate, organism) triple. Which one a run uses can be given per call, or once on the model adapter as params.kcatAggregation; an adapter that sets neither gets 'max', which is what GECKO has always used.

Input Arguments

kcatAggregation : char the per-call choice, or empty to fall back to the adapter. modelAdapter : ModelAdapter a loaded model adapter.

Returns

kcatAggregation : char: 'max' or 'median'.

See also

loadBRENDAdata, fuzzyKcatMatching