Utility functions for the MetaboLights repository
Source:R/MsBackendMetaboLights.R
MetaboLights-utils.RdMetaboLights is one of the main public repositories for deposition of metabolomics experiments including (raw) mass spectrometry (MS) and NMR data files and experimental/analysis results. The experimental metadata and results are stored as plain text files in ISA-tab format. Each MetaboLights experiment must provide a file describing the samples analyzed and at least one assay file that links between the experimental samples and the (raw and processed) data files with quantification of metabolites/features in these samples.
Each experiment in MetaboLights is identified with its unique identifier, starting with MTBLS followed by a number. The data (metadata files and MS/NMR data files) of an experiment are available through the repository's ftp server.
The functions listed here allow to query and retrieve information of a data set/experiment from MetaboLights.
mtbls_ftp_path: returns the FTP path for a provided MetaboLights ID. WithmustWork = TRUE(the default) the function throws an error if the path is not accessible (either because the data set does not exist or no internet connection is available). The function returns acharacter(1)with the FTP path to the data set folder.mtbls_list_files: returns the available files (and directories) for the specified MetaboLights data set (i.e., the FTP directory content of the data set). The function returns acharactervector with the relative file names to the absolute FTP path (mtbls_ftp_path()) of the data set. Parameterpatternallows to filter the file names and define which file names should be returned.
Arguments
- x
character(1)with the ID of the MetaboLights data set (usually starting with a MTBLS followed by a number).- mustWork
for
mtbls_ftp_path():logical(1)whether the validity of the path should be verified or not. By default (withmustWork = TRUE) the function throws an error if either the data set does not exist or if the folder can not be accessed (e.g. if no internet connection is available).- pattern
for
mtbls_list_files():character(1)defining a pattern to filter the file names, such aspattern = "^a_"to retrieve the file names of all assay files of the data set (i.e., files with a name starting with"a_"). This parameter is passed to thegrepl()function.
Value
For
mtbls_ftp_path():character(1)with the ftp path to the specified data set on the MetaboLights ftp server.For
mtbls_list_files():characterwith the names of the files in the data set's base ftp directory.
Examples
## Get the FTP path to the data set MTBLS2
mtbls_ftp_path("MTBLS2")
#> [1] "ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS2/"
## Retrieve available files (and directories) for the data set MTBLS2
mtbls_list_files("MTBLS2")
#> [1] "FILES"
#> [2] "a_MTBLS2_metabolite_profiling_mass_spectrometry.txt"
#> [3] "files-all.json"
#> [4] "i_Investigation.txt"
#> [5] "m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
#> [6] "s_MTBLS2.txt"
## Retrieve the available assay files (file names starting with "a_").
afiles <- mtbls_list_files("MTBLS2", pattern = "^a_")
afiles
#> [1] "a_MTBLS2_metabolite_profiling_mass_spectrometry.txt"
## Read the content of one file
a <- read.table(paste0(mtbls_ftp_path("MTBLS2"), afiles[1L]),
header = TRUE, sep = "\t", check.names = FALSE)
head(a)
#> Sample Name Protocol REF Parameter Value[Post Extraction]
#> 1 Ex1-Col0-48h-Ag-1 Extraction 200 µL methanol:water (30:70, v/v)
#> 2 Ex1-Col0-48h-Ag-2 Extraction 200 µL methanol:water (30:70, v/v)
#> 3 Ex1-Col0-48h-Ag-3 Extraction 200 µL methanol:water (30:70, v/v)
#> 4 Ex1-Col0-48h-Ag-4 Extraction 200 µL methanol:water (30:70, v/v)
#> 5 Ex1-cyp79-48h-Ag-1 Extraction 200 µL methanol:water (30:70, v/v)
#> 6 Ex1-cyp79-48h-Ag-2 Extraction 200 µL methanol:water (30:70, v/v)
#> Parameter Value[Derivatization] Extract Name Protocol REF
#> 1 NA Ex1-Col0-48h-Ag-1 Chromatography
#> 2 NA Ex1-Col0-48h-Ag-2 Chromatography
#> 3 NA Ex1-Col0-48h-Ag-3 Chromatography
#> 4 NA Ex1-Col0-48h-Ag-4 Chromatography
#> 5 NA Ex1-cyp79-48h-Ag-1 Chromatography
#> 6 NA Ex1-cyp79-48h-Ag-2 Chromatography
#> Parameter Value[Chromatography Instrument] Term Source REF
#> 1 Waters ACQUITY UPLC system MTBLS
#> 2 Waters ACQUITY UPLC system MTBLS
#> 3 Waters ACQUITY UPLC system MTBLS
#> 4 Waters ACQUITY UPLC system MTBLS
#> 5 Waters ACQUITY UPLC system MTBLS
#> 6 Waters ACQUITY UPLC system MTBLS
#> Term Accession Number
#> 1 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000877
#> 2 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000877
#> 3 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000877
#> 4 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000877
#> 5 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000877
#> 6 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000877
#> Parameter Value[Autosampler model]
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 NA
#> 6 NA
#> Parameter Value[Column model]
#> 1 ACQUITY UPLC HSS T3 (1.8 µm, 1 mm x 100 mm; Waters)
#> 2 ACQUITY UPLC HSS T3 (1.8 µm, 1 mm x 100 mm; Waters)
#> 3 ACQUITY UPLC HSS T3 (1.8 µm, 1 mm x 100 mm; Waters)
#> 4 ACQUITY UPLC HSS T3 (1.8 µm, 1 mm x 100 mm; Waters)
#> 5 ACQUITY UPLC HSS T3 (1.8 µm, 1 mm x 100 mm; Waters)
#> 6 ACQUITY UPLC HSS T3 (1.8 µm, 1 mm x 100 mm; Waters)
#> Parameter Value[Column type] Parameter Value[Guard column]
#> 1 reverse phase NA
#> 2 reverse phase NA
#> 3 reverse phase NA
#> 4 reverse phase NA
#> 5 reverse phase NA
#> 6 reverse phase NA
#> Labeled Extract Name Label Term Source REF Term Accession Number
#> 1 NA NA NA NA
#> 2 NA NA NA NA
#> 3 NA NA NA NA
#> 4 NA NA NA NA
#> 5 NA NA NA NA
#> 6 NA NA NA NA
#> Protocol REF Parameter Value[Scan polarity]
#> 1 Mass spectrometry positive
#> 2 Mass spectrometry positive
#> 3 Mass spectrometry positive
#> 4 Mass spectrometry positive
#> 5 Mass spectrometry positive
#> 6 Mass spectrometry positive
#> Parameter Value[Scan m/z range] Parameter Value[Instrument] Term Source REF
#> 1 100-1000 Bruker micrOTOF-Q II MTBLS
#> 2 100-1000 Bruker micrOTOF-Q II MTBLS
#> 3 100-1000 Bruker micrOTOF-Q II MTBLS
#> 4 100-1000 Bruker micrOTOF-Q II MTBLS
#> 5 100-1000 Bruker micrOTOF-Q II MTBLS
#> 6 100-1000 Bruker micrOTOF-Q II MTBLS
#> Term Accession Number
#> 1 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000633
#> 2 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000633
#> 3 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000633
#> 4 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000633
#> 5 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000633
#> 6 http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000633
#> Parameter Value[Ion source] Term Source REF
#> 1 electrospray ionization MS
#> 2 electrospray ionization MS
#> 3 electrospray ionization MS
#> 4 electrospray ionization MS
#> 5 electrospray ionization MS
#> 6 electrospray ionization MS
#> Term Accession Number Parameter Value[Mass analyzer]
#> 1 http://purl.obolibrary.org/obo/MS_1000073 quadrupole time-of-flight
#> 2 http://purl.obolibrary.org/obo/MS_1000073 quadrupole time-of-flight
#> 3 http://purl.obolibrary.org/obo/MS_1000073 quadrupole time-of-flight
#> 4 http://purl.obolibrary.org/obo/MS_1000073 quadrupole time-of-flight
#> 5 http://purl.obolibrary.org/obo/MS_1000073 quadrupole time-of-flight
#> 6 http://purl.obolibrary.org/obo/MS_1000073 quadrupole time-of-flight
#> Term Source REF Term Accession Number
#> 1 MTBLS http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000699
#> 2 MTBLS http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000699
#> 3 MTBLS http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000699
#> 4 MTBLS http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000699
#> 5 MTBLS http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000699
#> 6 MTBLS http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000699
#> MS Assay Name
#> 1 Ex1-Col0-48h-Ag-1_1-A,1_01_9818
#> 2 Ex1-Col0-48h-Ag-2_1-A,1_01_9820
#> 3 Ex1-Col0-48h-Ag-3_1-A,1_01_9822
#> 4 Ex1-Col0-48h-Ag-4_1-A,1_01_9824
#> 5 Ex1-cyp79-48h-Ag-1_1-B,1_01_9819
#> 6 Ex1-cyp79-48h-Ag-2_1-B,2_01_9821
#> Raw Spectral Data File Protocol REF
#> 1 FILES/MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818.d Data transformation
#> 2 FILES/MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820.d Data transformation
#> 3 FILES/MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822.d Data transformation
#> 4 FILES/MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824.d Data transformation
#> 5 FILES/MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819.d Data transformation
#> 6 FILES/MSpos-Ex1-cyp79-48h-Ag-2_1-B,2_01_9821.d Data transformation
#> Normalization Name
#> 1 Ex1-Col0-48h-Ag-1_1-A,1_01_9818
#> 2 Ex1-Col0-48h-Ag-2_1-A,1_01_9820
#> 3 Ex1-Col0-48h-Ag-3_1-A,1_01_9822
#> 4 Ex1-Col0-48h-Ag-4_1-A,1_01_9824
#> 5 Ex1-cyp79-48h-Ag-1_1-B,1_01_9819
#> 6 Ex1-cyp79-48h-Ag-2_1-B,2_01_9821
#> Derived Spectral Data File
#> 1 FILES/mzML/MSpos-Ex1-Col0-48h-Ag-1_1-A__1_01_9818.mzML
#> 2 FILES/mzML/MSpos-Ex1-Col0-48h-Ag-2_1-A__1_01_9820.mzML
#> 3 FILES/mzML/MSpos-Ex1-Col0-48h-Ag-3_1-A__1_01_9822.mzML
#> 4 FILES/mzML/MSpos-Ex1-Col0-48h-Ag-4_1-A__1_01_9824.mzML
#> 5 FILES/mzML/MSpos-Ex1-cyp79-48h-Ag-1_1-B__1_01_9819.mzML
#> 6 FILES/mzML/MSpos-Ex1-cyp79-48h-Ag-2_1-B__2_01_9821.mzML
#> Derived Spectral Data File
#> 1 FILES/mzData/MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818.mzData
#> 2 FILES/mzData/MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820.mzData
#> 3 FILES/mzData/MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822.mzData
#> 4 FILES/mzData/MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824.mzData
#> 5 FILES/mzData/MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819.mzData
#> 6 FILES/mzData/MSpos-Ex1-cyp79-48h-Ag-2_1-B,2_01_9821.mzData
#> Protocol REF Data Transformation Name
#> 1 Metabolite identification Ex1-Col0-48h-Ag-1_1-A,1_01_9818
#> 2 Metabolite identification Ex1-Col0-48h-Ag-2_1-A,1_01_9820
#> 3 Metabolite identification Ex1-Col0-48h-Ag-3_1-A,1_01_9822
#> 4 Metabolite identification Ex1-Col0-48h-Ag-4_1-A,1_01_9824
#> 5 Metabolite identification Ex1-cyp79-48h-Ag-1_1-B,1_01_9819
#> 6 Metabolite identification Ex1-cyp79-48h-Ag-2_1-B,2_01_9821
#> Metabolite Assignment File
#> 1 m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv
#> 2 m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv
#> 3 m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv
#> 4 m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv
#> 5 m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv
#> 6 m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv
#> Factor Value[genotype] Term Source REF Term Accession Number
#> 1 Col-0 NA NA
#> 2 Col-0 NA NA
#> 3 Col-0 NA NA
#> 4 Col-0 NA NA
#> 5 cyp79 NA NA
#> 6 cyp79 NA NA
#> Factor Value[replicate] Term Source REF Term Accession Number
#> 1 Exp1 NA NA
#> 2 Exp1 NA NA
#> 3 Exp1 NA NA
#> 4 Exp1 NA NA
#> 5 Exp1 NA NA
#> 6 Exp1 NA NA