The GNPS2 datasetcache collects and provides general information on data sets/experiments with their related MS data files for various repositories including MassIVE and MetaboLights. The resource is updated on a regular basis. MsBackendMassIVE provides utility functions to retrieve information from this resource directly in R:
gnps2_query(): query the datasetcache for metadata of data sets with the provided (MassIVE) dataset ID(s). Returns adata.framewith one row per file entry from the filename table.gnps2_usi_download_link(): retrieve the download link for a specific USI. Returns acharacter(1)with the link.
Arguments
- id
for
gnps2_query():characterwith the ID(s) of the MassIVE data set(s).- usi_pattern
for
gnps2_query():character(1)defining a pattern to filter the USI, such asusi_pattern = ".mzML"to retrieve the USI of all files of the data set (i.e., files with extension".mzML"). This parameter is passed to thegrepl()function.- filepath_pattern
for
gnps2_query():character(1)defining a pattern to filter thefilepath, such asfilepath_pattern = "metadata"to retrieve thefilepathof all files of the data set (i.e., files with metadata info). This parameter is passed to thegrepl()function.- usi
for
gnps2_usi_download_link():character(1)with the USI of a file in GNPS2 DB.
Value
For
gnps2_query(): adata.framewith the all information in the GNPS2 datasetcache database for the data set IDs provided.For
gnps2_usi_download_link(): acharacter(1)with the downlaod link of the USI.
Details
The gnps2_query() function queries the GNPS2 Datasette API
at https://datasetcache.gnps2.org/datasette/database.csv by executing a
SQL query on the filename table filtered by dataset IDs. It returns all
matching file metadata records. This metadata is used by downstream
functions to determine the FTP paths and to download files. The
gnps2_usi_download_link() makes a GET request to the GNPS2 dashboard to get
the download link of a specific USI.
Note
The Datasette API enforces a maximum limit of 50,000 rows per query. Longer results will thus be truncated.
Examples
## Get the GNPS2 table to the data set MSV000080547
gnps2_query("MSV000080547")
#> usi
#> 1 mzspec:MSV000080547:ccms_parameters/params.xml
#> 2 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample1.mzXML
#> 3 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample10.mzXML
#> 4 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample11.mzXML
#> 5 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample12.mzXML
#> 6 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample13.mzXML
#> 7 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample14.mzXML
#> 8 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample15.mzXML
#> 9 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample16.mzXML
#> 10 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample17.mzXML
#> 11 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample18.mzXML
#> 12 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample19.mzXML
#> 13 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample2.mzXML
#> 14 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample20.mzXML
#> 15 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample3.mzXML
#> 16 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample4.mzXML
#> 17 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample5.mzXML
#> 18 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample6.mzXML
#> 19 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample7.mzXML
#> 20 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample8.mzXML
#> 21 mzspec:MSV000080547:peak/Quant_assesment_QE/AG_spiked_sample9.mzXML
#> 22 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample1.mzML
#> 23 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample10.mzML
#> 24 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample11.mzML
#> 25 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample12.mzML
#> 26 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample13.mzML
#> 27 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample14.mzML
#> 28 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample15.mzML
#> 29 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample16.mzML
#> 30 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample17.mzML
#> 31 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample18.mzML
#> 32 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample19.mzML
#> 33 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample2.mzML
#> 34 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample20.mzML
#> 35 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample3.mzML
#> 36 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample4.mzML
#> 37 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample5.mzML
#> 38 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample6.mzML
#> 39 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample7.mzML
#> 40 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample8.mzML
#> 41 mzspec:MSV000080547:peak/Quant_assesment_QQQ/AG_spiked_sample9.mzML
#> filepath dataset
#> 1 ccms_parameters/params.xml MSV000080547
#> 2 peak/Quant_assesment_QE/AG_spiked_sample1.mzXML MSV000080547
#> 3 peak/Quant_assesment_QE/AG_spiked_sample10.mzXML MSV000080547
#> 4 peak/Quant_assesment_QE/AG_spiked_sample11.mzXML MSV000080547
#> 5 peak/Quant_assesment_QE/AG_spiked_sample12.mzXML MSV000080547
#> 6 peak/Quant_assesment_QE/AG_spiked_sample13.mzXML MSV000080547
#> 7 peak/Quant_assesment_QE/AG_spiked_sample14.mzXML MSV000080547
#> 8 peak/Quant_assesment_QE/AG_spiked_sample15.mzXML MSV000080547
#> 9 peak/Quant_assesment_QE/AG_spiked_sample16.mzXML MSV000080547
#> 10 peak/Quant_assesment_QE/AG_spiked_sample17.mzXML MSV000080547
#> 11 peak/Quant_assesment_QE/AG_spiked_sample18.mzXML MSV000080547
#> 12 peak/Quant_assesment_QE/AG_spiked_sample19.mzXML MSV000080547
#> 13 peak/Quant_assesment_QE/AG_spiked_sample2.mzXML MSV000080547
#> 14 peak/Quant_assesment_QE/AG_spiked_sample20.mzXML MSV000080547
#> 15 peak/Quant_assesment_QE/AG_spiked_sample3.mzXML MSV000080547
#> 16 peak/Quant_assesment_QE/AG_spiked_sample4.mzXML MSV000080547
#> 17 peak/Quant_assesment_QE/AG_spiked_sample5.mzXML MSV000080547
#> 18 peak/Quant_assesment_QE/AG_spiked_sample6.mzXML MSV000080547
#> 19 peak/Quant_assesment_QE/AG_spiked_sample7.mzXML MSV000080547
#> 20 peak/Quant_assesment_QE/AG_spiked_sample8.mzXML MSV000080547
#> 21 peak/Quant_assesment_QE/AG_spiked_sample9.mzXML MSV000080547
#> 22 peak/Quant_assesment_QQQ/AG_spiked_sample1.mzML MSV000080547
#> 23 peak/Quant_assesment_QQQ/AG_spiked_sample10.mzML MSV000080547
#> 24 peak/Quant_assesment_QQQ/AG_spiked_sample11.mzML MSV000080547
#> 25 peak/Quant_assesment_QQQ/AG_spiked_sample12.mzML MSV000080547
#> 26 peak/Quant_assesment_QQQ/AG_spiked_sample13.mzML MSV000080547
#> 27 peak/Quant_assesment_QQQ/AG_spiked_sample14.mzML MSV000080547
#> 28 peak/Quant_assesment_QQQ/AG_spiked_sample15.mzML MSV000080547
#> 29 peak/Quant_assesment_QQQ/AG_spiked_sample16.mzML MSV000080547
#> 30 peak/Quant_assesment_QQQ/AG_spiked_sample17.mzML MSV000080547
#> 31 peak/Quant_assesment_QQQ/AG_spiked_sample18.mzML MSV000080547
#> 32 peak/Quant_assesment_QQQ/AG_spiked_sample19.mzML MSV000080547
#> 33 peak/Quant_assesment_QQQ/AG_spiked_sample2.mzML MSV000080547
#> 34 peak/Quant_assesment_QQQ/AG_spiked_sample20.mzML MSV000080547
#> 35 peak/Quant_assesment_QQQ/AG_spiked_sample3.mzML MSV000080547
#> 36 peak/Quant_assesment_QQQ/AG_spiked_sample4.mzML MSV000080547
#> 37 peak/Quant_assesment_QQQ/AG_spiked_sample5.mzML MSV000080547
#> 38 peak/Quant_assesment_QQQ/AG_spiked_sample6.mzML MSV000080547
#> 39 peak/Quant_assesment_QQQ/AG_spiked_sample7.mzML MSV000080547
#> 40 peak/Quant_assesment_QQQ/AG_spiked_sample8.mzML MSV000080547
#> 41 peak/Quant_assesment_QQQ/AG_spiked_sample9.mzML MSV000080547
#> collection is_update update_name create_time
#> 1 0 NA 2023-12-14 19:58:42.070000
#> 2 Quant_assesment_QE 0 NA 2023-12-14 19:58:44.045000
#> 3 Quant_assesment_QE 0 NA 2023-12-14 19:58:46.297000
#> 4 Quant_assesment_QE 0 NA 2023-12-14 19:58:47.947000
#> 5 Quant_assesment_QE 0 NA 2023-12-14 19:58:49.627000
#> 6 Quant_assesment_QE 0 NA 2023-12-14 19:58:51.647000
#> 7 Quant_assesment_QE 0 NA 2023-12-14 19:58:53.567000
#> 8 Quant_assesment_QE 0 NA 2023-12-14 19:58:55.129000
#> 9 Quant_assesment_QE 0 NA 2023-12-14 19:58:57.441000
#> 10 Quant_assesment_QE 0 NA 2023-12-14 19:58:59.260000
#> 11 Quant_assesment_QE 0 NA 2023-12-14 19:59:00.921000
#> 12 Quant_assesment_QE 0 NA 2023-12-14 19:59:03.107000
#> 13 Quant_assesment_QE 0 NA 2023-12-14 19:59:04.590000
#> 14 Quant_assesment_QE 0 NA 2023-12-14 19:59:06.340000
#> 15 Quant_assesment_QE 0 NA 2023-12-14 19:59:08.534000
#> 16 Quant_assesment_QE 0 NA 2023-12-14 19:59:10.439000
#> 17 Quant_assesment_QE 0 NA 2023-12-14 19:59:12.271000
#> 18 Quant_assesment_QE 0 NA 2023-12-14 19:59:14.019000
#> 19 Quant_assesment_QE 0 NA 2023-12-14 19:59:15.700000
#> 20 Quant_assesment_QE 0 NA 2023-12-14 19:59:17.352000
#> 21 Quant_assesment_QE 0 NA 2023-12-14 19:59:19.533000
#> 22 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:19.667000
#> 23 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:19.879000
#> 24 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.014000
#> 25 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.108000
#> 26 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.257000
#> 27 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.396000
#> 28 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.512000
#> 29 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.594000
#> 30 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.667000
#> 31 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.758000
#> 32 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.844000
#> 33 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:20.919000
#> 34 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.016000
#> 35 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.099000
#> 36 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.196000
#> 37 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.302000
#> 38 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.395000
#> 39 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.460000
#> 40 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.600000
#> 41 Quant_assesment_QQQ 0 NA 2023-12-14 19:59:21.668000
#> size size_mb sample_type spectra_ms1 spectra_ms2 instrument_vendor
#> 1 5801 0 MASSIVE 0 0 NA
#> 2 77825878 74 MASSIVE 0 0 NA
#> 3 83053496 79 MASSIVE 0 0 NA
#> 4 71125835 67 MASSIVE 0 0 NA
#> 5 74646509 71 MASSIVE 0 0 NA
#> 6 81068518 77 MASSIVE 0 0 NA
#> 7 73759240 70 MASSIVE 0 0 NA
#> 8 66366696 63 MASSIVE 0 0 NA
#> 9 85580871 81 MASSIVE 0 0 NA
#> 10 76035689 72 MASSIVE 0 0 NA
#> 11 74473877 71 MASSIVE 0 0 NA
#> 12 88730540 84 MASSIVE 0 0 NA
#> 13 67938213 64 MASSIVE 0 0 NA
#> 14 76273532 72 MASSIVE 0 0 NA
#> 15 100373730 95 MASSIVE 0 0 NA
#> 16 80690230 76 MASSIVE 0 0 NA
#> 17 83600234 79 MASSIVE 0 0 NA
#> 18 76815466 73 MASSIVE 0 0 NA
#> 19 70473590 67 MASSIVE 0 0 NA
#> 20 71789865 68 MASSIVE 0 0 NA
#> 21 91403666 87 MASSIVE 0 0 NA
#> 22 3371947 3 MASSIVE 0 0 NA
#> 23 3371964 3 MASSIVE 0 0 NA
#> 24 3371949 3 MASSIVE 0 0 NA
#> 25 3371959 3 MASSIVE 0 0 NA
#> 26 3371938 3 MASSIVE 0 0 NA
#> 27 3371919 3 MASSIVE 0 0 NA
#> 28 3371888 3 MASSIVE 0 0 NA
#> 29 3371972 3 MASSIVE 0 0 NA
#> 30 3370398 3 MASSIVE 0 0 NA
#> 31 3371940 3 MASSIVE 0 0 NA
#> 32 3371928 3 MASSIVE 0 0 NA
#> 33 3371910 3 MASSIVE 0 0 NA
#> 34 3370336 3 MASSIVE 0 0 NA
#> 35 3371942 3 MASSIVE 0 0 NA
#> 36 3370377 3 MASSIVE 0 0 NA
#> 37 3371943 3 MASSIVE 0 0 NA
#> 38 3371988 3 MASSIVE 0 0 NA
#> 39 3370409 3 MASSIVE 0 0 NA
#> 40 3370378 3 MASSIVE 0 0 NA
#> 41 3371940 3 MASSIVE 0 0 NA
#> instrument_model file_processed filename
#> 1 NA No params.xml
#> 2 NA No AG_spiked_sample1.mzXML
#> 3 NA No AG_spiked_sample10.mzXML
#> 4 NA No AG_spiked_sample11.mzXML
#> 5 NA No AG_spiked_sample12.mzXML
#> 6 NA No AG_spiked_sample13.mzXML
#> 7 NA No AG_spiked_sample14.mzXML
#> 8 NA No AG_spiked_sample15.mzXML
#> 9 NA No AG_spiked_sample16.mzXML
#> 10 NA No AG_spiked_sample17.mzXML
#> 11 NA No AG_spiked_sample18.mzXML
#> 12 NA No AG_spiked_sample19.mzXML
#> 13 NA No AG_spiked_sample2.mzXML
#> 14 NA No AG_spiked_sample20.mzXML
#> 15 NA No AG_spiked_sample3.mzXML
#> 16 NA No AG_spiked_sample4.mzXML
#> 17 NA No AG_spiked_sample5.mzXML
#> 18 NA No AG_spiked_sample6.mzXML
#> 19 NA No AG_spiked_sample7.mzXML
#> 20 NA No AG_spiked_sample8.mzXML
#> 21 NA No AG_spiked_sample9.mzXML
#> 22 NA No AG_spiked_sample1.mzML
#> 23 NA No AG_spiked_sample10.mzML
#> 24 NA No AG_spiked_sample11.mzML
#> 25 NA No AG_spiked_sample12.mzML
#> 26 NA No AG_spiked_sample13.mzML
#> 27 NA No AG_spiked_sample14.mzML
#> 28 NA No AG_spiked_sample15.mzML
#> 29 NA No AG_spiked_sample16.mzML
#> 30 NA No AG_spiked_sample17.mzML
#> 31 NA No AG_spiked_sample18.mzML
#> 32 NA No AG_spiked_sample19.mzML
#> 33 NA No AG_spiked_sample2.mzML
#> 34 NA No AG_spiked_sample20.mzML
#> 35 NA No AG_spiked_sample3.mzML
#> 36 NA No AG_spiked_sample4.mzML
#> 37 NA No AG_spiked_sample5.mzML
#> 38 NA No AG_spiked_sample6.mzML
#> 39 NA No AG_spiked_sample7.mzML
#> 40 NA No AG_spiked_sample8.mzML
#> 41 NA No AG_spiked_sample9.mzML
## Get link for an USI
gnps2_usi_download_link("mzspec:MTBLS39:FILES/AM063A.cdf")
#> [1] "https://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063A.cdf"