Add MsBackendMetaboLights to the list of backends

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.15.10
+Version: 1.15.11
 Description: The Spectra package defines an efficient infrastructure
    for storing and handling mass spectrometry spectra and functionality to
    subset, process, visualize and compare spectra data. It provides different

NEWS.md

@@ -1,5 +1,9 @@
 # Spectra 1.15
 
+## Changes in 1.15.11
+
+- Add reference to `MsBackendMetaboLights`.
+
 ## Changes in 1.15.10
 
 - Add new `extractSpectra()` generic and implementation for `MsBackend`. Fixes

README.md

@@ -19,58 +19,81 @@ footprint.
 A (possibly incomplete) list of available backends (along with a link to the R
 package providing it) is shown below:
 
-- `MsBackendMemory` (package: *Spectra*): *default* backend which keeps all data
-  in memory. Optimized for fast processing.
+- `MsBackendCompDb` (package
+  [*CompoundDb*](https://github.com/rformassspectrometry/CompoundDb): provides
+  access to spectra data (spectra and peaks variables) from a *CompDb*
+  database. Has a small memory footprint because all data (except precursor m/z
+  values) are retrieved on-the-fly from the database.
+
 - `MsBackendDataFrame` (package: *Spectra*): alternative to the
   `MsBackendMemory` also keeping all data in memory, but supporting `S4` objects
   as spectra variables because the data is stored internally in a `DataFrame`.
-- `MsBackendMzR` (package: *Spectra*): by using the `mzR` package it supports
-  import of MS data from mzML, mzXML and CDF files. This backend keeps only
-  general spectra variables in memory and retrieves the peaks data (m/z and
-  intensity values) on-the-fly from the original data files. The backend has
-  thus a smaller memory footprint compared to in-memory backends.
+
 - `MsBackendHdf5Peaks` (package: *Spectra*): on-disk backend similar to
   `MsBackendMzR`, but the peaks data is stored in HDF5 files (general spectra
   variables are kept in memory).
-- `MsBackendMgf` (package
-  [*MsBackendMgf*](https://github.com/rformassspectrometry/MsBackendMgf): allows
-  to import/export data in mascot generic format (MGF). Extends the
-  `MsBackendDataFrame` and keeps thus all data, after import, in memory.
-- `MsBackendMsp` (package
-  [*MsbackendMsp*](https://github.com/rformassspectrometry/MsBackendMsp): allows
-  to import/export data in NIST MSP format. Extends the `MsBackendDataFrame` and
-  keeps thus all data, after import, in memory.
+
+- `MsBackendHmdbXml` (package
+  [*MsbackendHmdb*](https://github.com/rformassspectrometry/MsBackendHmdb)):
+  allows import of MS data from xml files of the Human Metabolome Database
+  (HMDB). Extends the `MsBackendDataFrame` and keeps thus all data, after
+  import, in memory.
+
 - `MsBackendMassbank` (package
   [*MsBackendMassbank*](https://github.com/rformassspectrometry/MsBackendMassbank)):
   allows to import/export data in MassBank text file format. Extends the
   `MsBackendDataFrame` and keeps thus all data, after import, in memory.
+
 - `MsBackendMassbankSql` (package
   [*MsBackendMassbank*](https://github.com/rformassspectrometry/MsBackendMassbank)):
   allows to directly connect to a MassBank SQL database to retrieve all MS data
   and variables. Has a minimal memory footprint because all data is retrieved
   on-the-fly from the SQL database.
+
+- `MsBackendMemory` (package: *Spectra*): *default* backend which keeps all data
+  in memory. Optimized for fast processing.
+
+- `MsBackendMetaboLights` (package
+  [*MsBackendMetaboLights*](https://github.com/rformassspectrometry/MsBackendMetaboLights)):
+  retrieves and caches MS data files from MetaboLights.
+
+- `MsBackendMgf` (package
+  [*MsBackendMgf*](https://github.com/rformassspectrometry/MsBackendMgf)): allows
+  to import/export data in mascot generic format (MGF). Extends the
+  `MsBackendDataFrame` and keeps thus all data, after import, in memory.
+
+- `MsBackendMsp` (package
+  [*MsbackendMsp*](https://github.com/rformassspectrometry/MsBackendMsp)): allows
+  to import/export data in NIST MSP format. Extends the `MsBackendDataFrame` and
+  keeps thus all data, after import, in memory.
+
+- `MsBackendMzR` (package: *Spectra*): by using the `mzR` package it supports
+  import of MS data from mzML, mzXML and CDF files. This backend keeps only
+  general spectra variables in memory and retrieves the peaks data (m/z and
+  intensity values) on-the-fly from the original data files. The backend has
+  thus a smaller memory footprint compared to in-memory backends.
+
+- `MsBackendOfflineSql` (package
+  [*MsBackendSql*](https://github.com/rformassspectrometry/MsBackendSql)):
+  stores all MS data in a SQL database and has thus a minimal memory footprint.
+  Does, in contrast to `MsBackendSql`, not keep an active SQL database
+  connection and can thus support parallel processing.
+
 - `MsBackendRawFileReader` (package
   [*MsBackendRawFileReader*](https://github.com/fgcz/MsBackendRawFileReader)):
   implements a backend for reading MS data from Thermo Fisher Scientific's raw
   data files using the manufacturer's NewRawFileReader .Net libraries. The
   package generalizes the functionality introduced by the `rawrr` package.
-- `MsBackendHmdbXml` (package
-  [*MsbackendHmdb*](https://github.com/rformassspectrometry/MsBackendHmdb)):
-  allows import of MS data from xml files of the Human Metabolome Database
-  (HMDB). Extends the `MsBackendDataFrame` and keeps thus all data, after
-  import, in memory.
+
 - `MsBackendSql` (package
   [*MsBackendSql*](https://github.com/rformassspectrometry/MsBackendSql)):
   stores all MS data in a SQL database and has thus a minimal memory footprint.
-- `MsBackendCompDb` (package
-  [*CompoundDb*](https://github.com/rformassspectrometry/CompoundDb): provides
-  access to spectra data (spectra and peaks variables) from a *CompDb*
-  database. Has a small memory footprint because all data (except precursor m/z
-  values) are retrieved on-the-fly from the database.
+
 - `MsBackendTimsTof` (package
   [*MsBackendTimsTof*](https://github.com/rformassspectrometry/MsBackendTimsTof):
   allows import of data from Bruker TimsTOF raw data files (using the
   `opentimsr` R package).
+
 - `MsBackendWeizMass` (package
   [*MsBackendWeizMass*](https://github.com/rformassspectrometry/MsBackendWeizMass):
   allows to access MS data from WeizMass MS/MS spectral databases.

vignettes/Spectra.Rmd

@@ -1244,38 +1244,51 @@ head(basename(dataStorage(sps_tmt)))
 A (possibly incomplete) list of R packages providing additional backends that
 add support for additional data types or storage options is provided below:
 
-- `r BiocStyle::Biocpkg("MsBackendMgf")`: support for import/export of mass
-  spectrometry files in mascot generic format (MGF).
-- `r BiocStyle::Biocpkg("MsBackendMsp")`: allows to import/export data in NIST
-  MSP format. Extends the `MsBackendDataFrame` and keeps thus all data, after
-  import, in memory.
-- `MsBackendMassbank` (package `r BiocStyle::Biocpkg("MsBackendMassbank")`):
-  allows to import/export data in MassBank text file format. Extends the
-  `MsBackendDataFrame` and keeps thus all data, after import, in memory.
-- `MsBackendMassbankSql` (package `r BiocStyle::Biocpkg("MsBackendMassbank")`):
-  allows to directly connect to a MassBank SQL database to retrieve all MS data
-  and variables. Has a minimal memory footprint because all data is retrieved
-  on-the-fly from the SQL database.
-- `r BiocStyle::Biocpkg("MsBackendSql")`: stores all MS data in a SQL database
-  and has thus a minimal memory footprint.
 - `MsBackendCompDb` (package `r BiocStyle::Biocpkg("CompoundDb")`): provides
   access to spectra data (spectra and peaks variables) from a *CompDb*
   database. Has a small memory footprint because all data (except precursor m/z
   values) are retrieved on-the-fly from the database.
-- `r Biocpkg("MsBackendRawFileReader")`: implements a backend for reading MS
-  data from Thermo Fisher Scientific's raw data files using the manufacturer's
-  NewRawFileReader .Net libraries. The package generalizes the functionality
-  introduced by the `r Biocpkg("rawrr")` package, see also
-  [@kockmann_rawrr_2021].
+
 - `MsBackendHmdbXml` (package
   [`MsbackendHmdb`](https://github.com/rformassspectrometry/MsBackendHmdb)):
   allows import of MS data from xml files of the Human Metabolome Database
   (HMDB). Extends the `MsBackendDataFrame` and keeps thus all data, after
   import, in memory.
+
+- `MsBackendMassbank` (package `r BiocStyle::Biocpkg("MsBackendMassbank")`):
+  allows to import/export data in MassBank text file format. Extends the
+  `MsBackendDataFrame` and keeps thus all data, after import, in memory.
+
+- `MsBackendMassbankSql` (package `r BiocStyle::Biocpkg("MsBackendMassbank")`):
+  allows to directly connect to a MassBank SQL database to retrieve all MS data
+  and variables. Has a minimal memory footprint because all data is retrieved
+  on-the-fly from the SQL database.
+
+- `MsBackendMetaboLights` (package `r
+  BiocStyle::Biocpkg("MsBackendMetaboLights")`): retrieves and caches MS data
+  files from the MetaboLights repository.
+
+- `MsBackendMgf`: (package `r BiocStyle::Biocpkg("MsBackendMgf")`): support for
+  import/export of mass spectrometry files in mascot generic format (MGF).
+
+- `MsBackendMsp`: (package `r BiocStyle::Biocpkg("MsBackendMsp")`): allows to
+  import/export data in NIST MSP format. Extends the `MsBackendDataFrame` and
+  keeps thus all data, after import, in memory.
+
+- `MsBackendRawFileReader` (package `r Biocpkg("MsBackendRawFileReader")`):
+  implements a backend for reading MS data from Thermo Fisher Scientific's raw
+  data files using the manufacturer's NewRawFileReader .Net libraries. The
+  package generalizes the functionality introduced by the `r Biocpkg("rawrr")`
+  package, see also [@kockmann_rawrr_2021].
+
+- `MsBackendSql` (package `r BiocStyle::Biocpkg("MsBackendSql")`): stores all MS
+  data in a SQL database and has thus a minimal memory footprint.
+
 - `MsBackendTimsTof` (package
   [`MsBackendTimsTof`](https://github.com/rformassspectrometry/MsBackendTimsTof):
   allows import of data from Bruker TimsTOF raw data files (using the
   `opentimsr` R package).
+
 - `MsBackendWeizMass` (package
   [`MsBackendWeizMass`](https://github.com/rformassspectrometry/MsBackendWeizMass):
   allows to access MS data from WeizMass MS/MS spectral databases.