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Add comparison between SQL databases to the vignette
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jorainer committed Nov 13, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: MsBackendSql
Title: SQL-based Mass Spectrometry Data Backend
Version: 1.3.0
Version: 1.3.1
Authors@R:
c(person(given = "Johannes", family = "Rainer",
email = "Johannes.Rainer@eurac.edu",
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7 changes: 7 additions & 0 deletions NEWS.md
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# MsBackendSql 1.3

## Changes in 1.3.1

- Add description on the use/advantages of different SQL database systems to the
vignette.

# MsBackendSql 1.1

## Changes in 1.1.5
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23 changes: 23 additions & 0 deletions vignettes/MsBackendSql.Rmd
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Expand Up @@ -363,6 +363,29 @@ The `MsBackendSql` outperforms the `MsBackendMzR` while, not unexpectedly, the
`MsBackendMemory` provides fasted access.


## Considerations for database systems/servers

The backends from the *MsBackendSql* package use standard SQL calls to retrieve
MS data from the database and hence any SQL database system (for which an R
package is available) is supported. SQLite-based databases would represent the
easiest and most user friendly solution since no database server administration
and user management is required. Indeed, performance of SQLite is very high,
even for very large data sets. Server-based databases on the other hand have the
advantage to enable a centralized storage and control of MS data (inclusive user
management etc). Also, such server systems would also allow data set or
server-specific configurations to improve performance.

A comparison between a SQLite-based with a MariaDB-based *MsBackendSql* database
for a large data set comprising over 8,000 samples and over 15,000,000 spectra
is available
[here](https://github.com/rformassspectrometry/MsBackendSql/issues/15). In
brief, performance to extract data was comparable and for individual spectra
variables even faster for the SQLite database. Only when more complex SQL
queries were involved (combining several primary keys or data fields) the more
advanced MariaDB database outperformed SQLite.



# Other properties of the `MsBackendSql`

The `MsBackendSql` backend does not support parallel processing since the
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