Biodb

An R package for connecting to chemical and biological databases.

With biodb you can:

• Access entries by accession number and let biodb download them for you.
• Take advantage of the cache system, that saves the results of all sent requests for you. If you send again the same request, the cached result will be used instead of contacting the database. The cache system can be disabled.
• Download whole databases and access entries by accession number locally.
• Rely on biodb to access correctly the database, respecting the published access policy (i.e.: not sending too much requests). biodb uses a special class for scheduling requests on each database.
• Switch from one database to another easily (providing they offer the same type of information), not changing a line in your code. This is because entries are populated with values found from the database, using always the same keys.
• Search for MS spectra by peaks in Massbank, Peakforest and in-house database.
• Search for MSMS spectra.
• Export any database into a CSV file.

License

This software is licensed under the GNU Affero General Public License version 3 (AGPL-3.0).

Installation

Install from GitHub

Using package devtools you can install Biodb directly from GitHub:

devtools::install_github('pkrog/biodb')

Install from local repository

First, you need to clone the GitHub repos:

git clone -b master https://github.com/pkrog/biodb.git

Then you install biodb using the devtools package:

devtools::install_local('/your/path/to/biodb')

Examples

• Retrieving some entries from ChEBI database.
• Exporting some entries of miRBase Mature into a CSV file.
• Search for MS spectra in Massbank Japan.
• Search for MSMS spectra in Massbank Japan.
• Integrating data from different databases.
• Checking a table of database IDs.
• Seach for compounds in KEGG Compound database.
• Extract spectra from Massbank to build a custom peak table.

Access documentation

Once in R, you can get documentation about main classes with the standard help function:

?biodb::Biodb

Some of the classes you can get help about are: Biodb, BiodbFactory, BiodbConfig, BiodbCache, BiodbDbsInfo, BiodbEntryFields, BiodbObserver, BiodbConn, BiodbEntry, MassdbConn, RemotedbConn.

Some vignettes are also available. To get a list of them run:

vignette(package = 'biodb')

To open a vignette in a browser, use its name:

vignette('init', package = 'biodb')

Contributing

If you wish to contribute to the biodb package, you first need to create an account under GitHub. You can then either to ask to become a contributor or fork the project and submit a merge request.

Debugging, enhancement or creation of a database connector or an entry parser are of course most welcome.

Running tests

Under UNIX and UNIX like systems (macOS, Linux, ...) you can run make test to run the tests. You will need to have R accessible from command line, and also to have installed the R package testthat.

The plain command make test will run the offline tests, which uses cache files recorded inside this repository under tests/res/offline-cache. All databases will be tested.

If you wish to test only some databases, you can specify them inside the environment variable DATABASES:

DATABASES=massbank.jp,chebi,mirbase.mature make test

If you want to run online tests, use the environment variable MODES to specify it:

MODES=online make test

The value quick.online for MODES turns off download of whole databases if they have already been downloaded and are stored inside the cache system. The value all for MODES run tests in all modes: online, quick.online and offline.

The two environment variables can be combined together.