Package: biodb 1.21.0

Pierrick Roger

biodb: Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Authors:Pierrick Roger [aut, cre], Alexis Delabrière [ctb]

biodb_1.21.0.tar.gz
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biodb_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
biodb/json (API)

# Install 'biodb' in R:
install.packages('biodb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://gitlab.com/rbiodb/biodb

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:biodb-1.21.0(bioc 3.24)biodb-1.20.0(bioc 3.23)

softwareinfrastructuredataimportkeggcpp

5.75 score 1 packages 31 scripts 56 exports 58 dependencies

Last updated from:cd5fba650d. Checks:4 WARNING, 10 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING208
linux-devel-arm64OK237
linux-devel-x86_64OK309
source / vignettesOK277
linux-release-arm64OK240
linux-release-x86_64OK269
macos-release-arm64OK190
macos-release-x86_64OK334
macos-oldrel-arm64OK153
macos-oldrel-x86_64OK445
windows-develWARNING347
windows-releaseWARNING195
windows-oldrelWARNING260
wasm-releaseOK176

Exports:abstractClassBiodbConfigBiodbConnBiodbConnBaseBiodbCsvEntryBiodbDbInfoBiodbDbsInfoBiodbEntryBiodbEntryFieldBiodbEntryFieldsBiodbFactoryBiodbHtmlEntryBiodbJsonEntryBiodbListEntryBiodbMainBiodbSdfEntryBiodbTxtEntryBiodbXmlEntrycheckDeprecatedCacheFoldersCompCsvFileConnCompCsvFileEntryCompSqliteConnCompSqliteEntrycreateBiodbTestInstanceCsvFileConndf2strerrorerror0getConnClassNamegetConnTypesgetDefaultCacheDirgetEntryClassNamegetEntryTypesgetLoggerlistTestRefEntrieslogDebuglogDebug0logInfologInfo0logTracelogTrace0lst2strMassCsvFileConnMassCsvFileEntryMassSqliteConnMassSqliteEntrynewInstProgressRangerunGenericTestsSqliteConntestContextTestRefEntriestestThatwarnwarn0

Dependencies:askpassbitbit64bitopsblobbriocachemcallrchkclicpp11crayonDBIdescdiffobjevaluatefastmapfsfscachegluehmsjsonlitelgrlifecyclemagrittrmemoiseopensslotelpkgbuildpkgconfigpkgloadplyrpraiseprettyunitsprocessxprogresspsR.methodsS3R.ooR.utilsR6rappdirsRcppRCurlrlangrprojrootRSQLiteschedsqlqstringistringrsystestthatvctrswaldowithrXMLyaml

Details on biodb
Introduction | Object oriented programming (OOP) model | Initialization & termination | Management classes | Configuration | Databases information | Accessing a custom CSV file with a biodb connector | Request scheduler | Entry fields information | Persistent cache system | Logging messages | Closing biodb instance | Session information | References
Rendered fromdetails.Rmdusingknitr::rmarkdown

Last update: 2025-09-29
Started: 2020-11-28

An introduction to biodb
Introduction | Installation | Initialization | Connecting to a database | Accessing entries | Getting entries | Getting all fields defined inside an entry | Getting field values from an entry | Exporting entries into a data frame | Searching for entries | Mass spectra | Mass spectra annotation with a compound database | Mass spectra annotation with a mass spectra database | MS/MS matching | Sources of documentation | Closing biodb instance | Session information | References
Rendered frombiodb.Rmdusingknitr::rmarkdown

Last update: 2025-09-29
Started: 2021-05-06

Manipulating entry objects
Introduction | Getting entries | Entry fields | Conversion | Memory usage | Copy | Merging databases | Merging the entries | Use a writable database | Closing biodb instance | Session information | References
Rendered fromentries.Rmdusingknitr::rmarkdown

Last update: 2025-09-29
Started: 2020-11-28

Readme and manuals

Help Manual

Help pageTopics
biodb: Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databasesbiodb-package biodb
Declares a class as abstract.abstractClass
Declares a method as abstractabstractMethod
A class for storing configuration values.BiodbConfig
The mother abstract class of all database connectors.BiodbConn
Base class of 'BiodbConn' for encapsulating all needed information for database access.BiodbConnBase
Entry class for content in CSV format.BiodbCsvEntry
A class for describing the characteristics of a database.BiodbDbInfo
A class for describing the available databases.BiodbDbsInfo
The mother abstract class of all database entry classes.BiodbEntry
A class for describing an entry field.BiodbEntryField
A class for handling description of all entry fields.BiodbEntryFields
A class for constructing biodb objects.BiodbFactory
Entry class for content in HTML format.BiodbHtmlEntry
Entry class for content in JSON format.BiodbJsonEntry
Entry class for content in list format.BiodbListEntry
The central class of the biodb package.BiodbMain
Entry class for content in SDF format.BiodbSdfEntry
A class for acknowledging messages during tests.BiodbTestMsgAck
Entry class for content in text format.BiodbTxtEntry
Entry class for content in XML format.BiodbXmlEntry
Check deprecated default cache folders.checkDeprecatedCacheFolders
Close match PPMcloseMatchPpm
Compound CSV File connector class.CompCsvFileConn
Compound CSV File entry class.CompCsvFileEntry
Class for handling a Compound database in SQLite format.CompSqliteConn
Compound SQLite entry class.CompSqliteEntry
Convert connector name into class prefix.connNameToClassPrefix
Creating a BiodbMain instance for tests.createBiodbTestInstance
CSV File connector class.CsvFileConn
Convert a data.frame into a string.df2str
Throw an error and log it too.error
Throw an error and log it too.error0
File template class.FileTemplate
Get connector class name.getConnClassName
Get connector types.getConnTypes
Get default cache folder.getDefaultCacheDir
Get entry class name.getEntryClassName
Get entry types.getEntryTypes
Get the main package logger.getLogger
List test reference entries.listTestRefEntries
Loads the contents of files in memory.loadFileContents
Log debug message.logDebug
Log debug message.logDebug0
Log information message.logInfo
Log information message.logInfo0
Log trace message.logTrace
Log trace message.logTrace0
Convert a list into a string.lst2str
Mass CSV File connector class.MassCsvFileConn
Mass CSV File entry class.MassCsvFileEntry
Class for handling a Mass spectrometry database in SQLite format.MassSqliteConn
Mass spectra SQLite entry class.MassSqliteEntry
Create a new BiodbMain instance.newInst
Progress class.Progress
Range class.Range
Run generic tests.runGenericTests
SQLite connector class.SqliteConn
Set a test context.testContext
A class for accessing the test reference entries.TestRefEntries
Run a test.testThat
Throw a warning and log it too.warn
Throw a warning and log it too.warn0