biodb
Bioc currentBiodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
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.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
106 26 exported
Complexity
3.2 avg / 16 max
Call network
106 nodes / 60 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
26,981
Files
190
Compiled share
1.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
56
Internal functions
375
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.12
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
3
Dep constraint coverage
9.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
AGPL-3
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-06-09
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 46%
- References docs
- 0%
Topics
Depended on by (10)
Bioconductor (10)
People
- Pierrick Roger author maintainer
- Alexis Delabrière contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("biodb")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.