# Bioconductor Organismdbi

The package enables a simple unified interface to several annotation packages each of...

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-organismdbi -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-organismdbi -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-organismdbi -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-organismdbi -g -a gemini-cli -y`

## Description

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# OrganismDbi

## Dependencies & Environment

> Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

- **Version:** 1.54.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6
- **Depends:** BiocGenerics, AnnotationDbi, Seqinfo, GenomicFeatures
- **Imports:** DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges
- **System requirements:** URL
- **Install:** `BiocManager::install("OrganismDbi")`

## When to Use
- **Unified Annotation Queries**: Querying multiple annotation resources (e.g., `TxDb` and `OrgDb`) simultaneously through a single unified interface using `select`.
- **Custom Meta-Package Building**: Building custom `OrganismDbi` meta-packages (like `Homo.sapiens`) that link genome-centric and gene-centric databases using `makeOrganismPackage`.
- **Feature Extraction**: Extracting genomic features (transcripts, exons, cds) mapped directly to gene symbols or other identifiers using `transcripts`, `exons`, or `cds`.
- **Grouped Feature Extraction**: Grouping genomic features by a specific identifier (e.g., by gene) using `transcriptsBy`, `exonsBy`, or `cdsBy`.

## When NOT to Use
- **Non-Model Organisms**: When working with non-model organisms that do not have pre-built `OrgDb` or `TxDb` packages available to link together.
- **Cyclic Graph Relationships**: When the relationships between your annotation packages present more than one pathway between any two nodes/objects (the package cannot handle cycles in the graph).

## Data Requirements
- **Annotation Packages**: Installed Bioconductor annotation packages (e.g., `org.Hs.eg.db`, `TxDb.Hsapiens.UCSC.hg19.knownGene`, `GO.db`).
- **Graph Data**: A list of short two-element character vectors representing foreign key relationships (e.g., `graphData`) when building custom packages.

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/genomics/organismdbi/SKILL.md