| name | bioconductor-organismdbi |
| 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. |
| when_to_use | Use when: 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). Not for: 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 pathwa |
| user-invocable | false |
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.
Key Parameters
- keys: The character vector of keys to search for in
select or keys.
- keytype: The type of input keys (e.g.,
"ENTREZID") provided to select or keys.
- columns: The columns of information to retrieve (e.g.,
c("TXNAME", "SYMBOL")) in select, transcripts, or transcriptsBy.
- by: The grouping factor (e.g.,
"gene") used in transcriptsBy.
- pkgname: The name of the custom package to create (e.g.,
"Homo.sapiens") in makeOrganismPackage.
- graphData: The list expressing how different packages relate to each other via foreign keys in
makeOrganismPackage.
Best Practices
- Inspect Fields: Use
keytypes() and columns() to inspect valid query fields before executing a search.
- Use Select: Prefer using the unified
select() method to retrieve multi-database annotations in a single tabular format.
- GRanges Integration: When extracting genomic ranges, use functions like
transcripts(Homo.sapiens, columns=...) to get GRanges objects pre-annotated with gene metadata.
- Consistent Builds: Take extra care to ensure that the different packages used in
makeOrganismPackage are from the same build (e.g., hg19).
Common Pitfalls
- Conflicting Package Schemas: Mixing incompatible
TxDb and OrgDb versions. Fix: Ensure the underlying TxDb and OrgDb packages correspond to the same genome assembly and annotation release.
- Non-Unique Columns: Having more than one example of each field across supporting packages. Fix: Ensure all values returned by
columns are unique across ALL of the supporting packages before using makeOrganismPackage.
- Graph Cycles: Providing a
graphData list with multiple pathways between nodes. Fix: Choose exactly one foreign key relationship to connect any two packages in your graph.
Alternatives
- AnnotationDbi: The base package for querying individual
OrgDb databases.
- GenomicFeatures: Specifically for managing and querying
TxDb transcript databases.
Citations
- Carlson M, Atiku Mustapha A (2026). OrganismDbi: A meta framework for Annotation Packages.
References
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