bioconductor-organismdbi

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

• Homepage: https://bioconductor.org/packages/OrganismDbi
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/OrganismDbi/inst/doc/OrganismDbi.pdf

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