bioconductor-keggrest

name: bioconductor-keggrestdescription: "A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see <https://www.kegg.jp/kegg/rest/>). Note that KEGGREST"when_to_use: "Use when: Exploring available KEGG databases and organisms using listDatabases() and keggList().; Retrieving specific KEGG entries, including amino acid (aaseq) or nucleotide (ntseq) sequences as AAStringSet or DNAStringSet objects using keggGet().; Downloading KEGG pathway maps as PNG images using keggGet() with the \"image\" option.; Searching for genes or compounds by keywords, chemical formulas, or exact . Not for: For commercial applications, use ReactomePA instead because the KEGG API is strictly restricted to academic use by academic institutions.; For offline or high-throughput batch queries of thousands of genes, use local annotation packages like org.Hs.e"user-invocable: false

KEGGREST

Dependencies & Environment

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

• Version: 1.52.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: httr, png, Biostrings
• Install: BiocManager::install("KEGGREST")

When to Use

• Exploring available KEGG databases and organisms using listDatabases() and keggList().
• Retrieving specific KEGG entries, including amino acid (aaseq) or nucleotide (ntseq) sequences as AAStringSet or DNAStringSet objects using keggGet().
• Downloading KEGG pathway maps as PNG images using keggGet() with the "image" option.
• Searching for genes or compounds by keywords, chemical formulas, or exact mass using keggFind().
• Converting between KEGG identifiers and external database IDs (e.g., NCBI Gene ID) using keggConv().

When NOT to Use

• For commercial applications, use ReactomePA instead because the KEGG API is strictly restricted to academic use by academic institutions.
• For offline or high-throughput batch queries of thousands of genes, use local annotation packages like org.Hs.eg.db instead to avoid server-side limitations.
• For complex pathway network topology analyses, use KEGGgraph or ROntoTools instead.

Data Requirements

• Valid Identifiers: Input queries must be valid KEGG identifiers (e.g., "hsa:10458", "path:hsa00010", "cpd:C00493") or supported external identifiers.
• Internet Connection: An active internet connection is required to query the live KEGG REST API.

Key Parameters

• database: The target KEGG database to query (e.g., "pathway", "organism", "compound", "genes").
• query: The search term, identifier, or vector of identifiers to retrieve (e.g., "hsa:10458").
• option: Specific query options for keggGet() (e.g., "aaseq", "ntseq", "image") or keggFind() (e.g., "formula", "exact_mass", "mol_weight").

Best Practices

• Verify the target organism's official KEGG code (e.g., "hsa" for human, "eco" for E. coli) using keggList("organism") before running queries.
• Limit keggGet() queries to a maximum of 10 identifiers at once, as the server restricts larger batches.
• Use keggLink() to find relationships across databases, such as retrieving all pathways associated with specific genes.

Common Pitfalls

• Truncated results from keggGet(): Occurs when supplying more than 10 inputs to keggGet(); fix this by batching requests into chunks of 10 or fewer.
• Invalid organism code: Using common names instead of the official 3-4 letter KEGG code returns empty results; fix this by looking up the code with keggList("organism").
• Commercial use violation: Occurs when using the package for non-academic purposes; fix this by switching to open-source databases like Reactome.

Alternatives

• ReactomePA: For pathway analysis using the open-source, commercially unrestricted Reactome database.
• clusterProfiler: For comprehensive enrichment analysis integrating KEGG and GO annotations locally.
• AnnotationDbi: For local, offline mapping of gene IDs without relying on web APIs.

Citations

• Tenenbaum D (2024). KEGGREST: Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). R package version 1.46.0.
• Kanehisa M, Goto S (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1), 27-30.

References

• Homepage: https://bioconductor.org/packages/KEGGREST
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html

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