biocontext_kb.core.kegg

biocontext_kb.core.kegg#

Functions#

get_kegg_id_by_gene_symbol(gene_symbol, organism_code)

Convert gene symbol to KEGG ID for use in subsequent API calls. Returns KEGG gene ID required for query_kegg().

query_kegg(operation[, database, target_db, ...])

Execute flexible KEGG API queries across pathways, genes, compounds, diseases, drugs. Use get_kegg_id_by_gene_symbol() first.

Package Contents#

biocontext_kb.core.kegg.get_kegg_id_by_gene_symbol(gene_symbol, organism_code)#

Convert gene symbol to KEGG ID for use in subsequent API calls. Returns KEGG gene ID required for query_kegg().

Returns:

KEGG gene ID string (e.g., ‘hsa:7157’) or error dict.

Return type:

str or dict

Parameters:

  • gene_symbol (Annotated[str, Field(description="Gene symbol (e.g., 'TP53' for human, 'Trp53' for mouse)")])

  • organism_code (Annotated[str, Field(description='Taxonomy ID: 9606 (human), 10090 (mouse), 10116 (rat), 562 (E. coli), 4932 (yeast)')])

biocontext_kb.core.kegg.query_kegg(operation, database=None, target_db=None, source_db=None, query=None, option=None, entries=None)#

Execute flexible KEGG API queries across pathways, genes, compounds, diseases, drugs. Use get_kegg_id_by_gene_symbol() first.

Returns:

Raw text response from KEGG API with requested data (pathways, genes, compounds, etc.) or error dict.

Return type:

str or dict

Parameters:

  • operation (Annotated[KeggOperation, Field(description='info, list, find, get, conv, link, or ddi')])

  • database (Annotated[Optional[Union[KeggDatabase, KeggOutsideDb, str]], Field(description='pathway, compound, genes, organism code (hsa, mmu, etc.), or other DB')])

  • target_db (Annotated[Optional[Union[KeggDatabase, KeggOutsideDb, str]], Field(description='Target DB for conversion/linking operations')])

  • source_db (Annotated[Optional[Union[KeggDatabase, KeggOutsideDb, str]], Field(description='Source DB for conversion/linking operations')])

  • query (Annotated[Optional[str], Field(description='Query string for FIND/LIST, or organism code for LIST')])

  • option (Annotated[Optional[Union[KeggOption, KeggFindOption, KeggRdfFormat]], Field(description='aaseq, ntseq, mol, formula, exact_mass, mol_weight, etc.')])

  • entries (Annotated[Optional[List[str]], Field(description="KEGG entry IDs (e.g., ['hsa:7157', 'hsa00010'])")])

Contents