Render a KEGG pathway as ASCII text optimized for LLM consumption.

Two styles available:

• 'chain': Linear reaction flow text showing substrate->enzyme->product chains. Robust and compact. Best for understanding reaction sequences.

• 'grid': 2D spatial layout using KGML coordinates. Shows the pathway topology with box-and-arrow rendering. Best for seeing spatial relationships.

Args: pathway_id: KEGG pathway ID (e.g. 'hsa00010' for human glycolysis). Must be organism-specific; reference pathways (map*) have limited KGML. style: 'chain' (default, linear text) or 'grid' (2D spatial layout). max_width: Maximum line width in characters (40-200, default 100). max_height: Grid mode only: maximum height in lines (20-80, default 40).

Search KEGG BRITE functional hierarchy databases.

Args: query: Hierarchy name (e.g. 'KEGG pathway', 'transporter', 'ribosome'). max_results: Maximum number of results to return (capped at 100).

Get the structure of a KEGG BRITE functional hierarchy.

BRITE entries are large A/B/C/D trees, not flat-file entries, so the result is a bounded summary: the level line counts, the leaf column names, and the labels of the top two levels.

Args: brite_id: KEGG BRITE hierarchy ID. Any form KEGG hands out works — 'br:ko00001' (canonical), 'ko00001' / 'br08303' (as listed by list_databases), or the bare '00001' / '08303' returned by search_brite. detail_level: 'summary' (default) or 'full' (adds raw_content, the raw hierarchy text — TRUNCATED, since the largest hierarchies are several megabytes).

Search KEGG compounds by name or chemical property.

Args: query: Search term (compound name, formula, or mass). search_type: 'name' (default), 'formula', 'exact_mass', 'mol_weight', or 'nop'. max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG compound entry.

Args: compound_id: KEGG compound ID (e.g. 'C00002' for ATP, 'C00031' for D-Glucose). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Get all reactions involving a KEGG compound.

Args: compound_id: KEGG compound ID (e.g. 'C00002'). max_results: Maximum number of reactions to return (capped at 100).

Fetch multiple KEGG entries in bulk (max 50 IDs).

Automatically chunks requests into groups of 10 to respect KEGG's API limit.

Args: entry_ids: List of KEGG entry IDs (e.g. ['C00002', 'C00031', 'C00033']). Can mix databases. Max 50 entries. detail_level: 'summary' (default, compact per-entry projection) or 'full' (complete flat-file parse — sequences and GENES lists make this large for 50 entries at once).

Convert KEGG IDs to/from external database identifiers.

Converts within one kind only, KEGG side <-> outside side: genes (organism code 'hsa' or T-number 'T01001') <-> ncbi-geneid / ncbi-proteinid / uniprot; chemistry (compound / drug / glycan) <-> pubchem / chebi. Cross-kind pairs such as compound<->uniprot are rejected by KEGG, and 'kegg' is not a database conv accepts.

Args: source_db: Source database — 'hsa', 'T01001', 'ncbi-geneid', 'ncbi-proteinid', 'uniprot', 'compound', 'drug', 'glycan', 'pubchem' or 'chebi'. target_db: Target database, from the same list and the opposite side of the pair (e.g. source_db='hsa' + target_db='uniprot', or source_db='chebi' + target_db='compound'). entry_ids: Optional list of specific IDs to convert. Bare ids are prefixed with source_db automatically ('1956' -> 'hsa:1956'). KEGG accepts at most 10 per request; longer lists are chunked and fetched concurrently rather than silently dropped. If None, converts the full source database (large: hsa <-> ncbi-geneid is ~700 KB).

Find related entries in another KEGG database for a given entry.

Args: entry_id: Source KEGG entry ID (e.g. 'hsa:1956', 'C00002', 'K00844'). target_db: Target database (e.g. 'pathway', 'disease', 'drug', 'ko', 'compound', 'reaction', 'module', 'genes'). max_results: Maximum number of pairs to return (capped at 100).

Get release information and statistics for a KEGG database.

Args: database: Database name (e.g. 'kegg', 'pathway', 'compound', 'drug', 'genome').

List organisms available in KEGG with their 3-4 letter codes and names.

KEGG has ~12,000 organisms, so the full list is large. Pass query to filter by organism code or name (e.g. 'Bacillus', 'hsa') instead of paging through everything.

Args: query: Case-insensitive substring filter on the organism code or name. Empty (the default) returns the first max_results organisms. max_results: Maximum number of organisms to return (capped at 100).

Search KEGG diseases by name or keyword.

Args: query: Disease name (e.g. 'diabetes', 'cancer', 'Alzheimer'). max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG disease entry.

Args: disease_id: KEGG disease ID (e.g. 'H00004' for colorectal cancer). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Search KEGG drugs by name, formula, or molecular weight.

Args: query: Drug name, formula, or mass value. search_type: 'name' (default), 'formula', 'exact_mass', or 'mol_weight'. max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG drug entry.

Args: drug_id: KEGG drug ID (e.g. 'D00001' for aspirin, 'D00564' for ibuprofen). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Get drug-drug interactions for one or more KEGG drugs.

Args: drug_ids: Single drug ID (e.g. 'D00001') or multiple IDs joined with '+' (e.g. 'D00001+D00564'). Max 10 entries. max_results: Maximum number of interactions to return (capped at 100).

Search KEGG enzymes by EC number or name.

Args: query: EC number (e.g. '1.1.1.1') or enzyme name (e.g. 'kinase', 'oxidase'). max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG enzyme (EC number).

Args: enzyme_id: EC number (e.g. '1.1.1.1') or prefixed ID (e.g. 'ec:1.1.1.1'). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Search for genes in a KEGG organism database.

Args: query: Search term (gene name, symbol, or description). organism_code: KEGG organism code (e.g. 'hsa' human, 'mmu' mouse, 'eco' E. coli). max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG gene entry.

Args: gene_id: KEGG gene ID in format 'organism:gene' (e.g. 'hsa:1956' for EGFR). detail_level: 'summary' (default, compact) or 'full' (complete parse with linked orthologs, pathways, xrefs, and references). include_sequence: If True and detail_level='full', fetches amino acid and nucleotide sequences.

Get KO (KEGG Orthology) entries and cross-organism orthologs for a gene.

Args: gene_id: KEGG gene ID (e.g. 'hsa:1956').

Search KEGG glycan database by keyword or composition.

Args: query: Glycan name or composition (e.g. 'GlcNAc', 'Man5', 'sialic acid'). max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG glycan entry.

Args: glycan_id: KEGG glycan ID (e.g. 'G00001'). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Search KEGG modules by keyword.

Args: query: Module name or pathway block (e.g. 'glycolysis', 'TCA cycle'). max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG module.

Args: module_id: KEGG module ID (e.g. 'M00001' for glycolysis core module). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Search KEGG Orthology (KO) entries by keyword.

Args: query: Gene function (e.g. 'hexokinase', 'ribosomal protein', 'cytochrome'). max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG Orthology (KO) entry.

Args: ko_id: KEGG KO identifier (e.g. 'K00844' for hexokinase). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Draw a KEGG pathway map as a PNG image, with gene boxes coloured by group.

The map is redrawn from KEGG's KGML layout (gene boxes, compounds, reactions and links to other maps), not copied from KEGG's image. Each gene box is split into one stripe per highlight group: coloured when the group has one of the box's KOs, grey when it doesn't. Returns the PNG plus an exact summary of what the image shows (per group: map KOs found and boxes coloured; per box: KOs and the groups that have them), so check the summary rather than describing the picture from memory.

Args: pathway_id: KEGG map number: 'map00010', 'ko00010', an organism map such as 'eco00010' (drawn as the KO reference map), or '00010'. Global and overview maps (011xx, 012xx) are refused. highlight: Optional {label: ids}, at most 8 groups (e.g. one per genome). Ids are KO ids ('K00844', 'ko:K00844', 'KEGG:K00844') or complete EC numbers ('2.7.1.1', 'EC:2.7.1.1'). One item may hold one gene's ids separated by spaces ('K00845 EC:2.7.1.2', or a GenBank db_xref string). A KO with no KO match is coloured through EC numbers only when one item carries every EC KEGG links to it; those KOs are listed under matched_by_ec.

Search KEGG pathways by keyword.

Args: query: Search term (e.g. 'glycolysis', 'TCA', 'insulin signaling'). organism_code: 3-4 letter organism code (e.g. 'hsa' for human, 'mmu' for mouse). Use 'map' for reference pathways. max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG pathway.

Args: pathway_id: KEGG pathway ID (e.g. 'hsa00010', 'map00010'). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse with all linked genes, compounds, reactions, references, and xrefs).

Get all genes associated with a KEGG pathway.

Args: pathway_id: KEGG pathway ID (e.g. 'hsa00010'). Use organism-specific IDs (e.g. 'pae00350' for P. aeruginosa) — reference pathways ('map*') are not supported by the KEGG gene link API. max_results: Maximum number of pairs to return (capped at 100).

Get all compounds (metabolites) associated with a KEGG pathway.

Args: pathway_id: KEGG pathway ID (e.g. 'map00010'). max_results: Maximum number of pairs to return (capped at 100).

Get all reactions in a KEGG pathway.

Args: pathway_id: KEGG pathway ID (e.g. 'hsa00010'). max_results: Maximum number of pairs to return (capped at 100).

Search KEGG reactions by keyword.

Args: query: Search term (reaction name or description). max_results: Maximum number of results to return (capped at 100).

Get detailed information for a KEGG reaction.

Args: reaction_id: KEGG reaction ID (e.g. 'R00756' for glucose phosphorylation). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).