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find_databases

Identify relevant biological databases from any search terms like gene, pathway, or disease. Use keywords to find 1-3 candidate databases to query.

Instructions

Database discovery — REQUIRED first step for any TogoMCP workflow.

Always call this BEFORE get_MIE_file() or run_sparql(). Pass any search terms you have (gene, pathway, drug target, variant, organism, disease, enzyme class, etc.) as keywords. Returns 1–3 candidate databases scoped to your terms — much more efficient than browsing the full catalog.

Workflow:

  1. find_databases(keywords=[...]) — identify 1–3 relevant databases.

  2. get_MIE_file(database) — learn each candidate's schema and SPARQL idioms.

  3. run_sparql() — query with the discovered structured properties.

Common keywords to try: "MANE" (Ensembl), "drug targets" (ChEMBL), "clinical variants" (ClinVar), "pathways" (Reactome), "variants" (gnomAD), "ortholog" (OMA), "expression" (Bgee).

If you have no search terms and want to browse the full catalog instead, see list_databases() — that tool is supplementary, not a substitute for this one.

Returns: List of dicts: {database, title, matched_keywords, categories, snippet} (or description when verbose=True). Sorted by number of matched keywords descending, then alphabetically by database name.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
keywordsNoKeyword or list of keywords (case-insensitive substring match against title, description, and the database's curated keywords field).
categoryNoCategory filter (substring, case-insensitive). Call list_categories() to see the available set.
matchNo'any' returns DBs matching at least one keyword (OR); 'all' requires every keyword to match (AND).any
verboseNoIf True, return the full description; if False (default), return a short snippet around the first match.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries full burden. It explains that it performs case-insensitive substring matching, returns a sorted list of dicts, and that verbose controls full description or snippet. It does not explicitly state that the tool is read-only with no side effects, but it is implied. A minor gap.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with a bold opening statement, a workflow list, examples, sibling tool distinction, and return format. Every sentence adds value; no redundancy. It is concise yet comprehensive.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool has 4 parameters and an output schema, the description is very complete: it explains the role in the workflow, parameter usage, output format, and distinguishes from siblings. The output schema exists separately, so description does not need to detail return fields, but it does so succinctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% for all 4 parameters. The description adds significant value beyond the schema by explaining the workflow, how to use keywords effectively, and the effect of verbose on output. It also provides examples for common keywords.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states that this tool is for database discovery, the required first step in any TogoMCP workflow. It specifies that it searches across databases using keywords and returns 1-3 candidates. It distinguishes from sibling `list_databases()` by explaining that `list_databases()` is for browsing the full catalog, while `find_databases()` is for scoped search.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly states when to use this tool: 'Always call this BEFORE get_MIE_file() or run_sparql().' It provides a numbered workflow and even suggests common keywords to try. It also tells when to use `list_databases()` instead (when no search terms and want to browse).

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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