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BioModels — Model Download Files

biomodels.model.files
Read-onlyIdempotent

List all downloadable file representations for a BioModels model by accession ID. Returns the main SBML file (primary format, compatible with COPASI, libSBML, JWS Online, Tellurium), plus auto-generated alternative formats: BioPAX Level 2 and 3 (OWL/RDF for pathway databases), MATLAB/Octave simulation scripts (.m files), and any author-supplied supplementary files. Each entry includes filename, description, MIME type, file size in bytes, MD5 checksum, and the direct download URL. Use to retrieve simulation-ready model files for computational biology workflows. CC0 Public Domain — EMBL-EBI BioModels Database

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
model_idYesBioModels accession identifier (e.g. "BIOMD0000000001"). Returns all downloadable file representations: SBML (primary), BioPAX levels 2 and 3, MATLAB/Octave scripts, and any author-provided supplementary files. Each entry includes the direct download URL, MIME type, file size, and MD5 checksum.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false. The description adds concrete behavioral context beyond annotations: it guarantees returning 'all' file representations, enumerates the formats with compatibility notes (e.g., SBML compatible with COPASI, libSBML), and discloses the CC0 license. No contradiction with annotations.

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

Conciseness4/5

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

The description is moderately sized and front-loaded with the core action. Every sentence contributes meaning—scope, formats, returned fields, use case, and license. A few details are repeated in the schema's parameter description, but the text remains efficient and well-structured.

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?

For a single-parameter, read-only list tool with an output schema, the description covers everything an agent needs: the exact accession ID input, the full set of return formats, the fields in each entry, the primary use case, and licensing. There are no hidden prerequisites, side effects, or pagination concerns that would impede correct invocation.

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

Parameters3/5

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

Schema description coverage is 100%; the model_id parameter is already fully documented in the schema, including an example ('BIOMD0000000001') and the list of returned formats. The general description reinforces the format list but adds no new parameter-specific semantics beyond what the schema provides, so baseline 3 applies.

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 opens with a specific verb and resource: 'List all downloadable file representations for a BioModels model by accession ID.' It clearly distinguishes this tool from sibling tools like biomodels.model.detail or biomodels.model.search by focusing on file representations and listing specific formats (SBML, BioPAX, MATLAB/Octave, supplementary).

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

Usage Guidelines4/5

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

The description gives a clear usage context: 'Use to retrieve simulation-ready model files for computational biology workflows.' It does not mention explicit alternatives or when-not-to-use conditions, but the use case is unambiguous enough for a simple list-style tool.

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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