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BioModels — Search Biological Models

biomodels.model.search
Read-onlyIdempotent

Search the BioModels repository for peer-reviewed mathematical models of biological and biomedical systems. BioModels is the world's primary repository for quantitative kinetic models, hosted by EMBL-EBI. Contains 3,200+ models in SBML format covering signaling pathways, metabolic networks, gene regulation, pharmacokinetics, circadian rhythms, disease dynamics (COVID-19, diabetes, cancer), and more. Returns model accession IDs (BIOMD prefix = curated, MODEL prefix = submitted), names, formats, submitter info, and URLs. Filter by curation status to restrict to manually validated models. CC0 Public Domain — European Bioinformatics Institute (EMBL-EBI)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoNumber of results to return (1–50, default 10)
queryYesKeyword to search for biological mathematical models — e.g. "insulin signaling", "circadian clock", "glucose metabolism", "COVID-19". Supports free-text and can include organism names, disease terms, pathway names, or author names.
offsetNoPagination offset — number of results to skip (default 0)
curation_statusNoFilter by curation status. "CURATED" returns only manually reviewed, peer-validated models from the BioModels curated branch (highest quality). "NON_CURATED" returns all submitted models including author-provided ones. Omit to search all models.

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

A4.1/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, and destructiveHint=false, so the safety profile is covered. The description adds useful behavioral context: it explains the return format (accession IDs with BIOMD vs MODEL prefixes), the scope of the repository, and the curation status filter semantics. It doesn't mention pagination behavior beyond the offset parameter, but the schema covers that.

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 well-structured and information-dense without being bloated. It front-loads the core purpose, then provides repository context, return value details, and filtering guidance. The only minor issue is that some repository background (hosted by EMBL-EBI, CC0 license) is useful but not essential for calling the tool.

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

Completeness4/5

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

The description is complete for a search tool: it covers what the tool does, what it returns, and how to filter. The output schema exists, so return values are documented. The only gap is that it doesn't explicitly state when to prefer this over biomodels.model.latest or biomodels.model.detail, but the sibling names make this reasonably clear.

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%, so the schema already documents all four parameters thoroughly. The description adds some value by explaining the BIOMD/MODEL prefix distinction and curation status meaning, but it doesn't add significant new parameter semantics beyond what the schema provides. Baseline 3 is appropriate.

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 states a specific verb ('Search') and resource ('BioModels repository'), and clearly distinguishes this tool from siblings like biomodels.model.detail, biomodels.model.files, and biomodels.model.latest by focusing on search across the repository. It also explains what the repository contains and what the search returns.

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 provides clear context on when to use this tool (searching for models by keyword) and mentions filtering by curation status. It doesn't explicitly name alternatives or exclusions, but the sibling names (detail, files, latest) make the distinction inferable. The curation_status parameter description adds practical guidance on when to use it.

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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