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BioContextAI Knowledgebase MCP

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bc_get_reactome_info_by_identifier

Retrieve biological pathways associated with a given molecular identifier from Reactome, with options to filter by species, p-value, and other parameters.

Instructions

Query the Reactome API identifier endpoint.

Use this endpoint to retrieve pathways associated with a given identifier. Always provide the species parameter to ensure the correct protein is returned.

Args: identifier (str): The identifier of the element to be retrieved base_url (str): Base URL for the Reactome API interactors (bool): Include interactors species (str or list): List of species to filter the result (accepts taxonomy ids, species names and dbId) page_size (int): Pathways per page page (int): Page number sort_by (str): Field to sort results by (e.g., "ENTITIES_PVALUE", "ENTITIES_FDR") order (str): Sort order ("ASC" or "DESC") resource (str): Resource to filter by (TOTAL includes all molecule types) p_value (float): P-value threshold (only pathways with p-value <= threshold will be returned) include_disease (bool): Set to False to exclude disease pathways min_entities (int): Minimum number of contained entities per pathway max_entities (int): Maximum number of contained entities per pathway importable_only (bool): Filter to only include importable resources timeout (int): Request timeout in seconds

Returns: dict: API response data or error information

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
identifierYesThe identifier of the element to be retrieved
base_urlNoBase URL for the Reactome APIhttps://reactome.org/AnalysisService
interactorsNoInclude interactors
speciesNoList of species to filter the result (accepts taxonomy ids, species names and dbId)
page_sizeNoPathways per page
pageNoPage number
sort_byNoField to sort results by (e.g., 'ENTITIES_PVALUE', 'ENTITIES_FDR')ENTITIES_PVALUE
orderNoSort order ('ASC' or 'DESC')ASC
resourceNoResource to filter by (TOTAL includes all molecule types)TOTAL
p_valueNoP-value threshold (only pathways with p-value <= threshold will be returned)
include_diseaseNoSet to False to exclude disease pathways
min_entitiesNoMinimum number of contained entities per pathway
max_entitiesNoMaximum number of contained entities per pathway
importable_onlyNoFilter to only include importable resources
timeoutNoRequest timeout in seconds

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior3/5

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

With no annotations provided, the description carries full burden for behavioral disclosure. It states the tool returns a dict with API response or error, which is helpful. However, it omits critical details such as idempotency, side effects, authentication requirements, rate limits, or the nature of the API call (GET vs POST). The focus is heavily on parameters rather than behavior.

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

Conciseness3/5

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

The description is well-structured with a front-loaded purpose sentence followed by an Args section. However, the Args section is a verbose list that largely duplicates the schema's property descriptions, making it longer than necessary. Every sentence could be more concise; for example, the parameter details could be summarized or omitted given the schema.

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

Completeness3/5

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

Given the tool's complexity (15 parameters, 1 required) and that an output schema exists, the description covers the basic purpose and parameter details. However, it lacks guidance on when to use this tool versus siblings, does not explain error handling beyond 'error information', and misses behavioral constraints. The output schema may cover return structure, but the description's contextual gaps remain.

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 baseline is 3. The description repeats the schema's parameter descriptions almost verbatim without adding new semantic information beyond the usage tip about species. While it lists all parameters, it does not provide deeper meaning or contextualize parameter interactions beyond what the schema already offers.

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 the tool queries the Reactome API identifier endpoint to retrieve pathways for a given identifier, using a specific verb ('Query') and resource ('Reactome API identifier endpoint'). It distinguishes from sibling tools like bc_query_kegg (different database) and bc_get_string_id, as it targets Reactome pathways.

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

Usage Guidelines3/5

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

The description advises to always provide the species parameter for correct results, which is a useful usage condition. However, it does not explicitly mention when not to use this tool or compare it with alternatives among the many sibling tools (e.g., bc_query_kegg for KEGG pathways). This limits guidance for an agent choosing among similar tools.

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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