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go_bp_enrichment

Analyze gene lists to identify overrepresented biological processes using Gene Ontology enrichment, helping interpret gene expression data and uncover functional implications.

Instructions

Perform Gene Ontology (GO) Biological Process enrichment analysis to understand what biological functions and processes are overrepresented in your gene list. This tool helps researchers interpret gene expression data, identify statistically significant biological processes, and uncover functional implications of genes from RNA-seq, microarray, or other high-throughput experiments. Use this when you need to: analyze gene functions, find enriched biological processes, perform functional profiling of gene lists, understand molecular mechanisms, interpret differentially expressed genes (DEGs), discover key biological pathways, annotate gene lists functionally, characterize gene sets involved in specific phenotypes, connect genes to their biological roles, or investigate what your genes do. The tool performs over-representation analysis (ORA) using the Enrichr API and GO Biological Process 2025 database, returning only statistically significant terms (adjusted p-value < 0.05) to provide meaningful biological insights while managing context usage. Perfect for transcriptomics analysis, systems biology studies, drug target identification, biomarker discovery, and understanding disease mechanisms. For multi-library analysis across different databases (KEGG, Reactome, etc.), use enrichr_analysis instead.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
genesYesList of gene symbols to analyze for GO BP enrichment (e.g., ['TP53', 'BRCA1', 'EGFR']). Can be from DEG analysis, candidate gene lists, or any gene set of interest.
descriptionNoOptional description for the gene list to help track analysesGene list for GO BP enrichment
outputFileNoOptional path to save complete results as TSV file. If specified, ALL significant terms will be saved to this file, regardless of maxTerms limit.
Behavior4/5

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

With no annotations provided, the description carries full burden and discloses important behavioral traits: it performs over-representation analysis using Enrichr API, returns only statistically significant terms (adjusted p-value < 0.05), and mentions context usage management. However, it doesn't specify rate limits, authentication needs, or error handling details.

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 front-loaded with core purpose but contains lengthy lists of use cases and applications that could be more concise. While informative, some sentences could be condensed without losing essential information.

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?

For a tool with no annotations and no output schema, the description provides substantial context about methodology, statistical thresholds, and sibling differentiation. However, it doesn't describe the return format or structure of results, which would be helpful given the absence of an output schema.

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 three parameters thoroughly. The description doesn't add meaningful parameter semantics beyond what's in the schema, maintaining the baseline score of 3 for high schema coverage.

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 specific action ('perform Gene Ontology Biological Process enrichment analysis') and resource ('gene list'), distinguishing it from the sibling tool enrichr_analysis by specifying it focuses on GO Biological Process 2025 database rather than multi-library analysis.

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?

Explicitly states when to use this tool ('analyze gene functions, find enriched biological processes...') and when to use the alternative ('For multi-library analysis across different databases... use enrichr_analysis instead'), providing clear context and exclusions.

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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