gene-evidence-matrix

name	gene_evidence_matrix
description	Build an evidence matrix linking a gene list to a phenotype, pathway, or biological question using literature and local knowledge.
category	bio/literature
version	1
requires_tools	["ncbi_eutils","uniprot_api","search_knowledge_base","python_repl"]
requires_network	true
user_invocable	true
tags	["evidence","gene-list","phenotype","matrix","literature"]
aliases	["evidence_table_builder"]
species	any
modality	literature
stage	interpretation
stability	evolving
safety_level	medium

Gene Evidence Matrix

Purpose

Summarize how strongly each gene in a list is supported by literature or local knowledge for a specific phenotype, pathway, or mechanism.

When to use

Use this skill when the user wants to compare several candidate genes against one biological question, such as exhaustion, apoptosis, interferon response, or cytokine signaling.

Required inputs

• genes: Candidate genes
• question: The phenotype, pathway, or mechanism of interest
• species (optional)

Steps

1. Normalize the gene list if needed.
2. Use search_knowledge_base for any local protocol, note, or playbook relevant to the question.
3. For each gene, use ncbi_eutils to search the gene plus the question.
4. Use uniprot_api for a concise function check when needed.
5. Use python_repl to assemble an evidence matrix with fields such as:
   • gene
   • evidence strength
   • mechanism hint
   • representative PMID or source
   • main caveat
6. Rank genes cautiously. Distinguish strong evidence from plausible speculation.

Output format

• Evidence matrix: Gene | Evidence strength | Mechanism hint | Source | Caveat
• Top supported genes
• Low-confidence or conflicting genes

Failure modes

• Sparse literature: say the matrix is preliminary.
• Conflicting evidence: keep both sides visible instead of forcing a consensus.
• Very large gene lists: summarize the top subset and suggest batching.

Examples

• "Build an evidence matrix for TOX, PDCD1, TIGIT, IFNG against T-cell exhaustion."
• "Which of these genes have evidence for interferon response activation?"