paper-triage

name	paper_triage
description	Triage a paper for biological relevance, extract the main claims, and separate evidence-backed takeaways from abstract-only impressions.
category	bio/literature
version	1
requires_tools	["ncbi_eutils","evidence_retrieval","evidence_review","python_repl"]
requires_network	true
user_invocable	true
tags	["paper-triage","abstract","literature","relevance"]
aliases	["abstract_triage","paper_relevance_check"]
species	any
modality	literature
stage	interpretation
stability	stable
safety_level	low

Paper Triage

Purpose

Decide whether a paper is worth deeper follow-up and summarize the strongest claims, methods, and limitations with clear provenance.

When to use

Use this skill when the user pastes an abstract, provides a title or PMID, or asks whether a paper is relevant to perturb-seq, single-cell RNA-seq, or a related biology question.

Required inputs

• paper details: abstract text, title, DOI, PMID, or citation fragment
• research question (optional): the biological question the user wants the paper judged against

Steps

1. Normalize what the user supplied: abstract-only, title-plus-question, or PMID/citation-backed request.
2. If a title, citation, or PMID is available, use ncbi_eutils or evidence_retrieval to ground the paper metadata before judging relevance.
3. If the user is asking a question about what the paper supports, use evidence_review to distinguish supported conclusions from unresolved claims whenever enough source material is available.
4. Use python_repl if helpful to organize the paper into a compact table covering relevance, methods, claims, and limitations.
5. If only abstract text is available, say explicitly that the triage is abstract-only and lower confidence than a metadata-backed or evidence-reviewed pass.
6. Return the triage result with provenance, caveats, and the most useful follow-up action.

Output format

• Biological context or assumptions: the disease, system, assay, or research question used to judge relevance.
• Evidence or source basis: whether the triage came from ncbi_eutils, evidence_retrieval, evidence_review, or abstract-only text.
• Relevance and claims: High / Medium / Low fit plus the main claims and key methods.
• Caveats or ambiguity: missing full text, abstract-only limitations, or unclear alignment with the user's question.
• Recommended next step: retrieve full evidence, compare with a second paper, or move into a deeper evidence review.

Failure modes

• No usable citation details: say the triage is provisional and based only on the pasted text.
• Metadata mismatch: call out title, PMID, or abstract inconsistencies before summarizing.
• Over-broad relevance question: ask what assay, disease, or mechanism the user cares about most.

Examples

• "Is this paper relevant to Perturb-seq in T cells?"
• "Triage this abstract and tell me whether it is worth reading in full."