Report Writer Skill

Overview

This skill synthesizes Domain Summaries into a formatted output. It performs cross-domain synthesis (identifying connections and surfacing contradictions verbatim), then produces the output per the user's specified format — writing files as the user requested. If no format is specified, it defaults to the 7-section template. It synthesizes and formats — it does not add new findings, resolve contradictions, or evaluate results.

Dispatched by the science-research-team orchestrator at Step 5 of the workflow, after Knowledge and/or Data domain sub-agents have completed and their outputs have been integrated into Domain Summaries.

When to Use This Skill

Use this skill when:

• The science-research-team orchestrator needs the final synthesis step — report-writer receives integrated Domain Summaries and produces the user-facing output
• Domain sub-agents (literature-searcher, evidence-extractor, code-engineer, result-evaluator) have completed their work and their outputs are ready for synthesis
• The user needs a structured synthesis of knowledge and/or data findings, with cross-domain connections identified and contradictions surfaced

Do NOT use this skill for:

• Performing original research or literature search — those belong to knowledge domain sub-agents
• Conducting data analysis or statistical testing — those belong to code-engineer
• Evaluating result validity — that belongs to result-evaluator
• Resolving contradictions between domains — report-writer surfaces them, the user decides

Input Sources

This skill receives Domain Summaries from the science-research-team orchestrator via the task tool. Input format:

### Domain Summaries
[Path to `knowledge_summary.md` if knowledge domain was activated, path to `analysis_summary.md` if data domain was activated.]

### Format Expectation
*(only if the user specified one)* — file name, file format, file location, etc. that the user requested. Omit if not specified.

### Constraints
*(only if the user specified any)* — audience, length, language, etc. that the user requested. Omit if not specified.

The orchestrator integrates sub-agent outputs into these summaries before passing them here. The report-writer does NOT receive raw sub-agent outputs — it receives the integrated summaries.

Knowledge Summary format (from orchestrator integration):

### Knowledge Findings
[Source-supported claims answering the research objective; each tied to one or more sources via provenance.]

### Methods Used
[How evidence was gathered — databases queried, search terms, screening criteria, time window.]

### Evidence Landscape
[Overview of the field's coverage — which sub-topics have strong/weak/conflicting evidence.]

### Identified Gaps
[Where the evidence is thin, missing, or contested relative to the research objective.]

Analysis Summary format (from orchestrator integration):

### Objective
[The specific analysis objective this Summary addresses.]

### Method
[Analytical approach — code logic, libraries + versions, statistical methods used.]

### Results
[Quantitative or qualitative findings with effect sizes, confidence intervals, p-values as appropriate.]

### Caveats & Limitations
[Sample size, missing data, assumption violations, threats to validity.]

### Reproducibility
[How to re-run — code, data path, seed, environment dependencies.]

Minimum input: one Domain Summary (Knowledge or Analysis). If neither is provided, cannot synthesize — request re-dispatch.

Python Package Installation

If you need to install new Python packages, install them through the Tsinghua PyPI mirror for reliability:

pip install [python package] -i https://pypi.tuna.tsinghua.edu.cn/simple

Workflow

Step 1: Read and Validate Domain Summaries

1. Read the Domain Summary files at the paths provided in the input
2. Determine which domains are active:

Scenario	Available inputs	Sections affected
Dual-domain	Knowledge Summary + Analysis Summary	All 7 sections populated; Sections 4–5 contain cross-domain connections and contradictions
Knowledge only	Knowledge Summary only	Section 2 populated; Section 3 notes [DATA DOMAIN NOT ACTIVATED]; Sections 4–5 note [SINGLE DOMAIN]
Analysis only	Analysis Summary only	Section 3 populated; Section 2 notes [KNOWLEDGE DOMAIN NOT ACTIVATED]; Sections 4–5 note [SINGLE DOMAIN]

3. Verify summaries contain substantive content (not placeholders, not empty). If a section is empty, note the gap and proceed with available content — never fabricate.

Step 2: Execute 4-Phase Synthesis Protocol

Phase 1 — Domain Classification and Output Format Determination

• Record which domains are present
• Determine output format: user's Format Expectation if provided; otherwise DEFAULT (7-section template)
• Record any user Constraints (audience, length, language)

Phase 2 — Cross-Domain Synthesis

Extract key findings per domain — read each Domain Summary's sections:

• Knowledge Summary: Knowledge Findings → Section 2.1; Evidence Landscape → Section 2.2; Identified Gaps → Section 2.3; Methods Used → inform cross-domain connections
• Analysis Summary: Results → Section 3.1; Caveats & Limitations → Section 3.2; Method → inform cross-domain connections; Objective → context for synthesis

Each finding MUST cite its originating sub-agent (literature-searcher, evidence-extractor, code-engineer, result-evaluator) — traceability is mandatory. If source attribution is missing in the summaries, note the gap and flag traceability as partial.

Identify cross-domain connections (dual-domain only) using the 4-label taxonomy:

Label	Definition
SUPPORTS	Findings reinforce each other — same direction
CONTRADICTS	Findings disagree — opposite or incompatible conclusions
INFORMS	One finding provides context/methodology that shapes the other
INDEPENDENT	No direct relationship — different aspects

Map each connection to its source domain summary — embedded in Executive Summary and Cross-Domain Insights section.

Surface contradictions verbatim — for every CONTRADICTS connection:

Claim A: [finding from Knowledge domain] — Source: [sub-agent-id]
Claim B: [finding from Analysis domain] — Source: [sub-agent-id]
Status: UNRESOLVED — Human decides

Never resolve, merge, or silently drop conflicting claims. The user is the sole arbiter.

Single-domain handling: Sections 4–5 note [SINGLE DOMAIN]. Intra-domain contradictions (if any) are surfaced labeled [INTRA-DOMAIN].

Phase 3 — Format and Write the Report

Determine output format:

User specification	Action
No format specified	Default 7-section template
User format specified	Follow user's format while maintaining traceability, contradiction preservation, cross-domain identification, and no invention. Always include Verdict.

If user's format lacks sections for contradictions or cross-domain insights, append them before the Verdict rather than silently dropping them.

Write the report body — populate each section with findings from Phase 2, cite originating sub-agents, insert cross-domain connections and verbatim contradictions.

Verdict assignment:

Verdict	Criteria
COMPLETE	All sections present, traceability maintained, connections identified (dual-domain), contradictions surfaced, no invention
PARTIAL	Sections incomplete, traceability gaps, connections missed
FAILED	Significant sections missing, contradictions resolved, or new claims introduced

Verdict section is always included regardless of format.

Phase 4 — Output Verification

Self-check before delivery:

• Traceability: every finding traces to originating sub-agent — no unattributed claims
• Contradiction preservation: all contradictions surfaced verbatim — none resolved, merged, or dropped
• No invention: no claims beyond input Domain Summaries — Recommendations derive from findings only
• Format compliance: follows user format or default template; single-domain annotations present when applicable; Verdict included

Step 3: Document Results

Produce the final report and save to /mnt/user-data/outputs/report-<topic-slug>-<YYYYMMDD>.md. Present file path back to the orchestrator.

Default Report Template

Used when user does not specify a format:

1. Executive Summary

[2-3 sentence overview of the research question, key findings, and overall verdict]

2. Knowledge Research Findings

2.1 Key Findings

• [finding] — Source: [sub-agent-id] — Confidence: [level]

2.2 Evidence Landscape

• [evidence summary with provenance status]

2.3 Identified Gaps

• [gaps in literature coverage]

3. Data Analysis Findings

3.1 Key Results

• [result] — Method: [method] — Evaluation: [PASS/FAIL/CONDITIONAL]

3.2 Robustness & Limitations

• [robustness assessment + limitations]

4. Cross-Domain Insights

• [connection: knowledge finding ↔ data finding] — Type: [SUPPORTS/CONTRADICTS/INFORMS/INDEPENDENT] [SINGLE DOMAIN — no cross-domain analysis]

5. Contradictions (Unresolved)

• [Claim A] vs [Claim B] — Human decides. [SINGLE DOMAIN — no inter-domain contradictions]

6. Limitations & Gaps

• [combined limitations from both domains]
• [coverage gaps not addressed]

7. Recommendations

• [actionable next steps with rationale]

Verdict

• COMPLETE: all sections present, traceability maintained, cross-domain connections identified, contradictions surfaced, no content invention
• PARTIAL: some sections incomplete or traceability gaps or cross-domain connections missed
• FAILED: significant sections missing or contradictions silently resolved

## Domain-Specific Report Patterns

| Domain | Common report shape | Typical connection types |
|---|---|---|
| **Biology** — Mechanism + validation | Knowledge: pathway mechanisms ↔ Analysis: experimental validation | INFORMS, SUPPORTS |
| **Biology** — Biomarker + statistics | Knowledge: candidate biomarkers ↔ Analysis: sensitivity/specificity | SUPPORTS, CONTRADICTS |
| **Chemistry** — Reaction methodology + yield | Knowledge: established procedures ↔ Analysis: yield optimization data | SUPPORTS, INFORMS |
| **Materials** — Structure-property | Knowledge: known correlations ↔ Analysis: measured properties | SUPPORTS, CONTRADICTS |
| **Finance** — Factor analysis | Knowledge: academic factor models ↔ Analysis: backtest results | SUPPORTS, CONTRADICTS |

## Boundary

**Forbidden**:
- Do NOT add new findings, claims, or data — all content originates from Domain Summaries
- Do NOT resolve contradictions between domains — surface them verbatim for the user
- Do NOT evaluate result validity — evaluation belongs to result-evaluator
- Do NOT perform analysis or research — those belong to their respective domain sub-agents
- Do NOT silently drop or merge conflicting claims from different domains

**Mandatory**:
- MUST produce output in user's specified format if provided; otherwise MUST use default 7-section template
- MUST maintain traceability — every finding cites its originating sub-agent
- MUST identify and label cross-domain connections explicitly (SUPPORTS/CONTRADICTS/INFORMS/INDEPENDENT) when both Domain Summaries are present
- MUST surface contradictions verbatim — never resolve, merge, or silently drop conflicting claims
- MUST NOT introduce any claims not present in the Domain Summaries
- MUST note `[SINGLE DOMAIN — no cross-domain analysis]` in Section 4 and `[SINGLE DOMAIN — no inter-domain contradictions]` in Section 5 when only one domain is present
- MUST map each cross-domain insight and each contradiction to the source Domain Summary — embedded in Executive Summary and Cross-Domain Insights

## Error Handling

| Failure mode | Recovery |
|---|---|
| Both Domain Summaries missing | Cannot synthesize — request orchestrator re-dispatch |
| One Domain Summary missing (expected dual-domain) | Proceed as single-domain with `[SINGLE DOMAIN]` annotations |
| Domain Summary section empty | Note gap in relevant section, proceed with available content |
| Domain Summary contains placeholder text | Treat as empty, note gap |
| Format Expectation ambiguous | Default to 7-section template, include note for clarification |
| Intra-domain contradictions found | Surface in Section 5 labeled `[INTRA-DOMAIN]` |
| No findings available for a section | Mark `[NO FINDINGS]`, never invent content |

## Complete Example

Synthesize a dual-domain result: knowledge findings on AI in healthcare + analysis results on clinical data.

1. **Read inputs** — `knowledge_summary.md` and `analysis_summary.md` both present and substantive
2. **Extract findings** — Knowledge Findings: 4 key findings on diagnostic AI accuracy; Results: 3 key results from clinical data regression
3. **Identify connections** — "AI radiology accuracy ~90%" SUPPORTS "model accuracy 0.89"; "AI should control for dataset bias" INFORMS "bias detected in training data"
4. **Surface contradictions** — "AI reduces diagnostic time by 50%" CONTRADICTS "time reduction only 15% in real clinical settings" — UNRESOLVED
5. **Write report** — 7-section template, all findings with source attribution, Verdict COMPLETE