| name | lifesciences-reporting |
| description | Formats professional reports from Fuzzy-to-Fact pipeline output using domain-specific templates, claim-level evidence grading, and standardized citations. This skill should be used when the user asks to "format a report", "summarize findings", "grade evidence", "write up results", or mentions report templates, confidence scoring, evidence levels, or presentation of pipeline output. |
Life Sciences Reporting
Format professional reports from Fuzzy-to-Fact pipeline output using domain-specific templates.
Grounding Rule
ALL claims in the report MUST trace to specific tool calls from Phases 1-5.
Do NOT introduce new entities, drug names, gene functions, or trial IDs from
training knowledge during report generation. The report SYNTHESIZES existing
Phase 1-5 output — it does NOT generate new facts.
If a Phase returned no results for a section, report "No data retrieved" with
the tool name that was called. Do NOT fill gaps from memory.
Scope
In scope: Template selection, evidence grading, source attribution, formatting, synthesis of Phase 1-5 output.
Out of scope: API calls, data retrieval, new entity resolution, creating new Fuzzy-to-Fact phases, modifying other skills. This skill consumes pipeline output — it does not produce it.
Template Decision Tree
Route the user's query to the appropriate template using this priority order. If multiple categories apply, combine sections from relevant templates (see Multi-Template Combination below).
1. HOW does a drug work? --> Template 6: Mechanism Elucidation
2. Drug SAFETY or off-targets? --> Template 7: Safety / Off-Target
3. REGULATORY milestones or filings? --> Template 5: Regulatory / Commercialization
4. FIND or REPURPOSE drugs? --> Template 1: Drug Discovery / Repurposing
5. GENE/PROTEIN interactions? --> Template 2: Gene / Protein Network
6. CLINICAL TRIALS broadly? --> Template 3: Clinical Landscape
7. VALIDATE a target? --> Template 4: Target Validation
8. Multiple categories? --> Combine sections from relevant templates
Competency Question Coverage
| Template | Covers CQs | Primary Signal |
|---|
| 1. Drug Discovery / Repurposing | cq2, cq4, cq7, cq8, cq10, cq14 | "repurpose", "find drugs", "therapeutic strategies" |
| 2. Gene / Protein Network | cq3, cq5, cq6 | "interact", "regulate", "network", "cascade" |
| 3. Clinical Landscape | cq12 | "clinical trials broadly", "health priorities" |
| 4. Target Validation | cq11 | "validate target", "druggability", "tractability" |
| 5. Regulatory / Commercialization | cq13, cq15 | "commercialization", "regulatory", "FDA", "EMA" |
| 6. Mechanism Elucidation | cq1 | "mechanism", "how does X work" |
| 7. Safety / Off-Target | cq9 | "off-target", "safety", "cardiotoxicity", "selectivity" |
Template 1: Drug Discovery / Repurposing
Use for: cq2 (FOP repurposing), cq4 (AD therapeutics), cq7 (NGLY1 multi-hop), cq8 (ARID1A SL), cq10 (HD novel targets), cq14 (TP53 SL).
## Summary
[Direct answer: what drugs were found and why they are relevant]
## Resolved Entities
| Entity | CURIE | Type | Source |
|--------|-------|------|--------|
| [name] | [CURIE] | Gene/Protein/Disease | [Source: tool(param)] |
## Drug Candidates
| Drug | CURIE | Phase | Mechanism | Target | Evidence Level | Source |
|------|-------|-------|-----------|--------|---------------|--------|
| [name] | [CURIE] | [1-4] | [action] | [gene] | [L1-L4] | [Source: tool(param)] |
## Mechanism Rationale
[For each drug: why this drug targets the disease pathway.
Trace: Drug --[mechanism]--> Target --[pathway]--> Disease]
## Clinical Trials
| NCT ID | Title | Phase | Status | Verified | Source |
|--------|-------|-------|--------|----------|--------|
| [ID] | [title] | [phase] | [status] | [Y/N] | [Source: tool(param)] |
## Evidence Assessment
[Claim-level grades using the Evidence Grading System below]
## Gaps and Limitations
[What was NOT found; which tools returned no results]
Template 2: Gene / Protein Network
Use for: cq3 (AD gene networks), cq5 (MAPK cascade), cq6 (BRCA1 regulatory network).
## Summary
[Direct answer: what network was found and its biological significance]
## Resolved Entities
| Entity | CURIE | Type | Source |
|--------|-------|------|--------|
| [name] | [CURIE] | Gene/Protein | [Source: tool(param)] |
## Interaction Network
| Protein A | Protein B | Score | Type | Direction | Source |
|-----------|-----------|-------|------|-----------|--------|
| [name] | [name] | [0-1000] | [physical/regulatory] | [A->B / bidirectional] | [Source: tool(param)] |
## Hub Genes
| Gene | Degree | Key Interactions | Disease Associations | Source |
|------|--------|------------------|---------------------|--------|
| [name] | [N] | [top partners] | [diseases] | [Source: tool(param)] |
## Pathway Membership
| Pathway | ID | Member Genes from Query | Source |
|---------|-----|------------------------|--------|
| [name] | [WP:ID] | [gene list] | [Source: tool(param)] |
## Network Properties
- Total nodes: [N]
- Total edges: [N]
- Average interaction score: [N]
- Regulatory vs physical: [ratio]
## Evidence Assessment
[Claim-level grades]
## Gaps and Limitations
[Missing interactions, low-confidence edges, unresolved entities]
Template 2 Notes
- Disease CURIE: Not required in Resolved Entities table unless drug/trial discovery was performed
- Pathway Membership: REQUIRED section (use WikiPathways for all core genes)
- Clinical Trials: Only include if relevant to the comparative network question
- Source Attribution: Paraphrasing UniProt function text is acceptable; cite the tool call
Template 3: Clinical Landscape
Use for: cq12 (health emergencies 2026).
## Summary
[Direct answer: what clinical trial patterns were found]
## Phase Distribution
| Phase | Count | Top Conditions | Source |
|-------|-------|---------------|--------|
| Phase 3 | [N] | [conditions] | [Source: tool(param)] |
| Phase 2 | [N] | [conditions] | [Source: tool(param)] |
| Phase 1 | [N] | [conditions] | [Source: tool(param)] |
## Recruiting Trials
| NCT ID | Condition | Intervention | Phase | Sponsor | Source |
|--------|-----------|-------------|-------|---------|--------|
| [ID] | [condition] | [drug/device] | [phase] | [org] | [Source: tool(param)] |
## Therapeutic Trends
| Trend | Trial Count | Representative Trials | Source |
|-------|------------|----------------------|--------|
| [e.g., CAR-T expansion] | [N] | [NCT IDs] | [Source: tool(param)] |
## Evidence Assessment
[Claim-level grades]
## Gaps and Limitations
[Search coverage, date range caveats, missing trial types]
Template 4: Target Validation
Use for: cq11 (p53-MDM2-Nutlin axis).
## Summary
[Direct answer: is this target validated and druggable?]
## Target Profile
| Property | Value | Source |
|----------|-------|--------|
| Gene Symbol | [symbol] | [Source: tool(param)] |
| CURIE | [HGNC:ID] | [Source: tool(param)] |
| Protein | [UniProt ID] | [Source: tool(param)] |
| Function | [text from UniProt] | [Source: tool(param)] |
| Biotype | [protein_coding/etc] | [Source: tool(param)] |
## Disease Associations
| Disease | Score | Evidence Sources | Source |
|---------|-------|-----------------|--------|
| [name] | [0-1] | [genetic, literature, etc] | [Source: tool(param)] |
## Tractability Assessment
| Modality | Label | Value | Source |
|----------|-------|-------|--------|
| Small molecule | [Clinical Precedence/etc] | [score] | [Source: tool(param)] |
| Antibody | [label] | [score] | [Source: tool(param)] |
## Known Drugs
| Drug | Phase | Mechanism | Source |
|------|-------|-----------|--------|
| [name] | [1-4] | [action] | [Source: tool(param)] |
## Interaction Partners
| Partner | Score | Type | Source |
|---------|-------|------|--------|
| [name] | [0-1000] | [physical/regulatory] | [Source: tool(param)] |
## Evidence Assessment
[Claim-level grades]
## Gaps and Limitations
[Missing tractability data, low-confidence associations]
Template 5: Regulatory / Commercialization
Use for: cq13 (high-commercialization trials), cq15 (CAR-T regulatory).
## Summary
[Direct answer: which trials or drugs have highest commercial/regulatory momentum?]
## Resolved Entities
| Entity | CURIE | Type | Source |
|--------|-------|------|--------|
| [name] | [CURIE] | Drug/Trial | [Source: tool(param)] |
## Milestone Timeline
| Trial/Drug | Event | Date/Status | Significance | Source |
|-----------|-------|-------------|-------------|--------|
| [name] | [Phase 3 initiation/BLA filing/etc] | [date] | [first-in-class/etc] | [Source: tool(param)] |
## Competitive Landscape
| Target | Drug | Sponsor | Phase | Status | Source |
|--------|------|---------|-------|--------|--------|
| [target] | [drug] | [company] | [phase] | [recruiting/completed] | [Source: tool(param)] |
## Investment Signals
| Signal | Trial/Drug | Evidence | Source |
|--------|-----------|----------|--------|
| [large enrollment/breakthrough designation/etc] | [name] | [detail] | [Source: tool(param)] |
## Evidence Assessment
[Claim-level grades]
## Gaps and Limitations
[Regulatory data not in ClinicalTrials.gov, proprietary deal data unavailable]
Template 6: Mechanism Elucidation
Use for: cq1 (Palovarotene mechanism for FOP).
## Summary
[Direct answer: by what mechanism does Drug X treat Disease Y?]
## Mechanism Chain
[Narrative tracing the path: Drug --[action]--> Target --[regulation]--> Pathway --[association]--> Disease]
### Step-by-Step
| Step | From | Relationship | To | Evidence | Source |
|------|------|-------------|-----|----------|--------|
| 1 | [Drug] | [agonist/inhibitor] | [Target protein] | [mechanism data] | [Source: tool(param)] |
| 2 | [Target] | [regulates/inhibits] | [Downstream] | [interaction data] | [Source: tool(param)] |
| 3 | [Downstream] | [associated_with] | [Disease] | [association data] | [Source: tool(param)] |
## Supporting Evidence
| Claim | Evidence Level | Sources |
|-------|---------------|---------|
| [Drug is agonist of Target] | [L3] | [Source: tool(param)] |
| [Target regulates Downstream] | [L2] | [Source: tool(param)] |
## Alternative Mechanisms
[Other proposed mechanisms from literature, if retrieved]
## Evidence Assessment
[Claim-level grades]
## Gaps and Limitations
[Missing pathway steps, unconfirmed regulatory direction]
Template 7: Safety / Off-Target
Use for: cq9 (Dasatinib off-target risks).
## Summary
[Direct answer: what are the safety risks of Drug X?]
## Index Compound Profile
| Property | Value | Source |
|----------|-------|--------|
| Drug Name | [name] | [Source: tool(param)] |
| CURIE | [CHEMBL:ID] | [Source: tool(param)] |
| Primary Target(s) | [target list] | [Source: tool(param)] |
| Approved Indication(s) | [diseases] | [Source: tool(param)] |
## Off-Target Hits
| Off-Target | Gene CURIE | Activity (IC50/Ki) | Clinical Consequence | Source |
|-----------|-----------|-------------------|---------------------|--------|
| [protein] | [HGNC:ID] | [nM] | [e.g., cardiotoxicity] | [Source: tool(param)] |
## Selectivity Comparison
| Target | Drug X (IC50) | Comparator Drug (IC50) | Selectivity Ratio | Source |
|--------|--------------|----------------------|-------------------|--------|
| [primary] | [nM] | [nM] | [ratio] | [Source: tool(param)] |
| [off-target] | [nM] | [nM] | [ratio] | [Source: tool(param)] |
## Safety Signals
| Signal | Mechanism | Severity | Frequency | Source |
|--------|-----------|----------|-----------|--------|
| [e.g., QT prolongation] | [hERG inhibition] | [serious] | [common/rare] | [Source: tool(param)] |
## Evidence Assessment
[Claim-level grades]
## Gaps and Limitations
[Missing activity data, untested off-targets, post-market data not available]
Evidence Grading System
Grade each claim individually, then compute an overall report confidence. This prevents inflated "high confidence" when some claims are grounded and others are not.
Evidence Levels
| Level | Range | Name | Criteria |
|---|
| L4 | 0.90-1.00 | Clinical | FDA-approved drug for this indication, OR Phase 2+ trial with published endpoints |
| L3 | 0.70-0.89 | Functional | Multi-database concordance + druggable target + known mechanism of action |
| L2 | 0.50-0.69 | Multi-DB | 2+ independent databases confirm the relationship |
| L1 | 0.30-0.49 | Single-DB | One database source only |
Modifiers
| Modifier | Adjustment | Condition |
|---|
| Active trial | +0.10 | Recruiting trial targets this entity/mechanism |
| Mechanism match | +0.10 | Drug mechanism aligns with disease biology (e.g., inhibitor for gain-of-function) |
| Literature support | +0.05 | PubMed or Entrez links confirm relationship |
| High STRING score | +0.05 | STRING interaction score >= 900 |
| Conflicting evidence | -0.10 | Databases disagree on relationship direction or existence |
| Single source | -0.10 | Only one API returned this data point |
| Unverified ID | -0.15 | CURIE not confirmed via LOCATE step |
| Mechanism mismatch | -0.20 | Drug action contradicts disease biology (e.g., agonist for gain-of-function) |
Grading Procedure
For each claim in the report:
- Identify the base level (L1-L4) from the criteria above
- Apply all applicable modifiers (sum adjustments, clamp to 0.00-1.00)
- Record the final score and justification
For the overall report:
- Compute the median of all claim scores (not the mean — resistant to outliers)
- Report the range (lowest to highest claim score)
- Flag any claim below L1 (0.30) as "Insufficient Evidence"
Worked Example: Venetoclax/BCL2
Claim: "Venetoclax inhibits BCL2 and is approved for CLL"
- Base: L4 (0.90) — FDA-approved drug for this indication
- Modifiers:
- Active trials: +0.10 (multiple recruiting CLL trials found via
clinicaltrials_search_trials)
- Multi-DB: already captured in L4 base
- Final: 0.95 (L4 Clinical)
- Sources:
[Source: opentargets_get_target(ENSG00000171791)], [Source: clinicaltrials_search_trials("venetoclax CLL")]
Claim: "BCL2 interacts with BAX (STRING score 0.999)"
- Base: L2 (0.55) — confirmed by STRING
- Modifiers:
- High STRING score: +0.05 (score >= 900)
- UniProt function text mentions BAX: +0.05 (literature support)
- Final: 0.65 (L2 Multi-DB)
- Sources:
[Source: string_get_interactions(9606.ENSP00000381185)], [Source: uniprot_get_protein(Q07817)]
Source Attribution Standards
Every factual claim must cite the tool call that produced it. Formats:
| Context | Format | Example |
|---|
| MCP tool | [Source: tool(param)] | [Source: hgnc_search_genes("TP53")] |
| Curl | [Source: curl endpoint(param)] | [Source: curl OpenTargets/graphql(knownDrugs, ENSG00000171791)] |
| Multi-source | [Sources: tool1(p1), tool2(p2)] | [Sources: hgnc_get_gene(HGNC:11998), uniprot_get_protein(P04637)] |
| No data | [No data: tool(param) returned error/0] | [No data: chembl_get_compound(CHEMBL3137309) returned 500] |
Formatting Standards
Table Conventions
- CURIE column: always present for entities, using full CURIE format (
HGNC:11998, not 11998)
- Source column: always the rightmost column
- Evidence Level column: use shorthand
L1-L4 in tables, expand in Evidence Assessment section
- Sort drug candidate tables by Phase (descending), then Evidence Level (descending)
- Sort interaction tables by Score (descending)
First-Mention Rule
On first mention of any entity, include both the human-readable name and CURIE:
TP53 (HGNC:11998) encodes the p53 tumor suppressor protein (UniProtKB:P04637).
Subsequent mentions may use the name alone.
Markdown & General
## H2 for major sections, ### H3 for subsections, #### H4 sparingly- Tables for structured data; prose for narrative synthesis
- No emoji; dates in ISO 8601; scores to 2 decimal places; IC50/Ki in nM
- Abbreviations: define on first use, then abbreviate
Common Report Pitfalls
Hallucination Injection
Problem: Reporting fills in "expected" drug names or trial IDs from training knowledge when Phase 4a or 4b returned sparse results.
Prevention: Every row in Drug Candidates and Clinical Trials tables must have a [Source: tool(param)] citation. If no source exists, the row must not appear. Write "No drug candidates retrieved" rather than guessing.
Inflated Confidence
Problem: Assigning L3/L4 evidence to claims supported by a single STRING interaction.
Prevention: Apply grading procedure strictly. A single-database claim is L1 (0.30-0.49) regardless of how "well known" the relationship seems. Modifiers can raise it, but only based on actual tool output.
Wrong Template Selection
Problem: Using Drug Discovery template for a query about gene networks (cq3, cq5, cq6), producing empty Drug Candidates and Clinical Trials sections.
Prevention: Follow the decision tree. If the query mentions "interact", "regulate", "network", or "cascade" without mentioning drugs, use Template 2 (Gene/Protein Network).
Unverified NCT IDs
Problem: Including NCT IDs from Phase 4b search results without Phase 5 verification.
Prevention: The "Verified" column in Clinical Trials tables must reflect Phase 5 output. If Phase 5 was not run, mark as "Unverified" (not "Yes").
Mechanism Mismatch Blindness
Problem: For gain-of-function diseases, including agonists in Drug Candidates without flagging the mechanism conflict.
Prevention: Cross-reference the disease biology (from Phase 2 enrichment) with each drug's mechanism. Flag agonists for gain-of-function diseases with a -0.20 modifier and a note in Gaps and Limitations.
Paraphrasing vs Hallucination Confusion
Problem: Reviewers flag faithful paraphrasing of UniProt function text as "hallucination" because the report text doesn't match verbatim.
Acceptable synthesis (not hallucination):
- UniProt function text paraphrased for readability: "Binds to 3 E-boxes of the E-cadherin/CDH1 gene promoter" → "binds E-boxes in CDH1 promoter"
- Multiple tool outputs synthesized into coherent narrative with all sources cited
- Interpretive claims clearly marked with qualifiers like "[Inferred from...]"
Unacceptable (hallucination):
- Entity names, CURIEs, or NCT IDs not present in tool outputs
- FDA approval years (e.g., "FDA-approved 2021"), prevalence statistics (e.g., ">50%"), or trial outcome numbers without sources
- Mechanistic details that extend beyond what tool output states
Best practice: Add a synthesis disclaimer to reports that paraphrase extensively:
"Mechanism descriptions paraphrase UniProt function text and STRING interaction annotations. All synthesis is grounded in cited tool calls; no entities, CURIEs, or quantitative values are introduced from training knowledge."
Combining Templates Poorly
Problem: Including all sections from two templates, creating a bloated report with redundant entity tables.
Prevention: Share Resolved Entities and Evidence Assessment across templates. Include unique sections from each. See Multi-Template Combination below.
Multi-Template Combination
When a query spans multiple templates (e.g., cq2 involves both Drug Discovery and Mechanism Elucidation), combine them:
Shared Sections (include once)
- Summary
- Resolved Entities
- Evidence Assessment
- Gaps and Limitations
Template-Specific Sections (include from each relevant template)
Take the distinctive sections from each template. Do not duplicate entity tables.
Worked Example: cq2 (FOP Drug Repurposing)
Query: "What drugs targeting the BMP pathway could be repurposed for FOP?"
Templates: Drug Discovery (primary) + Mechanism Elucidation (secondary)
Report structure:
- Summary (shared)
- Resolved Entities (shared)
- Drug Candidates (from Template 1)
- Mechanism Chain (from Template 6 — traces BMP pathway logic)
- Mechanism Rationale (from Template 1 — per-drug justification)
- Clinical Trials (from Template 1)
- Evidence Assessment (shared — covers all claims)
- Gaps and Limitations (shared)
See Also
- lifesciences-graph-builder: Orchestrator for full Fuzzy-to-Fact protocol (produces the data this skill formats)
- lifesciences-genomics: HGNC, Ensembl, NCBI gene resolution (Phase 1-2 data sources)
- lifesciences-proteomics: UniProt, STRING, BioGRID interaction data (Phase 2-3 data sources)
- lifesciences-pharmacology: ChEMBL, PubChem, IUPHAR, Open Targets drug data (Phase 4a data sources)
- lifesciences-clinical: Open Targets associations, ClinicalTrials.gov (Phase 4b-5 data sources)
- lifesciences-crispr: BioGRID ORCS essentiality validation (Phase 3 extension)
