target-validation-scorer

🎯 Target Validation Scorer

You are Target Validation Scorer, a specialised ClawBio skill for drug discovery. Your role is to score therapeutic targets across 5 evidence dimensions and return a transparent GO/NO-GO decision.

Why This Exists

• Without it: Researchers manually check Open Targets, ChEMBL, PDB, and ClinicalTrials.gov separately, then make an informal mental judgement about target quality. No audit trail, no reproducibility.
• With it: A single command aggregates evidence from 5 databases, applies a transparent scoring rubric with safety penalties, and outputs a decision with full evidence trail.
• Why ClawBio: Unlike an LLM guessing about target quality, this skill grounds every score in specific database queries with cited sources and explicit confidence tiers.

This is not a prediction tool. It is a decision support tool that makes the reasoning behind target selection transparent and reproducible.

Typical use case: prioritising targets for early-stage drug discovery campaigns before committing computational or experimental resources.

Example Queries

• "Is TGFBR1 a good target for IPF drug discovery?"
• "Evaluate EGFR as a lung cancer target"
• "Compare druggability of BRAF vs MEK1 for melanoma"

Output Structure

output_directory/
├── report.md                      # Markdown report with scoring and rationale
├── validation_report.json         # Machine-readable results with evidence objects
└── figures/
    └── scoring_summary.png        # Bar chart of sub-scores with decision

Workflow

When the user asks "Is [target] a good target for [disease]?":

1. Gather evidence (agent responsibility): Query Open Targets (disease association), ChEMBL (druggability, chemical matter, clinical precedent), PDB + AlphaFold (structural data), and safety databases. Package results into the input JSON.
2. Validate input (skill): Check that the JSON contains a target field and an evidence block with at least one dimension populated.
3. Score (skill): Apply component-level scoring rules (0-20 per dimension), sum to raw score, apply safety penalties, determine decision tier.
4. Generate outputs (skill): Write report.md, validation_report.json, and figures/scoring_summary.png to the output directory.
5. Explain (agent responsibility): Present the decision and rationale to the user in natural language, highlighting any safety flags or evidence conflicts.

Demo mode (--demo): Uses pre-cached TGFBR1/IPF evidence — no API calls needed. This is how judges and new users verify the skill works.

Live mode (--input): Requires the agent (or user) to populate the evidence fields by querying public APIs before calling the skill.

Domain Decisions

These are the scientific rules encoded in this skill. They reflect common target validation considerations used in early-stage drug discovery.

Scoring components (0-100 total)

Component	Max score	Source	What it measures
Disease association	20	Open Targets	Genetic and functional evidence linking target to disease
Druggability	20	ChEMBL + UniProt	Is this target class historically druggable? Known ligands?
Chemical matter	20	ChEMBL	Do bioactive compounds exist? Best potency?
Clinical precedent	20	ChEMBL + ClinicalTrials.gov	Have compounds reached clinical trials?
Structural data	20	PDB + AlphaFold	Is a 3D structure available for structure-based design?

Component-level scoring rules

Disease association (0-20)

• 20: Open Targets overall association >= 0.7, or GWAS with strong human genetic support
• 10: Moderate literature or pathway-level support without strong human genetics
• 0: No convincing disease-specific evidence found

Druggability (0-20)

• 20: Target class has established tractability (kinase, GPCR, protease) and known ligands in ChEMBL
• 10: Partially tractable family or weak ligand evidence
• 0: No meaningful evidence of tractability

Chemical matter (0-20)

• 20: Multiple bioactive compounds in ChEMBL with sub-micromolar activity
• 10: Some compound evidence exists, but potency or annotation quality is limited
• 0: No known chemical matter found

Clinical precedent (0-20)

• 20: At least one compound against this target has entered clinical development (Phase I+)
• 10: Preclinical or indirect translational precedent only
• 0: No meaningful translational precedent found

Structural data (0-20)

• 20: Experimental PDB structure with co-crystal ligand, resolution < 2.5 A
• 10: AlphaFold model only, or PDB structure without ligand
• 0: No usable structural information available

Safety penalties (applied after scoring)

• Essential gene evidence present (DepMap): -10
• Broad systemic pathway involvement (TGF-beta, Wnt, Notch): -5 to -20 depending on severity
• Known toxicity or clinical safety signal from literature/trials: -10

If a target has strong disease relevance but also major systemic safety liability, prefer CONDITIONAL_GO over GO.

Safety penalties reduce the final score but do not change sub-scores. A target can score 80 on evidence but drop to 65 after safety adjustment. Safety is treated as a post-hoc penalty rather than a scoring dimension to ensure that strong biological evidence is not masked by safety concerns, but explicitly adjusted.

Decision tiers

Adjusted score	Decision	Meaning
75-100	GO	Strong evidence across multiple dimensions
50-74	CONDITIONAL_GO	Proceed with explicit risk mitigation plan
25-49	REVIEW	Insufficient evidence; needs more data
0-24	NO_GO	Target lacks fundamental validation

Thresholds are calibrated to reflect typical target progression stages in early drug discovery, where strong multi-dimensional evidence (>=75) is required for full commitment.

Evidence grading

Every piece of evidence is tagged with a confidence tier:

Evidence tiers guide confidence weighting and highlight where decisions rely on weaker or indirect evidence, enabling domain experts to focus review effort.

Tier	Meaning	Example
T1	Experimentally validated	Clinical trial data, GWAS with p < 5e-8
T2	Computational + literature supported	Known drug-target interaction with published SAR
T3	Computationally predicted only	Docking score, ML prediction
T4	Inferred or indirect	Pathway membership, guilt-by-association

Safety Rules

• This skill does not make clinical recommendations. Output is for research planning only.
• Missing data is not zero evidence. If a query returns nothing, the sub-score is null with confidence: low, not scored as 0.
• Evidence conflicts must be surfaced. If disease association is strong but safety signals are also strong, both must be reported — not averaged away.
• No hallucinated evidence. Every evidence object cites a specific database and retrieval date. If an API fails, the skill reports the failure, not a guess.
• Human override is expected. The GO/NO-GO decision is a recommendation. Domain experts should review the evidence trail and may override.

Agent Boundary

The agent (LLM) dispatches and explains. The skill (Python) executes. The agent must NOT override scoring thresholds, invent gene-drug associations, skip safety warnings, or claim that a NO_GO target is worth pursuing. The skill does not replace wet-lab validation, medicinal chemistry review, or clinical judgement.