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drug-targets

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Causal drug-target and mechanism gene prioritization from public source records, drugs, drug classes, mechanisms, and candidate gene lists.

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How to use this skill

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Source SKILL.md: https://github.com/exon-research/genomi/blob/HEAD/skills/drug-targets/SKILL.md

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First, summarize what it does, its dependencies, license status if identifiable, and any risks. Show the exact files you propose to add under .agents/skills/drug-targets/. Do not write files or run scripts until I approve.

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Drug Targets

Use this skill for disease-scoped clinical drug-target retrieval, direct drug-target records, PharmaProjects-style target context, ChEMBL mechanism genes, DrugBank target context, or candidate-gene review for a drug, drug class, or mechanism.

Contract

  • Direct drug-target or mechanism evidence outranks target-disease association scores and GWAS-style association.
  • ChEMBL, DrugBank, and PharmaProjects-style records can support direct target claims when the source supports both the gene and the drug, class, mechanism, or indication context.
  • Open Targets association context is useful for review; direct drug-target evidence comes from source records that support the drug, class, or mechanism relationship.
  • Open Targets disease drug and clinical candidate records can retrieve disease-scoped clinical drug-target genes when the drug target comes from a mechanism-of-action row.
  • Treat returned rankings as source evidence. The agent decides whether the drug-target prior matches the question. When using cross-source comparison, use prior_fit before reading a panel as task-relevant and audit decision_evidence before answering.

Tool Flow

  1. phenotype.retrieve_disease_drug_targets retrieves Open Targets clinical drug candidate target genes for a supplied disease anchor.
  2. phenotype.compare_drug_target_evidence compares candidate genes against direct drug-side context: drug, drug class, or mechanism.
  3. If source support is missing, use research.list_sources to choose direct target sources, review them, and store narrow findings with research.record.
  4. Re-run the same selected tool after recording reviewed findings.

Example:

  • phenotype.retrieve_disease_drug_targets with {"disease":"asthma","genes":["ADRB2","IL13"]}
  • phenotype.compare_drug_target_evidence with {"drug_class":"beta agonist","phenotype":"asthma","genes":["ADRB2","IL13"],"source_records":[{"genes":["ADRB2"],"drug_class":"beta agonist","verified_fields":{"genes":["ADRB2"],"drug_class":"beta agonist"},"support_spans":[{"field":"genes","text":"source-backed ADRB2 text"}]}]}

Source Records

Prefer source records with:

  • genes: candidate target genes named by the source.
  • drug, drug_class, indication, or mechanism.
  • source_title, source_url, and source_type.
  • finding or text: short source-backed finding.
  • verified_fields and support_spans showing where the source supports the gene and drug-target or mechanism context.

Answering

Use a direct gene-symbol answer only when reviewed evidence supports the drug-target or mechanism relationship requested by the question. Otherwise state the source gap and summarize the strongest reviewed evidence without presenting it as the final target.

Cross-Capability Synthesis

A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.

Tools

phenotype.compare_drug_target_evidence

Compare candidate genes using direct drug-target or mechanism evidence only.

Use when: Returns direct drug-target, target-mechanism, ChEMBL, DrugBank, or PharmaProjects evidence for candidate genes.

Why necessary: Drug-target questions require direct target/mechanism evidence, which is distinct from disease association evidence.

Result semantics: Returns source-local drug-target evidence only; association-only evidence cannot create direct target support.

phenotype.retrieve_disease_drug_targets

Retrieve disease-scoped clinical drug-target genes from Open Targets drug candidate records.

Use when: Returns Open Targets clinical drug candidate target genes for a supplied disease anchor, with optional gene_membership projection for supplied candidate genes.

Why necessary: Clinical drug-target records answer therapeutic-target membership without implying causal genetics or treatment efficacy.

Result semantics: Returns disease-scoped clinical drug-target records and source-local ordering; the host agent decides how they apply. mode='gene_membership' projects the same source records into per-gene membership booleans and highest observed phase for supplied genes. Does not ingest agent-supplied evidence and does not infer treatment efficacy or final causal-gene answers.