bio-database-evidence
Unified biological database evidence owner. Use for gene annotation, variant clinical significance, cancer mutation evidence, GWAS trait associations, pathway mapping, target-disease evidence, protein structures, protein interaction networks, reference single-cell census queries, and cross-database biological ID mapping. Do not use for full single-cell analysis, bulk RNA-seq differential expression, BAM/VCF processing, protein embedding models, metabolic flux modeling, genomic interval ML, or flow-cytometry file parsing.
pinned to #34429a8updated 2 weeks ago
Ask your AI client: “install skills/bio-database-evidence”.
Requires the metahub MCP server installed in your client. Set up MCP.
mh install skills/bio-database-evidencemetahub onboarded this repo on the author's behalf.
If you own github.com/foryourhealth111-pixel/Vibe-Skills on GitHub, claim the listing to take over publishing. Your claim preserves the existing eval history and badges; only the curator label is replaced with verified-publisher on your next publish.
Stars
2,381
Last commit
2 weeks ago
Latest release
published
- #agent-framework
- #agent-skills
- #agentic-coding
- #ai-agents
- #ai-scientist
- #ai-skills
- #ai-workflow
- #automation
- #claude-code
- #codex
- #context-engineering
- #developer-tools
- #llm
- #multi-agent
- #prompt-engineering
- #skills
- #vibe-coding
- #vibecoding
- #workflow-automation
Evaluation report
WarningsAutomated checks the publisher passed at publish time — structure, docs, safety, and whether the artifact behaves as claimed.34429a8· 2 weeks ago
Kind-specific
31Skill: SKILL.md present
found at bundled/skills/bio-database-evidence/SKILL.md · frontmatter source: SKILL.md
Skill: body content present
333 words · 2,511 chars · 4 sections
Skill: triggers declaredwarn
No `trigger` phrases in SKILL.md frontmatter
Add `trigger:` lines so Claude knows when to activate this skill — e.g. `when building MCP servers` or `for diagram creation`.
Skill: allowed-tools scope
no allowed-tools restriction (Claude may use anything)
Release history
1- releasecurrent34429a8warn2 weeks ago
Contents
Use This Skill For
Use this skill when the main task is biological database lookup, annotation, or evidence gathering across one or more biological sources:
- Gene annotation, identifiers, RefSeq, Ensembl IDs, orthologs, VEP, GO, and genomic coordinates.
- Variant clinical significance, VUS interpretation support, ClinVar review status, cancer mutations, and COSMIC evidence.
- GWAS Catalog trait associations, rs IDs, p-values, summary statistics, and genetic epidemiology evidence.
- Pathway mapping, ID conversion, KEGG pathways, Reactome enrichment, disease pathways, and pathway evidence.
- Target-disease association evidence, tractability, safety, known drugs, and Open Targets evidence.
- Protein structure evidence from AlphaFold DB or RCSB PDB, including UniProt IDs, mmCIF/PDB downloads, pLDDT, PAE, and structure metadata.
- Protein-protein interaction evidence, STRING networks, hub proteins, and enrichment evidence.
- Reference single-cell data lookup from CELLxGENE Census when the user asks for census metadata or expression data, not full downstream analysis.
- Cross-database biological ID mapping and evidence tables across multiple resources.
Do Not Use This Skill For
- Single-cell RNA-seq analysis, clustering, UMAP, marker genes, cell annotation, AnnData/h5ad container editing, or scVI/scANVI batch-correction planning. Use
scanpy. - Bulk RNA-seq differential expression. Use
pydeseq2. - BAM, SAM, CRAM, VCF, pileup, coverage, or region extraction as a primary file-processing task.
- deepTools signal-track processing and heatmaps.
- Protein language models, embeddings, inverse folding, or protein-design workflows.
- Constraint-based metabolic modeling, FBA, or metabolic-engineering simulation.
- BED/genomic interval embeddings, genomic-region ML, or gene regulatory network inference.
- FCS or flow-cytometry file parsing.
Workflow
- Identify the biological entity type: gene, transcript, variant, pathway, target, protein structure, protein interaction, trait association, or reference cell population.
- Pick the narrowest source that answers the evidence question.
- Preserve source names, query terms, access dates, identifiers, and API caveats in the result.
- Return evidence in a table when comparing multiple sources.
- State when authentication, license, rate limits, or non-public access restricts a source.
Source Guide
See references/database-evidence-sources.md for source-specific boundaries and query notes.
Reviews
No reviews yet. Be the first.
Related
orchestration-patterns
>
migration-patterns
>
deployment-sop
>
mh install skills/bio-database-evidence