bio-database-evidence
Bio-database-evidence performs biological database lookups and evidence gathering across resources like ClinVar, GWAS Catalog, Open Targets, UniProt, and CELLxGENE Census. Use it when you need gene annotations, variant clinical significance, pathway mapping, protein structures, protein interactions, or cross-database ID mapping rather than computational analysis of sequencing data or molecular modeling.
git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills /tmp/bio-database-evidence && cp -r /tmp/bio-database-evidence/bundled/skills/bio-database-evidence ~/.claude/skills/bio-database-evidenceSKILL.md
# Bio Database Evidence ## 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 1. Identify the biological entity type: gene, transcript, variant, pathway, target, protein structure, protein interaction, trait association, or reference cell population. 2. Pick the narrowest source that answers the evidence question. 3. Preserve source names, query terms, access dates, identifiers, and API caveats in the result. 4. Return evidence in a table when comparing multiple sources. 5. 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.
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
Access real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API. Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market news/sentiment, insider transactions, GDP, CPI, treasury yields, gold/silver/oil prices, Bitcoin/crypto prices, forex exchange rates, or calculating technical indicators (SMA, EMA, MACD, RSI, Bollinger Bands). Requires a free API key from alphavantage.co.
Implement proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design. Use when architecting complex backend systems or refactoring existing applications for better maintainability.
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
Full-stack software development agent for design, implementation, testing, and deployment. Use when the user explicitly asks for end-to-end project creation, feature development, bug fixing, or code refactoring.
Primary retained Python toolkit for molecular biology sequence work. Preferred for sequence manipulation, FASTA/FASTQ/GenBank parsing, Bio.Entrez, BLAST workflows, alignments, structures, and phylogenetics. For biological database evidence lookup, use bio-database-evidence. For single-cell workflows use scanpy. For direct literature REST API, use pubmed-database.