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概要と使いどころ
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
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Statistics, probability, linear algebra, and mathematical foundations for data science
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World-class data science skill for statistical modeling, experimentation, causal inference, and advanced analytics. Expertise in Python (NumPy, Pandas, Scikit-learn), R, SQL, statistical methods, A/B testing, time series, and business intelligence. Includes experiment design, feature engineering, model evaluation, and stakeholder communication. Use when designing experiments, building predictive models, performing causal analysis, or driving data-driven decisions.
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Master discrete mathematics, logic, formal proofs, and computational thinking. Build the mathematical foundation for all computer science.
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Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.
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Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).
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Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.
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Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.
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Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confidence scores, protein interaction partners, or pathway enrichments.
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Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching.
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Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or retrieving functional annotations and publications. Don't use for sequence alignment, protein folding, or sequence similarity search (use specialized skills for those tasks).
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Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.
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Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
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Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find genes associated with a specific pathway/GO term, or explore the Gene Ontology hierarchy. Do not use for querying drug targets (use OpenTargets) or mechanistic signaling pathway diagrams (use KEGG).
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Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not when the user wants to infer protein function based on structural similarity.
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Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.
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Ancient text restoration, attribution, dating, contextualization, and embedding via Aeneas (Latin) / Ithaca (Ancient Greek). Use when asked to "restore", "attribute", "date", "contextualize", "find parallels", "where was it written", "when was it written", "embed", or "analyze" an ancient text, inscription, or epigraphic document, or when the user mentions "Aeneas", or "Ithaca".
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Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.
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Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.
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Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
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Query the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations, and keywords. Use when searching academic papers, resolving DOIs, downloading open-access PDFs, finding an author's publications, aggregating bibliometric data (citation counts, h-index, impact factor), exploring the research taxonomies, or performing DOI lookups.
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Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.
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Score, annotate, and analyze the functional impact of genetic variants using AlphaGenome Variant Impact (AVI) scores. Query variants in chr:pos:ref>alt format, annotate VCF/tabular callsets, perform saturation mutagenesis window scans (1-based closed chr:start-end), and extract GENCODE v46 GTF gene/exon/junction coordinates all via the AlphaGenome Atlas API.
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Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene symbols to JASPAR Matrix IDs, or getting TF metadata. Supports multiple output formats (MEME, TRANSFAC, PFM, JASPAR, YAML).
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