Skill rating

Ancient text restoration, attribution, dating, contextualization, and embedding via Aeneas (Latin) / Ithaca (Ancient Greek). Use when asked to "restore", "attribute", "date", "contextualize", "find pa

Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).

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

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 wit

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 mechan

Distills a completed user workflow or interaction into a reusable agent skill. Use when the user asks to turn their workflow, interaction, or multi-step process into a skill, or when they say "make th

Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure dis

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,

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 ho

Constructs deep-links and URLs for the AlphaGenome Atlas website. Supports generating single-variant exploration links (1-based chr:pos:ref>alt), genomic locus views (1-based closed chr:start-end), ca

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,

Search for scientific papers, preprints, and publications on arXiv. Extract metadata, abstracts, and download full-text PDFs or HTML versions of papers. Use when the user asks to find research papers,

Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when

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

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

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

Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic var

Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP).

Query, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data. Use for FDA adverse events, reca

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.

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/FAS

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-func

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 sym

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, confi

Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif,

Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Use when analyzing whether genomic variants or regions are evolut

Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rs

Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure simi

Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search fo

Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to dis

Search Europe PMC for scientific literature and download open-access full texts and PDFs. Retrieve full-text XML/plain text by PMCID, get citation lists and bibliography.

Browse, filter, and download life sciences, biology, and medical preprints from bioRxiv and medRxiv. Supports fetching paper metadata by DOI, and browsing by date range with category and keyword filte

Checks whether the uv Python package manager is installed and installs it if missing. Ensures uv is on PATH. Use when another skill requires uv as a prerequisite.

Instructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.

Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or retrieving functional annotations and publica

Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. In

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

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 s

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.