science-skills

In the author's own words, from each skill's SKILL.md — showing the first 30 of 40 files.

• alphafold-database-fetch-and-analyze

  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.

  skills/alphafold_database_fetch_and_analyze/SKILL.md on GitHub (opens in a new tab)

• alphagenome-atlas-website-links

  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), candidate summary tables, and AlphaGenome reference vs. alternate predictions. Use whenever visualizing, exploring, charting, or linking genetic variants and genomic loci on the AlphaGenome Atlas, or w…

  skills/alphagenome_atlas_website_links/SKILL.md on GitHub (opens in a new tab)

• alphagenome-single-variant-analysis

  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 enhanc…

  skills/alphagenome_single_variant_analysis/SKILL.md on GitHub (opens in a new tab)

• alphagenome-variant-impact-score

  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.

  skills/alphagenome_variant_impact_score/SKILL.md on GitHub (opens in a new tab)

• chembl-database

  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.

  skills/chembl_database/SKILL.md on GitHub (opens in a new tab)

• clinical-trials-database

  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.

  skills/clinical_trials_database/SKILL.md on GitHub (opens in a new tab)

• clinvar-database

  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.

  skills/clinvar_database/SKILL.md on GitHub (opens in a new tab)

• credentials

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

  skills/credentials/SKILL.md on GitHub (opens in a new tab)

• dbsnp-database

  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 rsID, returns variant type, gene associations, clinical significance, allele frequencies, and genomic coordinates (GRCh38).

  skills/dbsnp_database/SKILL.md on GitHub (opens in a new tab)

• embl-ebi-ols

  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 for terms, retrieve details, navigate hierarchies (parents, children, ancestors), look up properties and individuals, get autocomplete suggestions, or access ontology metadata and statistics.

  skills/embl_ebi_ols/SKILL.md on GitHub (opens in a new tab)

• encode-ccres-database

  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 you want to query regulatory annotations or raw experimental data across human cell types.

  skills/encode_ccres_database/SKILL.md on GitHub (opens in a new tab)

• ensembl-database

  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). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.

  skills/ensembl_database/SKILL.md on GitHub (opens in a new tab)

• foldseek-structural-search

  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, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.

  skills/foldseek_structural_search/SKILL.md on GitHub (opens in a new tab)

• gnomad-database

  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),…

  skills/gnomad_database/SKILL.md on GitHub (opens in a new tab)

• gtex-database

  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.

  skills/gtex_database/SKILL.md on GitHub (opens in a new tab)

• human-protein-atlas-database

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

  skills/human_protein_atlas_database/SKILL.md on GitHub (opens in a new tab)

• interpro-database

  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. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significantly expands annotation and sequence coverage with deep learning. Includes domain architecture (IDA) s…

  skills/interpro_database/SKILL.md on GitHub (opens in a new tab)

• jaspar-database

  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).

  skills/jaspar_database/SKILL.md on GitHub (opens in a new tab)

• literature-search-arxiv

  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, literature, or specific arXiv IDs.

  skills/literature_search_arxiv/SKILL.md on GitHub (opens in a new tab)

• literature-search-biorxiv

  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 filters. Keyword filtering is local, so date ranges MUST be narrow (1-4 weeks) with a category to prevent timeouts.

  skills/literature_search_biorxiv/SKILL.md on GitHub (opens in a new tab)

• literature-search-europepmc

  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.

  skills/literature_search_europepmc/SKILL.md on GitHub (opens in a new tab)

• literature-search-openalex

  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.

  skills/literature_search_openalex/SKILL.md on GitHub (opens in a new tab)

• ncbi-sequence-fetch

  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.

  skills/ncbi_sequence_fetch/SKILL.md on GitHub (opens in a new tab)

• openfda-database

  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, recalls, labeling, approvals, shortages, 510(k) clearances, NDC lookups, and any FDA safety or regulatory data query across all 28 API endpoints.

  skills/openfda_database/SKILL.md on GitHub (opens in a new tab)

• opentargets-database

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

  skills/opentargets_database/SKILL.md on GitHub (opens in a new tab)

• pdb-database

  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 similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.

  skills/pdb_database/SKILL.md on GitHub (opens in a new tab)

• predictingthepast

  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".

  skills/predictingthepast/SKILL.md on GitHub (opens in a new tab)

• protein-sequence-msa

  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 align…

  skills/protein_sequence_msa/SKILL.md on GitHub (opens in a new tab)

• protein-sequence-similarity-search

  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.

  skills/protein_sequence_similarity_search/SKILL.md on GitHub (opens in a new tab)

• pubchem-database

  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.

  skills/pubchem_database/SKILL.md on GitHub (opens in a new tab)

No skill matches that filter.

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