stanfish06/skillquarium - Page 2

claw-metagenomics

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

alphafold-skill

Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries

bindingdb-skill

Submit compact BindingDB REST API requests for ligand-target binding lookups by PDB, UniProt, or similarity search. Use when a user wants concise BindingDB summaries; save raw payloads only on request.

biobankjapan-phewas-skill

Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant

biorxiv-skill

Submit compact bioRxiv and medRxiv API requests for details, publication-linkage, and DOI lookups. Use when a user wants concise preprint metadata summaries

biostudies-arrayexpress-skill

Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries

cbioportal-skill

Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries

cellxgene-skill

Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries

chembl-skill

Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL summaries

citation-management

Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. Use when you need to find papers, verify citation information,…

clinvar-variation-skill

Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping

database-lookup

Query documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when a scientific, regulatory, financial, or other database-backed fact must be retrieved reproducibly from a named source rather than inferred from…

efo-ontology-skill

Submit compact EFO OLS4 requests for search, term lookup, children, and descendants. Use when a user wants concise EFO resolution or ontology-expansion summaries

encode-skill

Submit compact ENCODE REST API requests for object lookups, portal-style search, and metadata retrieval. Use when a user wants concise ENCODE summaries

ensembl-skill

Submit compact Ensembl REST API requests for lookup, overlap, cross-reference, and variation endpoints. Use when a user wants concise Ensembl summaries

epigraphdb-skill

Submit compact EpiGraphDB API requests for ontology, literature, MR, gene-drug, and support-path evidence. Use when a user wants concise EpiGraphDB summaries

eqtl-catalogue-skill

Submit compact eQTL Catalogue API requests for association retrieval and documented metadata endpoints. Use when a user wants concise public eQTL Catalogue summaries

eva-skill

Submit compact EVA REST requests for species metadata and archived variant lookups. Use when a user wants concise European Variation Archive summaries

gwas-catalog-skill

Submit compact GWAS Catalog REST API v2 requests for studies, associations, SNPs, EFO traits, genes, publications, loci, and metadata. Use when a user wants concise GWAS Catalog summaries

hmdb-skill

Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries

human-protein-atlas-skill

Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups. Use when a user wants concise Human Protein Atlas summaries; save raw JSON or HTML only on request.

ipd-skill

Submit compact IPD REST requests for HLA allele and cell-level metadata using the public IPD query API. Use when a user wants concise IPD summaries; save raw JSON or text only on request.

metabolights-skill

Submit compact MetaboLights requests for study discovery and study-level metabolomics metadata. Use when a user wants concise MetaboLights summaries

mgnify-skill

Submit compact MGnify API requests for microbiome studies, samples, and biome metadata. Use when a user wants concise MGnify summaries

paper-lookup

Search 10 academic literature APIs for papers, preprints, citations, and open-access full text, and return results with reproducible provenance. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall.…

pharmgkb-skill

Submit compact PharmGKB API requests for genes, variants, clinical annotations, dosing guidelines, and search. Use when a user wants concise PharmGKB summaries

polars-bio

High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.

pride-skill

Submit compact PRIDE Archive API requests for proteomics project discovery and project-level metadata. Use when a user wants concise PRIDE summaries

proteomexchange-skill

Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries

pubchem-pug-skill

Submit compact PubChem PUG REST requests for compound properties, descriptions, assay summaries, and substance metadata. Use when a user wants concise PubChem summaries

query-alphafold

Query AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".

quickgo-skill

Submit compact QuickGO requests for GO terms, annotations, and ontology traversal. Use when a user wants concise QuickGO summaries

rcsb-pdb-skill

Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request.

reactome-skill

Submit compact Reactome ContentService requests for pathway, event, participant, search, and diagram-related data. Use when a user wants concise Reactome summaries

rhea-skill

Submit compact Rhea reaction search requests for biochemical reactions and reaction IDs. Use when a user wants concise Rhea summaries

rnacentral-skill

Submit compact RNAcentral API requests for RNA entry browsing, single-entry lookup, and cross-reference retrieval. Use when a user wants concise RNAcentral summaries

string-skill

Submit compact STRING API requests for network, interaction partner, and enrichment endpoints. Use when a user wants concise STRING summaries

uniprot-skill

Submit compact UniProt REST API requests for UniProtKB, UniRef, UniParc, and FASTA stream endpoints. Use when a user wants concise UniProt summaries; save raw JSON or FASTA only on request.

mendelian-randomisation

Two-sample Mendelian Randomisation from GWAS summary statistics with IVW, MR-Egger, weighted median/mode, and full sensitivity analysis (Cochran Q, Egger intercept, Steiger, F-statistic, leave-one-out).

technology-selection

Guides technology selection and implementation of AI and ML features in .NET 8+ applications using ML.NET, Microsoft.Extensions.AI (MEAI), Microsoft Agent Framework (MAF), GitHub Copilot SDK, ONNX Runtime, and OllamaSharp. Covers the full spectrum from…