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Found 21 Skills
Regulatory variant interpretation -- GWAS association lookup, eQTL analysis, chromatin state annotation, regulatory element overlap, and trait ontology resolution. Connects GWAS Catalog, GTEx, ENCODE, RegulomeDB, OpenTargets, OLS ontology, and Ensembl regulatory features. Use when users ask about non-coding variants, GWAS hits, eQTLs, regulatory elements, enhancer/promoter variants, or trait-associated SNPs.
Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, ZINC, BindingDB), materials (Materials Project, COD), biology/genomics (Reactome, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, BioGRID, Gene Ontology, dbSNP, gnomAD, ENCODE, Human Protein Atlas, Human Cell Atlas), disease/clinical (COSMIC, Open Targets, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, World Bank, US Treasury), demographics (US Census, Eurostat, WHO). Use when looking up compounds, genes, proteins, pathways, variants, clinical trials, patents, economic indicators, or any public database API query.
Parse, navigate, and query materials science ontology structures — browse class hierarchies, inspect individual classes and their properties, look up object and data property definitions with domain/range, search for ontology terms by keyword, and parse or summarize raw OWL/XML files. Currently supports CMSO and ASMO; the broader OCDO ecosystem (CDCO, PODO, PLDO, LDO) is planned. Use when exploring what classes or properties an ontology provides, finding the right CMSO term for a crystal structure or simulation concept, understanding parent-child class relationships, or onboarding to an unfamiliar materials ontology, even if the user only says "what ontology terms describe my FCC copper simulation" or "show me the CMSO class hierarchy."
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
Expert in aggregating, processing, and synthesizing information from multiple sources into coherent insights. Use when building knowledge graphs, ontologies, RAG systems, or extracting insights across documents. Triggers include "knowledge graph", "ontology", "synthesize information", "GraphRAG", "insight extraction", "cross-document analysis".
Typed knowledge graph for structured agent memory and composable skills. Use when creating/querying entities (Person, Project, Task, Event, Document), linking related objects, enforcing constraints, planning multi-step actions as graph transformations, or when skills need to share state. Trigger on "remember", "what do I know about", "link X to Y", "show dependencies", entity CRUD, or cross-skill data access.
Use when designing database schemas, need to model domain entities and relationships clearly, building knowledge graphs or ontologies, creating API data models, defining system boundaries and invariants, migrating between data models, establishing taxonomies or hierarchies, user mentions "schema", "data model", "entities", "relationships", "ontology", "knowledge graph", or when scattered/inconsistent data structures need formalization.
Generates hierarchical knowledge graphs via Recursive Pareto Principle for optimised schema construction. Produces four-level structures (L0 meta-graph through L3 detail-graph) where each level contains 80% fewer nodes while grounding 80% of its derivative, achieving 51% coverage from 0.8% of nodes via Pareto³ compression. Use when creating domain ontologies or knowledge architectures requiring: (1) Atomic first principles with emergent composites, (2) Pareto-optimised information density, (3) Small-world topology with validated node ratios (L1:L2 2-3:1), or (4) Bidirectional construction. Integrates with graph (η≥4 validation), abduct (refactoring), mega (SuperHyperGraphs), infranodus (gap detection). Triggers: 'schema generation', 'ontology creation', 'Pareto hierarchy', 'recursive graph', 'first principles decomposition'.
Create production-ready skills from expert knowledge. Extracts domain expertise and system ontologies, uses scripts for deterministic work, loads knowledge progressively. Use when building skills that must work reliably in production.