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Found 19 Skills
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).
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.
Implements knowledge graphs for AI-enhanced relational knowledge. Covers ontology design, graph database selection (Neo4j, Neptune, ArangoDB, TigerGraph), entity extraction, hybrid graph-vector architecture, query patterns, and AI integration. Use when implementing knowledge graphs, designing ontologies, extracting entities and relationships, selecting a graph database, or building hybrid graph-vector search. Use for knowledge graph, ontology design, entity resolution, graph RAG, hallucination detection. For architecture selection and governance, use the knowledge-base-manager skill. For document retrieval pipelines, use the rag-implementer skill.
Master metaphysics and ontology - the study of being, existence, and fundamental reality. Use for: existence, being, substance, identity, causation, modality, time, universals. Triggers: 'ontological', 'metaphysical', 'what exists', 'substance', 'essence', 'existence', 'being', 'identity', 'persistence', 'causation', 'modality', 'possible worlds', 'universals', 'particulars', 'properties', 'abstract objects', 'time', 'change', 'composition'.
9 knowledge graphs skills. Trigger: building knowledge graphs, connecting concepts, ontology design. Design: graph construction, traversal, and visualization for research knowledge.
Creates, updates, validates, and displays the architectural DNA of a project through two shared documents: docs/specs/architecture.md (technology stack, architectural rules, security constraints, AI guardrails) and docs/specs/ontology.md (domain glossary / Ubiquitous Language). Use BEFORE brainstorm as a project setup step, or at any point in the SDD lifecycle to validate specs/tasks against architecture principles. Triggers on 'create constitution', 'update constitution', 'constitution check', 'validate against constitution', 'project principles', 'architectural guardrails', 'setup project architecture', 'define ontology'.
Use when designing and building knowledge graphs from unstructured data. Invoke when user mentions entity extraction, schema design, LPG vs RDF, graph data model, ontology alignment, knowledge graph construction, or building a KG for RAG. Provides extraction pipelines, schema patterns, and data model selection guidance.
Master African philosophical traditions including Ubuntu, Africana philosophy, and postcolonial thought. Use for: communitarian ethics, personhood, African metaphysics, decolonial philosophy. Triggers: 'Ubuntu', 'African philosophy', 'Africana', 'communitarian', 'postcolonial', 'decolonial', 'sage philosophy', 'ethnophilosophy', 'Negritude', 'African humanism', 'ubuntu ethics', 'communalism', 'African ontology', 'personhood Africa', 'I am because we are'.
This skill should be used when the user asks to "model agent mental states", "implement BDI architecture", "create belief-desire-intention models", "transform RDF to beliefs", "build cognitive agent", or mentions BDI ontology, mental state modeling, rational agency, or neuro-symbolic AI integration. Part of the context engineering skill suite — also activates when the user mentions "context engineering" or "context-engineering" in the context of belief-based agent reasoning.
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.
Specification-first AI development powered by Ouroboros. Socratic questioning exposes hidden assumptions before writing code. Evolutionary loop (Interview → Seed → Execute → Evaluate → Evolve) runs until ontology converges. Ralph mode persists until verification passes — the boulder never stops. Use when user says "ralph", "ooo", "don't stop", "must complete", "until it works", "keep going", "interview me", or "stop prompting".
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.