「ontology」の検索結果

Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and workflow integrations. Use for reproducible biological data curation or a LaminDB lakehouse.

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Mint a tamper-evident, post-quantum-signed receipt for a consequential agent action (deploy, delete, pay, grant-access, model decision) so it can be verified later from the certificate alone. Use when an autonomous agent takes a side-effecting action that may need to be proven later, or when satisfying EU AI Act Article 12 record-keeping. Three decisions: whether an action needs a receipt, minting it, verifying it. Signing is delegated to the open-source OpenAgentOntology package. Not after-the-fact log analysis; not a hosted notary; not a legal opinion.

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

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Submit compact ChEBI 2.0 API requests for chemical search, compound lookup, ontology traversal, and structure metadata. Use when a user wants concise ChEBI summaries

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Submit compact Bgee SPARQL requests for healthy wild-type expression metadata and ontology-aware lookup patterns. Use when a user wants concise Bgee summaries; save raw results only on request.

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

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Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.

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Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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Expert guidance for the Fabric CLI (`fab`) and the Fabric and Power BI REST APIs: workspaces, items, lakehouses, notebooks, pipelines, semantic models, reports, capacities, OneLake, deployment and admin. Also estimates the capacity units (CU) an operation will consume and its impact on the capacity before running it. Automatically invoke whenever the user mentions Fabric, Power BI Service, a Fabric or Power BI workspace, a capacity or F SKU, OneLake, `fab`, or asks to create, run, refresh, schedule, deploy or delete anything in Fabric, including preview items such as Plan, Ontology, Graph or Copilot.

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SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.

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InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell comm

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The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag

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Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.

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Open-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets. Integrates with Nextflow, Snakemake, W&B, scVI. For scRNA-seq use scanpy; for ontology lookups use bionty.

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Map construction data to standard ontologies. Create semantic mappings between different data schemas

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Design and implement Purpose-Based Access Control (PBAC) architecture including purpose ontology definition, policy engine configuration, audit logging of purpose verification at query time, and integration with existing IAM systems. Enforces GDPR Article 5(1)(b) purpose limitation technically.

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The **Coherence Composer** is an epistemological skill that validates structural consistency and explores counterfactual worlds while respecting constraints from both **Commitment Tracker** (ontology) and **Opacity Detector** (epistemology).

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CatColab Ologs (Ontology Logs) - category-theoretic knowledge representation where objects are concepts and morphisms are functional relationships. Foundation for database schemas and conceptual modeling.

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Design, build, evaluate, or teach graph-based systems. Use for knowledge graphs, ontology/schema design, entity/relation/event extraction, entity resolution and fusion, GraphRAG or graph memory, and agent/task dependency graphs with concurrency, joins, failure handling, verification, or human gates.

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Query the Open Targets Platform GraphQL API for target-disease associations, genetic and clinical evidence, tractability and safety liabilities, target prioritisation metrics, known drugs and mechanisms of action, and disease ontology. Use this skill for target identification and validation, target-disease evidence review, druggability assessment, drug repurposing, and resolving gene, disease, and drug names to Ensembl, MONDO, and ChEMBL identifiers. Also trigger when a query mentions Open Targets, platform.opentargets.org, association scores, tractability buckets, or api.platform.opentargets.org.

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Builds and audits a concept-ontology for a regelrecht corpus to decide and verify reference types — cross-law source-binding vs intra-law source-binding vs open-norm leaf vs external-fact leaf — and to catch concept conflation across laws. Core principle: a value's reference type is fixed by WHO derives it, and a binding is sound only when producer and consumer denote the SAME concept; the lexical surface (the word in the text) is not the concept. Detects false friends (one term, different concepts — e.g. a register-based vs a factual "naar de omstandigheden"-based residence/ingezetene concept), orphan plain-params (a value a regulation actually derives, modeled as a brute input), negation/complement re-entry (¬X modeled as an independent leaf next to X), and duplication (one concept re-entered as several independent leafs, losing the single-source-of-truth invariant). Produces a law-level glossary and a stelsel-level concept map with sound same-concept binding edges and flagged lexical-match-but-concept-mismatch edges. Use when deciding whether a value should be cross-law/intra-law/leaf, when the same term means different things across laws, or when a binding might silently conflate concepts.

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Evaluate and review GO-CAM (Gene Ontology Causal Activity Model) activities / annotons — molecular-function typing, has-input, causal relations, complexes, evidence — and check their consistency with gene annotation reviews. Use when reviewing cached GO-CAMs under gocams/, filling a GoCamReview YAML (gocams/<id>/<id>-review.yaml), or grounding a module in GO-CAM models.

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Obsidian Claw is an ontology-building skill that transforms chaotic notes, raw ideas, voice dumps, and meeting transcripts into a structured, interlinked knowledge base inside Obsidian. Use this skill whenever the user wants to: add new notes to their Obsidian vault and auto-link them to existing ones, build a concept graph or knowledge map, surface forgotten related discussions ("you talked about this with investor X 3 months ago"), extract entities and relationships from unstructured text, or turn scattered thoughts into wiki-style atomic notes. Also trigger when the user mentions "second brain", "Zettelkasten", "PKM", "personal knowledge management", "note graph", "knowledge graph", "link my notes", "organize my vault", "connect ideas", or asks Claude to "remember" something across sessions using Obsidian. If the user is doing anything with Obsidian notes and wants intelligence layered on top, use this skill.

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Comprehensive ethics expert covering virtue ethics, deontology, consequentialism, and applied ethical dilemmas

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