「ontology」の検索結果

Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifiers via Identifiers.org, maps lab shorthand with ZOOMA, and builds Ontobee term pages. Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or deciding HPO vs HP. Triggers include "ontology term", "ontology ID", "CURIE", "controlled vocabulary", "UBERON", "CL:", "MONDO", "HPO", "EFO", "ChEBI", "NCBITaxon", "GO term", "PATO", "Zooma", "Bioregistry", "Identifiers.org", "Ontobee", "annotate this tissue/cell type/disease", and any request to emit or verify an identifier shaped like PREFIX:0001234.

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Plan and diagnose FIPA-style ontology-service interactions while keeping declared ontology relations, provider capability, and application authorization separate. NOT for treating an ontology mapping as provider authority or guaranteed interoperability.

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Model and publish semantic definitions in Auto Ontology. Use for terms, relationships, measures, imports, and governed results—not deployment or querying.

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Set up or troubleshoot the Auto Ontology runtime. Use for Helm (the official install), Docker Compose, developer setup, and MCP connection to an existing deployment.

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Query Auto Ontology and validate generated SQL, rows, and answers. Use for MCP or REST access, readiness, authentication, conversations, and grounded questions.

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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.

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Manages Fabric IQ Ontology items, including entity and relationship types, data bindings, and definition updates, plus schema, lineage, grounding, and graph-walk exploration. Use for ontology modelling and traversal. For natural-language questions over a Power BI report use fabriciq.

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

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Agent A5 - Paradigm & Worldview Advisor - Philosophical foundations for research design. Covers ontology, epistemology, axiology, and methodology alignment. Use when: establishing philosophical foundations, justifying methodological choices, writing positionality statements Triggers: paradigm, 패러다임, ontology, epistemology, worldview, 세계관, philosophical foundations, 철학적 기초

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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).

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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

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Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nomenclature or gene coordinates. Use for QTL support, cross-strain comparison, mouse model selection, and ontology-driven phenotype discovery. Use monarch-database for disease-gene-phenotype knowledge graphs; ensembl-database for mouse genome annotations.

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Guide for annotating ENCODE peaks with genomic features using ChIPseeker and GREAT. Use when users need to assign peaks to genes, determine genomic feature distribution (promoter, intron, intergenic), or perform gene ontology enrichment of peak-associated genes. Trigger on: peak annotation, ChIPseeker, GREAT, peak to gene, genomic feature, promoter enrichment, gene ontology, peak distribution, TSS distance, nearest gene.

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Framework for coordinating meaning across autonomous agents that use different conceptual models, vocabularies, and knowledge representations. Treats ontologies as first-class negotiable resources rather than hardcoded implementation details.

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METAINFORMANT rules for directory src/metainformant/ontology/query. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory src/metainformant/ontology/workflow. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory src/metainformant/ontology/annotation. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory src/metainformant/ontology/core. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory src/metainformant/ontology/pathway_enrichment. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory src/metainformant/ontology/visualization. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory src/metainformant/ontology. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory scripts/ontology. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory examples/ontology. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory docs/ontology. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。