'ontology' 검색 결과

Match scientific labels to ontology identifiers, standardized IDs for concepts such as tissues, cell types, and diseases. Checks existing IDs, labels, obsolete terms, and prefixes to support metadata annotation, submission preparation, and table audits.

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• Annotating tissue, cell type, or disease fields with standard IDs
• Auditing metadata tables for incorrect IDs and labels
• Checking obsolete terms and available replacements

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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Look up Gene Ontology terms, which classify gene functions, and their links to gene products through QuickGO. Get concise summaries, explore broader or narrower terms, and save full responses when needed.

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• Looking up GO term details
• Checking GO annotations for a gene product
• Exploring broader and narrower GO terms

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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Search EFO, a structured vocabulary, look up individual terms, and retrieve their immediate children or broader descendants through OLS4. Get concise summaries for term identification and hierarchy exploration, with full responses saved when needed.

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• Find EFO terms related to a search word
• Look up details for a specific EFO term
• Explore immediate children and broader descendants

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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Create signed records for consequential agent actions such as deployments, deletions, and payments. Decide which actions need evidence, record the agent, action, target, and policy, then verify the resulting certificate offline to detect later changes.

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• Creating signed records for production deployments
• Preserving evidence of deletions and payments
• Recording access grants for later review

Query EpiGraphDB for trait classifications, related literature, genetic evidence, and gene–drug relationships. Get concise summaries with limited result counts, or save the complete response when you need the underlying data.

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• Find ontology terms for a disease or trait
• Look up drugs associated with a gene
• Summarize literature and genetic evidence

Clarify the philosophical assumptions behind a research project and check whether they fit the proposed methods. Get a reasoned research stance, draft proposal wording, and guidance for explaining how the researcher's background and values shape the study.

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• Clarifying philosophical foundations for a research proposal
• Explaining why the chosen research methods fit the study
• Drafting a statement about the researcher's position

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/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/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/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/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. 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/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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