「annotation」の検索結果

Retrieve protein sequences, annotation, and structures from UniProtKB, the RCSB PDB, and AlphaFold DB. Use this skill to resolve a gene or protein name to a UniProt accession, pull sequences and FASTA files, find binding sites and domains, search the PDB by UniProt accession, sequence, ligand, or text, download mmCIF/PDB coordinates and biological assemblies, fetch AlphaFold models with their pLDDT confidence, and check whether a structure is actually usable before docking or simulating it. Also trigger on UniProt accessions, PDB ids, rest.uniprot.org, search.rcsb.org, files.rcsb.org, alphafold.ebi.ac.uk, id mapping, SEQRES, or missing residues.

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Reorganize label-heavy or netlist-like electronic schematics into human-readable functional diagrams with visible local wiring while preserving proven connectivity. Use for schematic readability correction, overlapping wires or symbols, visually floating connectors or support logic, functional-sheet restructuring, bus presentation, layout annotations, or multi-EDA handoff across KiCad, Altium, EasyEDA, EAGLE/Fusion, gEDA/Lepton, SPICE/netlist, and PDF/image sources.

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Design data models with Pydantic schemas, comprehensive validation rules, type annotations, and relationship mappings.

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Use when designing, redrawing, or validating research-paper figures and tables, including Matplotlib plots, LaTeX tables, benchmarks, captions, legends, annotations, color, and typography. Preserves exact evidence and checks rendered PDFs for clipping, overlap, and readability.

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Review AI Gene Review pull requests and curation changes for GO term quality, evidence support, core function identification, and annotation action justification. Use for PR review comments, review follow-up automation, and QA of gene review YAML.

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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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Review computational protein or gene function predictions and fill PredictionReview YAML files using the COR/CNN/LSP/UNC/PLI/NPI/REP biological-validity taxonomy. Use for ProtNLM, DeepECTF, BioReason/GO-GPT, InterPro2GO, PANTHER/IBA, CLEAN, GloEC, MAPred, ProteinInfer, or other predicted EC/GO annotations, including audits of the evidence and reasoning in existing prediction reviews.

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Reverse engineers binaries with Binary Ninja using its analysis stack and Python API to enumerate functions, navigate IL levels (LLIL/MLIL/HLIL), and automate annotation and extraction. Activates for requests to reverse a binary with Binary Ninja, script the Binary Ninja API, or work with its intermediate languages.

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Before designing, training, or auditing ANY model that replicates human-annotated labels, audit the annotation protocol's INPUT — the exact document/evidence the human labelers consulted — and give the model that same input. Use when: (1) designing a classifier/LLM extractor whose target is a hand-coded label set, (2) a label-replication model shows low recall concentrated in a label subset and the diagnosis on offer is "the label's information is not in the features", (3) reviewers propose construct splits (e.g. "designation vs record-evident"), adjudication sittings, or per-domain stop rules to explain residual disagreement with gold, (4) validating an extraction pipeline against labels transcribed from a source document. Symptom of the underlying failure: elaborate theory accumulates to explain why gold is "partially unpredictable" when the model was simply never shown the document the annotators read.

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Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models, cross-reference with clinical trials and drug databases, or conduct any disease-focused, pathology-driven, or clinical variant interpretation workflow. Covers the full pipeline from disease-tissue mapping through GWAS variant annotation, heritability enrichment, cancer epigenomics, drug target identification, and clinical trial cross-referencing. Integrates ENCODE with Open Targets, PubMed, ClinicalTrials.gov, and bioRxiv.

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Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

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Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and which transcription factors control them?" by layering expression, chromatin accessibility, histone marks, and TF binding data. Follows the Mawla et al. 2023 framework for cross-assay integration of islet cell type-specific data. Handles chromatin state annotation (ChromHMM), enhancer-gene linkage, TF motif enrichment, and cell type-specific regulatory element identification. Use for ANY multi-omic analysis, enhancer discovery, regulatory network construction, or epigenomic characterization using ENCODE data.

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Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs bulk profiles. Covers platform differences (10X Chromium, Smart-seq2, Drop-seq), quality limitations of single-cell data, multimodal integration (RNA+ATAC), and cross-study reproducibility concerns. Also use for cell type annotation, gene detection limits, dropout artifacts, and single-cell data structure in ENCODE.

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Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with confidence annotations. Handles cross-lab batch effects, broad vs narrow marks, and ENCODE blocklist filtering.

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Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinical significance, pathogenic variant, variant classification, clinical variant, disease variant, VUS, benign, likely pathogenic.

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Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, genome-wide association, SNP association, trait association, GWAS Catalog, disease association, risk variant, lead SNP, LD proxy.

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Smart code scanner that detects Spring Boot patterns and routes to appropriate skills. Use when editing Java or Kotlin files in Spring Boot projects, working with pom.xml/build.gradle containing spring-boot-starter, or when context suggests Spring Boot development. Detects annotations (@RestController, @Entity, @EnableWebSecurity, @SpringBootTest) to determine relevant skills and provides contextual guidance. Uses progressive automation - auto-invokes for low-risk patterns (web-api, data, DDD), confirms before loading high-risk skills (security, testing, verify).

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Design annotation pipelines that produce reliable training labels — guidelines, agreement measurement, and quality control.

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Label smarter, not more — pick the most informative examples for annotation to maximize model gains per label.

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Documenting As-Is and To-Be business processes for a Salesforce project as swim-lane diagrams — one lane per actor, explicit decision points, parallel and exception/sad paths, and per-step automation-tier annotations that drive downstream build decisions. Trigger keywords: As-Is To-Be salesforce process, swim lane salesforce, business process map, automation candidate identification, sad path documentation, process actor mapping, manual residue. NOT for Opportunity stage and exit-criteria design — use admin/sales-process-mapping. NOT for picking Flow vs Apex for one requirement — use admin/process-automation-selection.

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The Kotlin target-language layer for Skmtc generators (@skmtc/lang-kotlin): base factories, KtSnippet, the seven entity kinds, packages-from-paths imports, the head+value render model, KtAnnotation and the composition classes, sanitization and @SerialName placement, plus the current-API worked example (the shipped gen-kotlin-* packages are API-stale — do not copy their call shapes). Use ALONGSIDE skmtc-generator whenever a generator emits Kotlin. Headings mirror skmtc-lang-typescript.

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Remove AI-generated code smells (slop) from branch changes or an explicit file list. Locks behavior with regression tests FIRST, then runs categorized cleanup via parallel `deep` agents in batches of 5, then verifies with quality gates. Covers 10 slop categories including performance equivalences, excessive complexity (object annotations, if/elif variant chains), and oversized modules (250+ pure LOC with mandatory modular refactoring). MUST USE when the user asks to "remove slop", "clean AI code", "deslop", "clean up AI-generated code", "remove AI slop", or wants to clean up AI-generated patterns from recent changes. Triggers - "remove ai slops", "clean ai code", "deslop", "cleanup AI generated", "remove AI slop", "clean up AI-generated code", "strip slop", "ai-slop cleanup".

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Use when writing Playwright tests, fixing flaky tests, debugging failures, implementing Page Object Model, configuring CI/CD, optimizing performance, mocking APIs, handling authentication or OAuth, testing accessibility (axe-core), file uploads/downloads, date/time mocking, WebSockets, geolocation, permissions, multi-tab/popup flows, mobile/responsive layouts, touch gestures, GraphQL, error handling, offline mode, multi-user collaboration, third-party services (payments, email verification), console error monitoring, global setup/teardown, test annotations (skip, fixme, slow), test tags (@smoke, @fast, @critical, filtering with --grep), project dependencies, security testing (XSS, CSRF, auth), performance budgets (Web Vitals, Lighthouse), iframes, component testing, canvas/WebGL, service workers/PWA, test coverage, i18n/localization, Electron apps, or browser extension testing. Covers E2E, component, API, visual, accessibility, security, Electron, and extension testing.

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Quantitative agent evaluation using 4-metric framework (correctness/step_ratio/tool_call_ratio/latency_ratio) with ideal trajectory annotation and capability-categorical taxonomy. Use when measuring agent efficiency, comparing agent variants, or gating new agents through correctness→efficiency phases. Complements harness-eval (SE benchmarks) and evaluator-optimizer (qualitative rubric).

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