SessionStart
01Hook Claude Code
Runs when a session starts, running an inline shell check. From ai4curation/ai-gene-review.
24 2d ago A
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original BSD-3-Clause
PostToolUse
02Hook Claude Code
Runs after a tool call finishes for Edit, MultiEdit and Write tool calls, executing validate_ai_review_hook.py and validate_rule_review_hook.py (2 commands). From ai4curation/ai-gene-review.
24 2d ago A
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original BSD-3-Clause
PreToolUse
03Hook Claude Code
Runs before the agent uses a tool for Edit, MultiEdit and Write tool calls, executing protect_files_hook.py and validate_ai_review_pretool_hook.py (2 commands). From ai4curation/ai-gene-review.
24 2d ago A
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copy · 86% BSD-3-Clause
Settings file Claude Code
Agent settings declaring 3 hook events (SessionStart, PostToolUse, PreToolUse).
24 2d ago A
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original BSD-3-Clause
Skill Claude CodeCodex
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.
24 2d ago A 50 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use this agent when you need to systematically review existing GO annotations for a gene and make curation decisions based on literature evidence and functional analysis. This agent should be called after seeding the SPECIES/GENE/GENE-ai-review.yaml file, which seeds each annotation with action: PENDING; these should…
24 2d ago A 72 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use this agent when you need to perform custom bioinformatics analyses on genes or proteins that go beyond standard database lookups. This includes situations where existing domain/family annotations from UniProt are insufficient, when you need to verify dubious annotations, or when you need to perform comparative…
24 2d ago A 78 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Work with BioReason-Pro predictions and reasoning traces for protein function. Use when: comparing BioReason outputs against curated reviews, converting web exports to YAML, reviewing reasoning trace quality, or running the SFT/RL comparison. Triggers: "bioreason", "GO-GPT predictions", "reasoning trace review"…
24 2d ago A 83 tokens
original BSD-3-Clause
boss
09Skill Claude CodeCodex
Use ONLY when the user explicitly asks to orchestrate parallel external agents (Codex or Claude Code) in tmux sessions via tp (tmux-pilot). Or when a user tells you that you're the boss or orchestrator. You can also use this if you are an operclaw agent. NEVER auto-invoke for a generic "do this in parallel" request.…
24 2d ago A 95 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use this agent when you need to synthesize and distill the core functions of a gene from multiple information sources (textual summaries, reviewed annotations, bioinformatics analysis) and populate the corefunctions section of a gene review YAML file. This agent should be called after completing the gene research…
24 2d ago A 81 tokens
original BSD-3-Clause
Skill Claude CodeCodex
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/ /…
24 2d ago A 90 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Curate, review, or repair ai-gene-review ModuleReview YAML documents under modules/, including pathway/module boundary setting, parts and variant modeling, annoton-level molecular functions, representative UniProt/PTN grounding, module deep-research provenance, validation, rendering, and project batch updates.
24 2d ago A 61 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use when running or wiring OpenScientist for AI Gene Review gene-function hypotheses, especially blinded comparisons against local bioinformatics analyses.
24 2d ago C 32 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use this agent when you need to create a pathway summary for a gene after completing the main gene review. This agent should be invoked specifically to generate GENE-pathway.md files that summarize the gene's role in biological pathways with proper citations and mermaid diagrams.
24 2d ago A 58 tokens
original BSD-3-Clause
pm
15Skill Claude CodeCodex
Manage and drive forward an ongoing project, tracked in projects/ dir.
24 2d ago A 15 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use this agent when you need to extract and summarize key findings from scientific references that are relevant to a gene's function. This agent should be used after references have been identified in a gene review to provide detailed supporting evidence from the literature. The agent will look up cached publications…
24 2d ago A 87 tokens
original BSD-3-Clause
Skill Claude CodeCodex
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 DeepECTF, BioReason/GO-GPT, InterPro2GO, PANTHER/IBA, CLEAN, GloEC, MAPred, ProteinInfer, or other predicted EC/GO annotations.
24 2d ago A 83 tokens
original BSD-3-Clause
review
18Skill Claude CodeCodex
Review, either de-novo, or augment the review of an existing one. A list of deep research providers may be specified.
24 2d ago A 28 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use this agent when you need to review UniProt annotation rules (ARBA, UniRule) for quality, biological accuracy, and GO annotation appropriateness. This agent performs comprehensive analysis of rule condition sets, evaluates literature support, assesses taxonomic scope, and recommends curation actions.
24 2d ago A 60 tokens
original BSD-3-Clause
Instructions file GitHub Copilot
Instructions for ai4curation/ai-gene-review, a project described as: Demonstration of AI review of existing functional annotations.
24 2d ago A 5 tokens
copy · 100% BSD-3-Clause
Instructions file CodexOpenCode
Instructions for ai4curation/ai-gene-review, a project described as: Demonstration of AI review of existing functional annotations.
24 2d ago A 4 tokens
copy · 100% BSD-3-Clause
Instructions file
Instructions for ai4curation/ai-gene-review, covering ai instructions for ai-gene-review, project overview, repository layout, gene review guidelines and description field quality.
24 2d ago A 6,666 tokens
original BSD-3-Clause
Plugin Claude Code
Plugin marketplace listing 7 plugins: ontology-access-kit, ai4curation-configuration, run-deep-research, configure-w3id, editing-obo-ontologies.
24 3mo ago A
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Instructions file GitHub Copilot
Copilot instructions for ai4curation/curation-skills, a project described as: Claude skills for a variety of curation and knowledge-based tasks. We currently have 3 skills included, but intend to grow this.
24 3mo ago A 4 tokens