{
  "ok": true,
  "resource": {
    "id": "RES_40398D759800",
    "resource_type": "skill",
    "canonical_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/arboreto",
    "name": "arboreto",
    "summary_en": "Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.",
    "summary_zh": "使用可扩展算法（GRNBoost2、GENIE3）从基因表达数据推断基因调控网络（GRN）。在分析转录组数据（批量RNA-seq、单细胞RNA-seq）以识别转录因子-靶基因关系和调控相互作用时使用。支持大规模数据集的分布式计算。",
    "description_en": "Arboreto is a Python library for inferring gene regulatory networks (GRNs) from gene expression data. It provides scalable algorithms GRNBoost2 and GENIE3, and supports distributed computation via Dask for large-scale datasets. The skill includes guidance for basic GRN inference, algorithm selection, distributed computing, integration with pySCENIC, and reproducibility practices. It is designed for analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions.",
    "description_zh": "Arboreto是一个Python库，用于从基因表达数据推断基因调控网络（GRN）。它提供可扩展的算法GRNBoost2和GENIE3，并支持通过Dask进行分布式计算以处理大规模数据集。该技能包括基本GRN推断、算法选择、分布式计算、与pySCENIC集成以及可重复性实践的指导。它旨在分析转录组数据（批量RNA-seq、单细胞RNA-seq），以识别转录因子-靶基因关系和调控相互作用。",
    "provider_name": "K-Dense-AI",
    "homepage_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto",
    "endpoint_url": null,
    "source_url": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/arboreto/SKILL.md",
    "icon_url": null,
    "cover_image_url": null,
    "capabilities": [
      "data.analyze",
      "data.transform",
      "compute.execute"
    ],
    "categories": [
      "data",
      "research",
      "other"
    ],
    "industries": [
      "health",
      "general"
    ],
    "protocols": [
      "agent-skills"
    ],
    "auth": {
      "type": "none",
      "required": false
    },
    "pricing": {
      "model": "free"
    },
    "input_schema": {},
    "output_schema": {},
    "metadata": {
      "content_language": "en",
      "translation_status": "original-only",
      "license": {
        "spdx_id": "MIT",
        "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE"
      },
      "github": {
        "repository": "K-Dense-AI/scientific-agent-skills",
        "owner": "K-Dense-AI",
        "path": "skills/arboreto/SKILL.md",
        "commit": "1e5eeffbdad3749125afe7ab48a39694e27f181c",
        "stars": 42124,
        "forks": 3870,
        "updated_at": "2026-09-03T02:47:03Z"
      },
      "skill": {
        "compatibility": null,
        "allowed_tools": null,
        "content_hash": "230eac5da0a0dcdeafaf3f4141ccc21aee5385edf8718f87ec47e6c44a75bb1f",
        "line_count": 284
      },
      "review_gate": {
        "passed": true,
        "reasons": [],
        "policy_version": "review-gate-v1",
        "evaluated_at": "2026-09-03T06:20:38.549Z"
      }
    },
    "latest_version": "1e5eeffbdad3",
    "status": "listed",
    "health_status": "unknown",
    "source_kind": "imported",
    "source_agent": "aiworkshub-skill-reviewer",
    "trust": {
      "signal": "none",
      "reason": "No suspicious or malicious evidence.",
      "signals": {
        "yellow": 0,
        "red": 0
      }
    },
    "review_summary": {
      "method_version": "capability-evidence-v2",
      "capability_definition": "strong",
      "contract_completeness": "strong",
      "access_friction": "low",
      "operational_transparency": "strong",
      "evidence_strength": "source_inspected",
      "use_readiness": "ready_for_guidance",
      "reviewed_at": "2026-09-03T06:20:39.362Z"
    },
    "experience_count": 0,
    "verified_experience_count": 0,
    "usage_count": 0,
    "success_rate": null,
    "first_seen_at": "2026-09-03T02:50:27.303Z",
    "last_seen_at": "2026-09-03T06:20:38.768Z",
    "published_at": "2026-09-03T06:20:38.768Z",
    "created_at": "2026-09-03T02:50:27.303Z",
    "updated_at": "2026-09-03T06:20:39.362Z",
    "api_url": "https://aiworkshub.io/api/v1/resources/RES_40398D759800",
    "reviews_url": "https://aiworkshub.io/api/v1/resources/RES_40398D759800/reviews",
    "public_url": "https://aiworkshub.io/resources/RES_40398D759800",
    "distribution": {
      "canonical_identity": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/arboreto",
      "syndicatable": true,
      "origins": [
        {
          "registry_url": "https://github.com/",
          "upstream_resource_id": "K-Dense-AI/scientific-agent-skills:skills/arboreto/SKILL.md",
          "upstream_record_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/arboreto",
          "relation": "syndicated",
          "metadata": {
            "source": "github-skill-import"
          },
          "first_seen_at": "2026-09-03T02:50:27.303Z",
          "last_seen_at": "2026-09-03T06:20:38.768Z"
        }
      ]
    },
    "tools": [],
    "review_profile": {
      "schema_version": "aiworkshub.resource-review/0.2",
      "method_version": "capability-evidence-v2",
      "review_state": {
        "identity": "verified",
        "source": "verified",
        "connectivity": "unknown",
        "contract": "strong",
        "safe_use": "untested",
        "real_use": "unobserved"
      },
      "assessment": {
        "capability_definition": "strong",
        "contract_completeness": "strong",
        "access_friction": "low",
        "operational_transparency": "strong",
        "evidence_strength": "source_inspected",
        "use_readiness": "ready_for_guidance"
      },
      "profile": {
        "capabilities": [
          {
            "id": "data.analyze",
            "weight": 90,
            "confidence": 90,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "data.transform",
            "weight": 70,
            "confidence": 80,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "compute.execute",
            "weight": 80,
            "confidence": 85,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          }
        ],
        "domains": [
          {
            "id": "bioinformatics",
            "weight": 90,
            "confidence": 90,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "genomics",
            "weight": 85,
            "confidence": 85,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "data-science",
            "weight": 70,
            "confidence": 80,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          }
        ],
        "workflow_roles": [
          "analyze",
          "transform",
          "execute"
        ]
      },
      "capability_units": [
        {
          "id": "skill:arboreto",
          "kind": "skill_action",
          "capability_id": "data.analyze",
          "effect": "unknown",
          "open_world": false,
          "idempotency": "idempotent",
          "confirmation": "explicit policy",
          "input_contract": "natural_language",
          "output_contract": "natural_language",
          "accepts": [
            "task context"
          ],
          "produces": [
            "task result"
          ],
          "runtime_auth": {},
          "pricing": {},
          "evidence_ids": [
            "source-inspection"
          ],
          "metadata": {}
        }
      ],
      "access": {
        "distribution_license": {
          "spdx_id": "MIT",
          "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE"
        },
        "runtime_auth": {},
        "runtime_pricing": {},
        "dependencies": [
          "arboreto (Python package)",
          "dask",
          "distributed",
          "numpy",
          "pandas",
          "scikit-learn",
          "scipy"
        ]
      },
      "operational_flags": [],
      "trust": {
        "signal": "none",
        "evidence_ids": [],
        "reason": "No suspicious or malicious evidence."
      },
      "fit": {
        "good_for": [
          "Inferring gene regulatory networks from gene expression data",
          "Analyzing bulk RNA-seq and single-cell RNA-seq data",
          "Identifying transcription factor-target gene relationships",
          "Large-scale distributed computation"
        ],
        "not_for": [
          "Directly performing differential expression analysis",
          "Visualizing networks",
          "Running pySCENIC downstream analysis"
        ]
      },
      "evidence": [
        {
          "id": "source-record",
          "type": "source_record",
          "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/arboreto/SKILL.md",
          "observation": "Submitted Skill record for arboreto; declared license MIT.",
          "observed_at": "2026-09-03T02:47:03Z",
          "payload": {}
        },
        {
          "id": "source-inspection",
          "type": "source_inspection",
          "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/arboreto/SKILL.md",
          "observation": "The Skill source was fetched and inspected (9416 bytes; SHA-256 230eac5da0a0dcdeafaf3f4141ccc21aee5385edf8718f87ec47e6c44a75bb1f).",
          "observed_at": "2026-09-03T06:20:31.145Z",
          "payload": {}
        }
      ],
      "unknowns": [
        "Actual runtime behavior and performance on real datasets",
        "Compatibility with specific versions of arboreto and dependencies",
        "Whether the skill has been tested in real-world use cases",
        "Exact input and output schemas beyond natural language description"
      ],
      "id": "REV_45CA25E6D283",
      "resource_id": "RES_40398D759800",
      "evaluator_type": "platform_ai",
      "provider": "deepseek",
      "model": "deepseek-v4-flash",
      "review_scope": "source-inspected-skill",
      "created_at": "2026-09-03T06:20:39.362Z"
    }
  }
}