{
  "artifact_types": [
    {
      "artifact_type": "CandidateVulnerability",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "DrugResponse",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "DrugResponseEvidence",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "FeatureEvidence",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "FeatureEvidence",
      "schema_version": "2.0.0",
      "title": "FeatureEvidence artifact version 2"
    },
    {
      "artifact_type": "FunctionalDependency",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "GeneAssociation",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "MolecularSignature",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "MolecularSignature",
      "schema_version": "2.0.0",
      "title": "MolecularSignature artifact version 2"
    },
    {
      "artifact_type": "MolecularStatePrediction",
      "schema_version": "1.0.0",
      "title": "MolecularStatePrediction artifact"
    },
    {
      "artifact_type": "PathwayActivity",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "ProteinAssociation",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "ProteinValidationEvidence",
      "schema_version": "1.0.0"
    },
    {
      "artifact_type": "SubtypePrediction",
      "schema_version": "1.0.0"
    }
  ],
  "artifacts": [],
  "datasets": [
    {
      "access_review_required": true,
      "checksum": null,
      "connector_id": "depmap",
      "data_location": null,
      "dataset_id": "DEPMAP_CRISPR_GENE_EFFECT",
      "description": "Planned harmonized CRISPR gene-effect dataset; release and semantics are not yet locked.",
      "downloaded": false,
      "layer": "CURATED",
      "provenance_location": "datasets/provenance/DEPMAP_CRISPR_GENE_EFFECT.yaml",
      "schema_version": "1.0.0",
      "source": "Cancer Dependency Map",
      "status": "planned",
      "version": "pending-source-lock"
    },
    {
      "access_classification": "open",
      "access_review_required": true,
      "checksum": null,
      "connector_id": "gdc",
      "data_category": "Clinical",
      "data_location": null,
      "data_type": "Case and Sample Metadata",
      "dataset_id": "GDC_TCGA_BRCA_CASE_METADATA",
      "description": "Planned immutable TCGA-BRCA case/sample metadata source snapshot required for deterministic research-cohort construction; no source snapshot is locked. Curated linkages receive a separate dataset identity.",
      "downloaded": false,
      "genome_build": null,
      "layer": "RAW",
      "provenance_location": "datasets/provenance/GDC_TCGA_BRCA_CASE_METADATA.yaml",
      "schema_version": "1.0.0",
      "source": "NCI Genomic Data Commons",
      "source_project": "TCGA-BRCA",
      "status": "planned",
      "version": "pending-source-lock",
      "workflow": "GDC API metadata snapshot"
    },
    {
      "access_classification": "open",
      "access_review_required": true,
      "checksum": null,
      "connector_id": "gdc",
      "data_category": "Transcriptome Profiling",
      "data_location": null,
      "data_type": "Gene Expression Quantification",
      "dataset_id": "GDC_TCGA_BRCA_RNA",
      "description": "Planned immutable TCGA-BRCA STAR Counts source dataset; the GDC source release and file inventory are not yet locked. Curated expression receives a separate dataset identity.",
      "downloaded": false,
      "genome_build": "GRCh38",
      "layer": "RAW",
      "provenance_location": "datasets/provenance/GDC_TCGA_BRCA_RNA.yaml",
      "schema_version": "1.0.0",
      "source": "NCI Genomic Data Commons",
      "source_project": "TCGA-BRCA",
      "status": "planned",
      "version": "pending-source-lock",
      "workflow": "STAR - Counts"
    },
    {
      "access_classification": "open",
      "access_review_required": true,
      "checksum": null,
      "connector_id": "gdc",
      "data_category": "Simple Nucleotide Variation",
      "data_location": null,
      "data_type": "Masked Somatic Mutation",
      "dataset_id": "GDC_TCGA_BRCA_SOMATIC_MUTATIONS",
      "description": "Planned immutable open TCGA-BRCA masked somatic mutation MAF source dataset; the GDC source release and file inventory are not yet locked. Curated mutation data receives a separate dataset identity.",
      "downloaded": false,
      "genome_build": "GRCh38",
      "layer": "RAW",
      "provenance_location": "datasets/provenance/GDC_TCGA_BRCA_SOMATIC_MUTATIONS.yaml",
      "schema_version": "1.0.0",
      "source": "NCI Genomic Data Commons",
      "source_project": "TCGA-BRCA",
      "status": "planned",
      "version": "pending-source-lock",
      "workflow": "Aliquot Ensemble Somatic Variant Merging and Masking"
    },
    {
      "access_review_required": true,
      "checksum": null,
      "connector_id": "gdsc",
      "data_location": null,
      "dataset_id": "GDSC_DRUG_RESPONSE",
      "description": "Planned harmonized GDSC response dataset; licensed release and response semantics are unresolved.",
      "downloaded": false,
      "layer": "CURATED",
      "provenance_location": "datasets/provenance/GDSC_DRUG_RESPONSE.yaml",
      "schema_version": "1.0.0",
      "source": "Genomics of Drug Sensitivity in Cancer",
      "status": "planned",
      "version": "pending-source-lock"
    },
    {
      "access_review_required": true,
      "checksum": null,
      "connector_id": "pdc",
      "data_location": null,
      "dataset_id": "PDC_PROTEOMICS",
      "description": "Planned harmonized proteomics dataset; study, source release, and processing are unresolved.",
      "downloaded": false,
      "layer": "CURATED",
      "provenance_location": "datasets/provenance/PDC_PROTEOMICS.yaml",
      "schema_version": "1.0.0",
      "source": "NCI Proteomic Data Commons",
      "status": "planned",
      "version": "pending-source-lock"
    },
    {
      "access_review_required": true,
      "checksum": null,
      "connector_id": "prism",
      "data_location": null,
      "dataset_id": "PRISM_DRUG_RESPONSE",
      "description": "Planned harmonized PRISM response dataset; release, dose, and viability semantics are unresolved.",
      "downloaded": false,
      "layer": "CURATED",
      "provenance_location": "datasets/provenance/PRISM_DRUG_RESPONSE.yaml",
      "schema_version": "1.0.0",
      "source": "PRISM Repurposing",
      "status": "planned",
      "version": "pending-source-lock"
    }
  ],
  "dependency_graph": {
    "edges": [
      {
        "from": "P001",
        "minimum_release": "1.0.0",
        "required_artifacts": [
          {
            "artifact_type": "MolecularSignature",
            "schema_version": "2.0.0"
          },
          {
            "artifact_type": "FeatureEvidence",
            "schema_version": "2.0.0"
          }
        ],
        "to": "P002"
      }
    ],
    "nodes": [
      "P001",
      "P002",
      "P003"
    ],
    "topological_order": [
      "P001",
      "P002",
      "P003"
    ]
  },
  "generated_at": "2026-09-07T17:35:14.010313Z",
  "projects": [
    {
      "candidate_projections": [
        {
          "approval": "candidate",
          "cancer": "TCGA-BRCA",
          "input_modality": "bulk RNA expression (GDC STAR-Counts tpm_unstranded as log2(TPM + 1))",
          "metadata_path": "tasks/T001_tp53-mutation-state/imported-candidate.yaml",
          "model_checksum": "sha256:0d5a50eb0b881d749e6eb43535eb8583d63fdae866ae7abc421b9aa0543a0707",
          "model_id": "tcga-brca-tp53-logreg-1.0.0",
          "parity_verification": {
            "absolute_difference": 5.551115123125783e-17,
            "state": "verified",
            "tolerance": 1e-12
          },
          "payload_availability": "not_in_repository",
          "project_id": "P001",
          "provenance": {
            "gdc_release": "Data Release 45.0 - December 04, 2025",
            "legacy_platform": "AmbioSpire single-project platform",
            "patient_level_data_in_projection": false,
            "source": "NCI Genomic Data Commons open processed data",
            "synthetic": false
          },
          "release_status": "not_released",
          "schema_version": "1.0.0",
          "scientific_purpose": "Research-only estimation of the TP53 somatic-mutation-state label from TCGA-BRCA bulk RNA expression.",
          "target": "TP53 somatic-mutation-state label",
          "task_id": "T001"
        }
      ],
      "datasets": [
        {
          "dataset_id": "GDC_TCGA_BRCA_RNA",
          "layer": "RAW",
          "required": true,
          "version": "pending-source-lock"
        },
        {
          "dataset_id": "GDC_TCGA_BRCA_SOMATIC_MUTATIONS",
          "layer": "RAW",
          "required": true,
          "version": "pending-source-lock"
        },
        {
          "dataset_id": "GDC_TCGA_BRCA_CASE_METADATA",
          "layer": "RAW",
          "required": true,
          "version": "pending-source-lock"
        }
      ],
      "dependencies": [],
      "description": "Research-only molecular-state modeling project with independently versioned task contracts. T001 includes metadata and read-only compatibility validation for the completed legacy TCGA-BRCA TP53 candidate. The current platform specification remains unapproved and cannot pass G0 or produce a release.",
      "entrypoint": "pipeline.project:MolecularStateExplorerProject",
      "produced_artifacts": [
        {
          "artifact_type": "MolecularStatePrediction",
          "schema_version": "1.0.0"
        },
        {
          "artifact_type": "MolecularSignature",
          "schema_version": "2.0.0"
        },
        {
          "artifact_type": "FeatureEvidence",
          "schema_version": "2.0.0"
        }
      ],
      "project_id": "P001",
      "project_name": "Molecular State Explorer",
      "required_artifacts": [],
      "schema_version": "1.0.0",
      "slug": "molecular-state-explorer",
      "status": "active",
      "task_registry": "tasks/registry.yaml",
      "validation_gates": [
        "G0",
        "G1",
        "G2",
        "G3",
        "G4",
        "G5",
        "G6",
        "G7"
      ],
      "version": "0.3.0",
      "web": {
        "enabled": true,
        "navigation": {
          "category": "Explorers",
          "label": "Molecular State Explorer",
          "order": 10
        },
        "routes": [
          {
            "label": "Overview",
            "path": "/projects/molecular-state-explorer"
          }
        ]
      }
    },
    {
      "datasets": [
        {
          "dataset_id": "GDC_TCGA_BRCA_RNA",
          "layer": "CURATED",
          "required": true,
          "version": "pending-source-lock"
        },
        {
          "dataset_id": "DEPMAP_CRISPR_GENE_EFFECT",
          "layer": "CURATED",
          "required": true,
          "version": "pending-source-lock"
        },
        {
          "dataset_id": "PRISM_DRUG_RESPONSE",
          "layer": "CURATED",
          "required": true,
          "version": "pending-source-lock"
        },
        {
          "dataset_id": "GDSC_DRUG_RESPONSE",
          "layer": "CURATED",
          "required": true,
          "version": "pending-source-lock"
        },
        {
          "dataset_id": "PDC_PROTEOMICS",
          "layer": "CURATED",
          "required": true,
          "version": "pending-source-lock"
        }
      ],
      "dependencies": [
        {
          "minimum_release": "1.0.0",
          "project_id": "P001",
          "required_artifacts": [
            {
              "artifact_type": "MolecularSignature",
              "schema_version": "2.0.0"
            },
            {
              "artifact_type": "FeatureEvidence",
              "schema_version": "2.0.0"
            }
          ]
        }
      ],
      "description": "Contract scaffold for integrating molecular-state evidence with functional, pharmacological, and proteomic evidence to evaluate candidate vulnerabilities. No vulnerability analysis or validation is implemented.",
      "entrypoint": "pipeline.project:CancerVulnerabilityExplorerProject",
      "produced_artifacts": [
        "FunctionalDependency",
        "CandidateVulnerability",
        "DrugResponseEvidence",
        "ProteinValidationEvidence"
      ],
      "project_id": "P002",
      "project_name": "Cancer Vulnerability Explorer",
      "required_artifacts": [
        {
          "artifact_type": "MolecularSignature",
          "schema_version": "2.0.0"
        },
        {
          "artifact_type": "FeatureEvidence",
          "schema_version": "2.0.0"
        }
      ],
      "schema_version": "1.0.0",
      "slug": "cancer-vulnerability-explorer",
      "status": "scaffold",
      "validation_gates": [
        "G0",
        "G1",
        "G2",
        "G3",
        "G4",
        "G5",
        "G6",
        "G7"
      ],
      "version": "0.1.0",
      "web": {
        "enabled": true,
        "navigation": {
          "category": "Explorers",
          "label": "Cancer Vulnerability Explorer",
          "order": 20
        },
        "routes": [
          {
            "label": "Overview",
            "path": "/projects/cancer-vulnerability-explorer"
          }
        ]
      }
    },
    {
      "datasets": [],
      "dependencies": [],
      "description": "Research-only contract scaffold for a tumor-normal whole-genome somatic SNV/indel caller generalization benchmark. No scientific execution, validation, or release is implemented.",
      "entrypoint": "pipeline.project:CancerGenomeVariantExplorerProject",
      "produced_artifacts": [],
      "project_id": "P003",
      "project_name": "Cancer Genome Variant Explorer",
      "required_artifacts": [],
      "schema_version": "1.0.0",
      "slug": "cancer-genome-variant-explorer",
      "status": "scaffold",
      "task_registry": "tasks/registry.yaml",
      "validation_gates": [
        "G0",
        "G1",
        "G2",
        "G3",
        "G4",
        "G5",
        "G6",
        "G7"
      ],
      "version": "0.1.0",
      "web": {
        "enabled": false,
        "navigation": {
          "category": "Explorers",
          "label": "Cancer Genome Variant Explorer",
          "order": 30
        },
        "routes": []
      }
    }
  ],
  "releases": [],
  "schema_version": "1.0.0"
}