{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@type": "CreativeWork",
      "@id": "ro-crate-metadata.json",
      "conformsTo": {
        "@id": "https://w3id.org/ro/crate/1.1"
      },
      "about": {
        "@id": "./"
      }
    },
    {
      "@type": "Dataset",
      "@id": "./",
      "name": "E-DICE-R Research Object \u2014 RO-R3HCC1",
      "identifier": "RO-R3HCC1",
      "datePublished": "2026-09-27T05:04:40.562758+00:00",
      "engine": "E-DICE-Core",
      "engineVersion": "0.1.0",
      "nsfTag": "NSF-EDICE-PHASE-I",
      "integrityHash": "5fdb51005e1b62ce",
      "hasPart": [
        {
          "@id": "#result"
        },
        {
          "@id": "#admissibility-evidence"
        },
        {
          "@id": "#trust"
        },
        {
          "@id": "#targets"
        },
        {
          "@id": "#billing"
        },
        {
          "@id": "#evidence-chain"
        },
        {
          "@id": "#performance"
        }
      ]
    },
    {
      "@type": "ComputationalResult",
      "@id": "#result",
      "name": "GPU Docking Result",
      "description": "De novo molecules generated and docked against R3HCC1 via smina on g4dn.xlarge.",
      "target": "R3HCC1",
      "action": "gpu_docking",
      "totalCompounds": 10,
      "bestVina": -7.4,
      "bestSMILES": "O=C(NCc1ccc(F)cc1)c1cc2ccccc2[nH]1",
      "qed": "0.752",
      "mw": "268.3",
      "substrate": "gpu",
      "decision": "DOCKED",
      "top5": [
        {
          "rank": 1,
          "smiles": "O=C(NCc1ccc(F)cc1)c1cc2ccccc2[nH]1",
          "vina": -7.4
        },
        {
          "rank": 2,
          "smiles": "O=C(Nc1cccc(C(F)(F)F)c1)c1ccncc1",
          "vina": -7.1
        },
        {
          "rank": 3,
          "smiles": "O=C(Cc1cccc2nccnc12)NCc1ccccc1",
          "vina": -7.0
        },
        {
          "rank": 4,
          "smiles": "O=C(Nc1ccncc1)Sc1cccc2nccnc12",
          "vina": -6.9
        },
        {
          "rank": 5,
          "smiles": "O=C(C=CC=C1C=NCN=C1)NCc1ccccc1",
          "vina": -5.3
        }
      ]
    },
    {
      "@type": "AdmissibilityEvidence",
      "@id": "#admissibility-evidence",
      "name": "Four-Metric Admissibility Gate",
      "nimScore": 0.6167,
      "criticConfidence": 0.7,
      "thresholds": {
        "S": 0.75,
        "sigma_sq": 0.5,
        "R_theta": 0.05,
        "R_h": 2.0
      },
      "gateType": "all-or-nothing",
      "note": "All four metrics must independently pass."
    },
    {
      "@type": "GovernanceTrust",
      "@id": "#trust",
      "name": "Governance Chain",
      "pqmStatus": "ISSUED",
      "qcmTrust": 1.0,
      "qdmSubstrate": "gpu",
      "parityStatus": "VALIDATED",
      "ledgerLogged": true,
      "ledgerHash": "5fdb51005e1b62ce",
      "roCrateUri": "s3://edicer-dev-research-objects-865950114883/ro-crates/RO-R3HCC1/ro-crate-metadata.json"
    },
    {
      "@type": "TargetPanel",
      "@id": "#targets",
      "name": "Multi-Target Docking Panel",
      "primaryTarget": "R3HCC1",
      "totalTargetsHit": 0,
      "targets": [],
      "note": "Populated at query time with all targets sharing this compound."
    },
    {
      "@type": "BillingRecord",
      "@id": "#billing",
      "name": "Compute Cost Ledger",
      "data": {
        "total_cost": "0.72",
        "updated": "2026-05-26T16:21:18.115075+00:00",
        "data": "{\"gene\": \"R3HCC1\", \"internal_cost_usd\": \"0.72\", \"retail_price_usd\": \"650.00\", \"margin_pct\": \"99.9\", \"pharma_benchmark_usd\": \"10000000\", \"cost_reduction_vs_pharma\": \"15384\", \"cost_reduction_vs_internal\": \"13888888\", \"services\": {\"discovery_scan\": {\"description\": \"Lambda + DynamoDB\", \"duration_sec\": 30, \"internal_usd\": \"0.05\", \"retail_usd\": \"50.00\"}, \"pre_filters\": {\"description\": \"Lambda (GTEx/UniProt/OpenTargets API)\", \"duration_sec\": 15, \"internal_usd\": \"0.02\", \"retail_usd\": \"25.00\"}, \"pdb_retrieval\": {\"description\": \"AlphaFold API + S3\", \"duration_sec\": 5, \"internal_usd\": \"0.01\", \"retail_usd\": \"10.00\"}, \"denovo_generation\": {\"description\": \"Lambda (RDKit/SELFIES)\", \"duration_sec\": 60, \"internal_usd\": \"0.08\", \"retail_usd\": \"75.00\"}, \"gpu_docking\": {\"description\": \"AWS Batch g4dn.xlarge (smina)\", \"duration_sec\": 600, \"internal_usd\": \"0.53\", \"retail_usd\": \"350.00\"}, \"scoring\": {\"description\": \"Lambda (5-dim scorer)\", \"duration_sec\": 5, \"internal_usd\": \"0.01\", \"retail_usd\": \"40.00\"}, \"ro_crate\": {\"description\": \"Lambda + S3 (RO-Crate + Object Lock)\", \"duration_sec\": 3, \"internal_usd\": \"0.01\", \"retail_usd\": \"50.00\"}, \"evidence_chain\": {\"description\": \"DynamoDB + S3 immutable ledger\", \"duration_sec\": 2, \"internal_usd\": \"0.01\", \"retail_usd\": \"50.00\"}}, \"compute_type\": \"gpu\", \"instance\": \"g4dn.xlarge\", \"timestamp\": \"2026-05-26T16:21:18.115075+00:00\"}",
        "retail_price": "650.00"
      }
    },
    {
      "@type": "EvidenceChain",
      "@id": "#evidence-chain",
      "name": "Pipeline Evidence Chain",
      "stepsComplete": 10,
      "steps": {
        "step_10_cdx": {
          "cdx_rationale": "",
          "cdx_type": "Diagnostic",
          "cdx_use": "Novel \u2014 needs functional validation",
          "pathway": "RNA binding / unknown function",
          "pubmed_prostate": 0,
          "source": "Cortex CDx Classification Engine",
          "status": "CLASSIFIED",
          "target_novelty": "TARGET_NOVEL (0 prostate publications)",
          "timestamp": "2026-05-28T23:22:12.676874+00:00"
        },
        "step_1_discovery": {
          "action": "Gene scan \u2014 identified R3HCC1 as novel target",
          "decision": "NOVEL \u2014 promoted to hero candidate",
          "result": "Cancer type: Pancreatic. Zero ChEMBL compounds.",
          "source": "TCGA/GDC",
          "timestamp": "2026-05-22T06:08:16.088617+00:00"
        },
        "step_2_physician_analysis": {
          "action": "Full multi-omics analysis of R3HCC1",
          "clinical_angle": "Disrupt adaptive splicing in pancreatic cancer",
          "result": "Pathway: R3HCC1 \u2192 RNA processing \u2192 splicing regulation \u2192 tumor adaptation. Hypothesis: R3HCC1 regulates RNA processing enabling tumor adaptive splicing. Blocking it disrupts cancer-specific transcript variants.",
          "source": "Physician Agent (9 sub-agents)",
          "timestamp": "2026-05-22T06:08:16.088617+00:00"
        },
        "step_3_bio_validation": {
          "corrected_vina": -4.2,
          "correction_method": "AlphaFold 20% uncertainty correction",
          "flags": [
            "ALPHAFOLD_ONLY"
          ],
          "gates_passed": 4,
          "gates_total": 4,
          "original_vina": -5.3,
          "source": "Biological Validation Gate",
          "status": "PASS",
          "timestamp": "2026-06-01T20:54:53.549852570+00:00",
          "trust_level": "MEDIUM"
        },
        "step_3_governance": {
          "action": "Admissibility gate + governance ledger",
          "decision": "APPROVED \u2014 passed confidence threshold",
          "source": "Fuzzy Brain",
          "timestamp": "2026-05-22T06:08:16.088617+00:00"
        },
        "step_4_gpu_docking": {
          "job_id": "f1c378fb-1baf-4c9b-9464-8f5d50212233",
          "n_molecules": 3,
          "n_poses": 5,
          "pose_variance": 0.013,
          "source": "GPU Docking Worker (smina) [Rust]",
          "status": "COMPLETE",
          "timestamp": "2026-06-01T20:54:53.549852570+00:00",
          "vina_score": -5.3
        },
        "step_5_scoring": {
          "affinity_band": "B",
          "cap_reason": "All gates pass \u2014 ready for next stage",
          "grade": "B+",
          "next_action": "Generate more diverse analogs \u2192 improve binding",
          "source": "5-Dimension Scorer (Rust inline) v6",
          "status": "COMPLETE",
          "timestamp": "2026-06-01T20:54:53.549852570+00:00",
          "total_score": 0.6035,
          "vina_score": -5.3
        },
        "step_6_billing": {
          "internal_cost_usd": "0.20",
          "retail_price_usd": "650.00",
          "source": "Governed Billing Ledger",
          "status": "COMPLETE",
          "timestamp": "2026-06-01T20:54:53.549852570+00:00"
        },
        "step_8_npead": {
          "chemistry_score": 1.0,
          "grade_logged": "B+",
          "is_membrane": false,
          "outcome_fed_to_maml": true,
          "pose_variance": 0.013,
          "source": "NPEAD Learning System",
          "status": "LOGGED",
          "timestamp": "2026-06-01T20:54:53.549852570+00:00",
          "vina_logged": -5.3
        },
        "step_9_intelligence": {
          "brain_bus_consulted": true,
          "cross_target_patterns": true,
          "failure_taxonomy_checked": true,
          "learned_knowledge_consulted": true,
          "smos_memories_queried": true,
          "source": "Cortex Intelligence Layer",
          "status": "COMPLETE",
          "timestamp": "2026-06-01T20:54:53.549852570+00:00"
        }
      }
    },
    {
      "@type": "PerformanceMetrics",
      "@id": "#performance",
      "totalMs": 0,
      "nimMs": 0,
      "substrateMs": 0,
      "scorer": "smina_gpu"
    },
    {
      "@type": "Disclaimer",
      "@id": "#disclaimer",
      "text": "COMPUTATIONAL HYPOTHESIS \u2014 REQUIRES EXPERT VALIDATION BEFORE EXPERIMENTAL COMMITMENT"
    }
  ]
}