{
  "@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-PIWIL2",
      "identifier": "RO-PIWIL2",
      "datePublished": "2026-09-27T05:04:31.643566+00:00",
      "engine": "E-DICE-Core",
      "engineVersion": "0.1.0",
      "nsfTag": "NSF-EDICE-PHASE-I",
      "integrityHash": "1eb771d67b6da26d",
      "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 PIWIL2 via smina on g4dn.xlarge.",
      "target": "PIWIL2",
      "action": "gpu_docking",
      "totalCompounds": 31,
      "bestVina": -7.9,
      "bestSMILES": "O=C(NCc1ccc2[nH]ccc2c1)c1cc2ccccc2[nH]1",
      "qed": "0.53",
      "mw": "289.3",
      "substrate": "gpu",
      "decision": "DOCKED",
      "top5": [
        {
          "rank": 1,
          "smiles": "O=C(NCc1ccc2[nH]ccc2c1)c1cc2ccccc2[nH]1",
          "vina": -7.9
        },
        {
          "rank": 2,
          "smiles": "Cc1ccc(CNC(=O)c2cc3ccccc3[nH]2)cc1",
          "vina": -7.7
        },
        {
          "rank": 3,
          "smiles": "CNc1ccc(CNC(=O)c2cc3ccccc3[nH]2)cc1",
          "vina": -7.6
        },
        {
          "rank": 4,
          "smiles": "O=C(NCc1ccccc1)c1cc2ccccc2[nH]1",
          "vina": -7.5
        },
        {
          "rank": 5,
          "smiles": "CN(C(=O)c1ccccc1)c1nc(-c2ccccc2)cs1",
          "vina": -7.5
        }
      ]
    },
    {
      "@type": "AdmissibilityEvidence",
      "@id": "#admissibility-evidence",
      "name": "Four-Metric Admissibility Gate",
      "nimScore": 0.6583,
      "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": "1eb771d67b6da26d",
      "roCrateUri": "s3://edicer-dev-research-objects-865950114883/ro-crates/RO-PIWIL2/ro-crate-metadata.json"
    },
    {
      "@type": "TargetPanel",
      "@id": "#targets",
      "name": "Multi-Target Docking Panel",
      "primaryTarget": "PIWIL2",
      "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\": \"PIWIL2\", \"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": 2,
      "steps": [
        {
          "step_1_discovery": {
            "action": "Gene scan \u2014 identified PIWIL2 as novel target",
            "decision": "NOVEL \u2014 promoted to hero candidate",
            "result": "Cancer type: Prostate / Pancreatic. Zero ChEMBL compounds.",
            "source": "TCGA/GDC",
            "timestamp": "2026-05-21T14:05:17.890757+00:00"
          },
          "step_2_physician_analysis": {
            "action": "Full multi-omics analysis of PIWIL2",
            "clinical_angle": "Eliminate cancer stem cells driving recurrence",
            "result": "Pathway: PIWIL2 \u2192 piRNA \u2192 transposon silencing \u2192 stem cell maintenance. Hypothesis: PIWIL2 maintains cancer stem cell populations through piRNA-mediated epigenetic silencing. Inhibiting PIWIL2 depletes the therapy-resistant stem cell pool.",
            "source": "Physician Agent (9 sub-agents)",
            "timestamp": "2026-05-21T14:05:17.890757+00:00"
          },
          "step_3_bio_validation": {
            "corrected_vina": -5.8,
            "correction_method": "No correction needed (experimental structure, soluble)",
            "flags": [],
            "gates_passed": 4,
            "gates_total": 4,
            "original_vina": -5.8,
            "source": "Biological Validation Gate",
            "status": "PASS",
            "timestamp": "2026-06-01T20:56:02.547441494+00:00",
            "trust_level": "HIGH"
          },
          "step_3_governance": {
            "action": "Admissibility gate + governance ledger",
            "decision": "APPROVED \u2014 passed confidence threshold",
            "source": "Fuzzy Brain",
            "timestamp": "2026-05-21T14:05:17.890757+00:00"
          },
          "step_4_gpu_docking": {
            "job_id": "83ad6748-da18-4689-89f3-91d270604a60",
            "n_molecules": 1,
            "n_poses": 5,
            "pose_variance": 0.037,
            "source": "GPU Docking Worker (smina) [Rust]",
            "status": "COMPLETE",
            "timestamp": "2026-06-01T20:56:02.547441494+00:00",
            "vina_score": -5.8
          },
          "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": "2026-06-01T20:56:02.547441494+00:00",
            "total_score": 0.613,
            "vina_score": -5.8
          },
          "step_6_billing": {
            "internal_cost_usd": "0.19",
            "retail_price_usd": "650.00",
            "source": "Governed Billing Ledger",
            "status": "COMPLETE",
            "timestamp": "2026-06-01T20:56:02.547441494+00:00"
          },
          "step_8_npead": {
            "chemistry_score": 1.0,
            "grade_logged": "B+",
            "is_membrane": false,
            "outcome_fed_to_maml": true,
            "pose_variance": 0.037,
            "source": "NPEAD Learning System",
            "status": "LOGGED",
            "timestamp": "2026-06-01T20:56:02.547441494+00:00",
            "vina_logged": -5.8
          },
          "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": "2026-06-01T20:56:02.547441494+00:00"
          }
        },
        {
          "step": "wetlab_order_generated",
          "gene": "PIWIL2",
          "order_id": "WL-PIWIL2-20260812",
          "timestamp": "2026-08-12T01:58:16.026631+00:00",
          "estimated_cost": "$22,000\u2013$36,000",
          "timeline": "6\u201310 weeks",
          "compound_smiles": "O=C(NCc1ccc2[nH]ccc2c1)c1cc2ccccc2[nH]1",
          "vina_score": "-7.9",
          "grade": "A",
          "trust_level": "MEDIUM",
          "hash": "d131fee21e943b7901cb3ca0e607d8d08a51d6b2a5339bd916c7a07850efd06b"
        }
      ]
    },
    {
      "@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"
    }
  ]
}