{
  "@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-SLC25A37",
      "identifier": "RO-SLC25A37",
      "datePublished": "2026-09-27T05:04:25.822724+00:00",
      "engine": "E-DICE-Core",
      "engineVersion": "0.1.0",
      "nsfTag": "NSF-EDICE-PHASE-I",
      "integrityHash": "ab20668207cc115e",
      "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 SLC25A37 via smina on g4dn.xlarge.",
      "target": "SLC25A37",
      "action": "gpu_docking",
      "totalCompounds": 10,
      "bestVina": -7.4975,
      "bestSMILES": "N=C1C=CC=CC1=NN=CSCC(=O)Nc1ccccc1",
      "qed": "0.379",
      "mw": "298.4",
      "substrate": "gpu",
      "decision": "DOCKED",
      "top5": [
        {
          "rank": 1,
          "smiles": "N=C1C=CC=CC1=NN=CSCC(=O)Nc1ccccc1",
          "vina": -7.4975
        },
        {
          "rank": 2,
          "smiles": "O=S(=O)(N=Cc1ccccc1)c1ccc(O)cc1",
          "vina": -7.1705
        },
        {
          "rank": 3,
          "smiles": "NC(=O)c1ccncc1Sc1ccccnccnc1",
          "vina": -7.0403
        },
        {
          "rank": 4,
          "smiles": "O=C(C=CN=C1C=CC=CC1)NC1=CC=CCO1",
          "vina": -7.0135
        },
        {
          "rank": 5,
          "smiles": "CC=CC=CC=NN=CSCC(=O)NC1=CC=C1",
          "vina": -6.62
        }
      ]
    },
    {
      "@type": "AdmissibilityEvidence",
      "@id": "#admissibility-evidence",
      "name": "Four-Metric Admissibility Gate",
      "nimScore": 0.6248,
      "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": "ab20668207cc115e",
      "roCrateUri": "s3://edicer-dev-research-objects-865950114883/ro-crates/RO-SLC25A37/ro-crate-metadata.json"
    },
    {
      "@type": "TargetPanel",
      "@id": "#targets",
      "name": "Multi-Target Docking Panel",
      "primaryTarget": "SLC25A37",
      "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\": \"SLC25A37\", \"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": 17,
      "steps": {
        "candidates_docked": 0,
        "candidates_generated": 1,
        "decided_by": "gpu-batch-rs (autonomous pipeline)",
        "decision": "FAILED_NO_VIABLE_COMPOUNDS",
        "job_id": "85865d61-b780-4c4c-ac5a-991bf3058a52",
        "next_step": "Redock with expanded scaffold library",
        "reason": "All generated de novo compounds rejected by G4-G5 quality gates (pose variance or vina threshold)",
        "step_0_provenance": {
          "approved_at": "",
          "approved_by": "auto_approved",
          "compute_type": "GPU docking (GNINA + Uni-Dock)",
          "initiated_by": "platform",
          "job_definition": "cortex-docking-gpu",
          "job_id": "15a8a6bb-af84-486b-aaa5-8c4496f61648",
          "timestamp": "2026-07-14T03:18:37.822006773+00:00"
        },
        "step_3_bio_validation": {
          "corrected_vina": null,
          "correction_method": "UNVALIDATABLE: membrane protein, no experimental structure",
          "flags": [
            "REJECT_MEMBRANE: 6 TM helices \u2014 unreliable",
            "ALPHAFOLD_ONLY"
          ],
          "gates_passed": 3,
          "gates_total": 4,
          "original_vina": -7.4975,
          "source": "Biological Validation Gate",
          "status": "CORRECTED",
          "timestamp": "2026-07-14T03:18:37.822006773+00:00",
          "trust_level": "REJECTED"
        },
        "step_4_gpu_docking": {
          "job_id": "15a8a6bb-af84-486b-aaa5-8c4496f61648",
          "n_molecules": 8,
          "n_poses": 1,
          "pose_variance": 0.0,
          "source": "GPU Docking Worker (Uni-Dock) [Rust]",
          "status": "COMPLETE",
          "timestamp": "2026-07-14T03:18:37.822006773+00:00",
          "vina_score": -7.4975
        },
        "step_5_scoring": {
          "affinity_band": "B+",
          "cap_reason": "Cortex upgraded: B \u2192 A (BioBrain=0.64, vina suggested B)",
          "grade": "A",
          "next_action": "Investigate target druggability \u2192 try alternative scaffolds",
          "source": "5-Dimension Scorer (Rust inline) v6",
          "status": "COMPLETE",
          "timestamp": "2026-07-14T03:18:37.822006773+00:00",
          "total_score": 0.4519,
          "vina_score": -7.4975
        },
        "step_6_billing": {
          "internal_cost_usd": "0.21",
          "retail_price_usd": "650.00",
          "source": "Governed Billing Ledger",
          "status": "COMPLETE",
          "timestamp": "2026-07-14T03:18:37.822006773+00:00"
        },
        "step_7_governance": {
          "approved": true,
          "confidence": 0.3,
          "decision_type": "Rejection",
          "evidence_signals": [
            "membrane_redock_failed",
            "COUNTER: Pipeline memory: prior docking was STRONG",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"In 2 sentences, explain WHY SLC25A37 is a promising cancer drug target for prostate cancer cancer. Use ONL",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"The algorithm decided the next step (see ALGORITHM DECISIONS above). EXPLAIN why that decision makes sense",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"Looking at the route intelligence and bottleneck data: what does blocking SLC25A37 mean for tumor evolutio",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"If the intervention package includes SLC25A37 as part of a gene combination, explain the BIOLOGICAL RATION",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"In 2 sentences, explain WHY SLC25A37 is a promising cancer drug target for prostate cancer cancer. Use ONL",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"The algorithm decided the next step (see ALGORITHM DECISIONS above). EXPLAIN why that decision makes sense",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"Looking at the route intelligence and bottleneck data: what does blocking SLC25A37 mean for tumor evolutio",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"If the intervention package includes SLC25A37 as part of a gene combination, explain the BIOLOGICAL RATION",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"In 2 sentences, explain WHY SLC25A37 is a promising cancer drug target for prostate cancer cancer. Use ONL",
            "COUNTER: SMOS memory (authority 0.6): {\"question\": \"The algorithm decided the next step (see ALGORITHM DECISIONS above). EXPLAIN why that decision makes sense"
          ],
          "new_state": "B",
          "old_state": "A+",
          "reason": "APPROVED: 1/1 governance checks passed",
          "source": "Governance Check Gate",
          "timestamp": "2026-07-10T02:35:36.521414391+00:00"
        },
        "step_8_npead": {
          "chemistry_score": 0.668,
          "grade_logged": "A",
          "is_membrane": false,
          "outcome_fed_to_maml": true,
          "pose_variance": 0.0,
          "source": "NPEAD Learning System",
          "status": "LOGGED",
          "timestamp": "2026-07-14T03:18:37.822006773+00:00",
          "vina_logged": -7.4975
        },
        "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": "2026-07-14T03:18:37.822006773+00:00"
        },
        "step_master_brain": {
          "action": "generate",
          "chosen_by": "",
          "consensus": {
            "arbitration": "",
            "llm_said": "",
            "rule_said": ""
          },
          "context": {
            "authority": 0.5,
            "failures": 0,
            "inhibitors": 20,
            "runs": 3
          },
          "directives": {
            "explore_ratio": 0.5,
            "focus": "balanced",
            "scaffold_hint": "",
            "weight_overrides": {}
          },
          "method": "rules_only",
          "rationale": "Standard generation \u2014 no signals require special handling",
          "risk": "",
          "timestamp": "2026-07-02T02:32:13.540254Z"
        },
        "timestamp": "2026-06-13T11:30:35.212579604+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"
    }
  ]
}