{
  "@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-ADAM28",
      "identifier": "RO-ADAM28",
      "datePublished": "2026-09-27T05:04:41.803460+00:00",
      "engine": "E-DICE-Core",
      "engineVersion": "0.1.0",
      "nsfTag": "NSF-EDICE-PHASE-I",
      "integrityHash": "5042a441c1199e79",
      "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 ADAM28 via smina on g4dn.xlarge.",
      "target": "ADAM28",
      "action": "gpu_docking",
      "totalCompounds": 10,
      "bestVina": -6.7,
      "bestSMILES": "O=C(Nc1ccncc1)Sc1cccc2nccnc12",
      "qed": "0.73",
      "mw": "282.3",
      "substrate": "gpu",
      "decision": "DOCKED",
      "top5": [
        {
          "rank": 1,
          "smiles": "O=C(Nc1ccncc1)Sc1cccc2nccnc12",
          "vina": -6.7
        },
        {
          "rank": 2,
          "smiles": "O=C(C=CCc1cnccn1)NCC1=CC=CC1",
          "vina": -6.4
        },
        {
          "rank": 3,
          "smiles": "C#CC(O)=CC=C[SH](=O)(NC=C1C=CC=[N+]=C1)OO",
          "vina": -6.1
        },
        {
          "rank": 4,
          "smiles": "N=CC=CC=CC(=O)NCC1=CCC=C1",
          "vina": -5.8
        },
        {
          "rank": 5,
          "smiles": "CC(O)=CC=CS(=O)(=O)Nc1ccccc1",
          "vina": -5.6
        }
      ]
    },
    {
      "@type": "AdmissibilityEvidence",
      "@id": "#admissibility-evidence",
      "name": "Four-Metric Admissibility Gate",
      "nimScore": 0.5583,
      "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": "5042a441c1199e79",
      "roCrateUri": "s3://edicer-dev-research-objects-865950114883/ro-crates/RO-ADAM28/ro-crate-metadata.json"
    },
    {
      "@type": "TargetPanel",
      "@id": "#targets",
      "name": "Multi-Target Docking Panel",
      "primaryTarget": "ADAM28",
      "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\": \"ADAM28\", \"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": "Prognostic",
          "cdx_use": "Invasion/metastasis risk",
          "pathway": "Metalloprotease / ECM remodeling",
          "pubmed_prostate": 1,
          "source": "Cortex CDx Classification Engine",
          "status": "CLASSIFIED",
          "target_novelty": "TARGET_KNOWN (1 prostate pubs)",
          "timestamp": "2026-05-28T23:22:12.676874+00:00"
        },
        "step_1_discovery": {
          "action": "Gene scan \u2014 identified ADAM28 as novel target",
          "decision": "NOVEL \u2014 promoted to hero candidate",
          "result": "Cancer type: Prostate / Pancreatic. Zero ChEMBL compounds.",
          "source": "TCGA/GDC",
          "timestamp": "2026-05-22T10:51:13.511129+00:00"
        },
        "step_2_physician_analysis": {
          "action": "Full multi-omics analysis of ADAM28",
          "clinical_angle": "Anti-invasive: block ECM remodeling at tumor-stroma interface",
          "result": "Pathway: ADAM28 \u2192 metalloprotease \u2192 ECM remodeling \u2192 invasion + metastasis. Hypothesis: ADAM28 cleaves extracellular matrix and growth factor binding proteins enabling invasion. Inhibiting ADAM28 blocks matrix degradation at invasion front.",
          "source": "Physician Agent (9 sub-agents)",
          "timestamp": "2026-05-22T10:51:13.511129+00:00"
        },
        "step_3_bio_validation": {
          "corrected_vina": -5.4,
          "correction_method": "Single-pass membrane correction +1.0",
          "flags": [
            "CAUTION_MEMBRANE",
            "ALPHAFOLD_ONLY"
          ],
          "gates_passed": 4,
          "gates_total": 4,
          "original_vina": -6.4,
          "source": "Biological Validation Gate",
          "status": "PASS",
          "timestamp": "2026-06-01T21:10:58.503394650+00:00",
          "trust_level": "MEDIUM"
        },
        "step_3_governance": {
          "action": "Admissibility gate + governance ledger",
          "decision": "APPROVED \u2014 passed confidence threshold",
          "source": "Fuzzy Brain",
          "timestamp": "2026-05-22T10:51:13.511129+00:00"
        },
        "step_4_gpu_docking": {
          "job_id": "ad6a761c-781f-4e01-bf24-b9786b5a75f4",
          "n_molecules": 1,
          "n_poses": 5,
          "pose_variance": 0.107,
          "source": "GPU Docking Worker (smina) [Rust]",
          "status": "COMPLETE",
          "timestamp": "2026-06-01T21:10:58.503394650+00:00",
          "vina_score": -6.4
        },
        "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": "2026-06-01T21:10:58.503394650+00:00",
          "total_score": 0.6344,
          "vina_score": -6.4
        },
        "step_6_billing": {
          "internal_cost_usd": "0.20",
          "retail_price_usd": "650.00",
          "source": "Governed Billing Ledger",
          "status": "COMPLETE",
          "timestamp": "2026-06-01T21:10:58.503394650+00:00"
        },
        "step_8_npead": {
          "chemistry_score": 1.0,
          "grade_logged": "B+",
          "is_membrane": false,
          "outcome_fed_to_maml": true,
          "pose_variance": 0.107,
          "source": "NPEAD Learning System",
          "status": "LOGGED",
          "timestamp": "2026-06-01T21:10:58.503394650+00:00",
          "vina_logged": -6.4
        },
        "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": "2026-06-01T21:10:58.503394650+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"
    }
  ]
}