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        "state": "partial",
        "title": "Claudin18.2 defines a prognostically distinct subgroup of intrahepatic cholangiocarcinoma via CD8+ T-cell exclusion.",
        "doi": "10.3389/fonc.2025.1636367",
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        "journal": "Frontiers in oncology",
        "year": 2025,
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                            "Characteristics",
                            "Total (N=83)",
                            "Claudin18.2 expression",
                            "χ2",
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                            "Positive",
                            "Negative"
                        ],
                        [
                            "Age (years)",
                            "",
                            "",
                            "",
                            "0.019",
                            "0.89"
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                        [
                            "≤ 65",
                            "55 (66.3%)",
                            "13 (65.0%)",
                            "42 (66.7%)",
                            "",
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                        [
                            ">65",
                            "28 (33.7%)",
                            "7 (35.0%)",
                            "21 (33.3%)",
                            "",
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                        [
                            "Sex",
                            "",
                            "",
                            "",
                            "2.29",
                            "0.13"
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                        [
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                            "26 (31.3%)",
                            "9 (45.0%)",
                            "17 (27.0%)",
                            "",
                            ""
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                        [
                            "Male",
                            "57 (68.7%)",
                            "11 (55.0%)",
                            "46 (73.0%)",
                            "",
                            ""
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                        [
                            "Tumor size (cm)",
                            "",
                            "",
                            "",
                            "4.59",
                            "0.032*"
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                        [
                            "≤ 5",
                            "45 (54.2%)",
                            "15 (75.0%)",
                            "30 (47.6%)",
                            "",
                            ""
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                        [
                            ">5",
                            "38 (45.8%)",
                            "5 (25.0%)",
                            "33 (52.8%)",
                            "",
                            ""
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                        [
                            "Tumor number",
                            "",
                            "",
                            "",
                            "",
                            "0.032*"
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                        [
                            "1",
                            "70 (83.1%)",
                            "20 (100.0%)",
                            "50 (79.4%)",
                            "",
                            ""
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                        [
                            "≥2",
                            "13 (16.9%)",
                            "0 (0.0%)",
                            "13 (20.6%)",
                            "",
                            ""
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                        [
                            "Histological grade",
                            "",
                            "",
                            "",
                            "H = 0.25",
                            "0.62"
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                        [
                            "Well/Moderate",
                            "64 (77.1%)",
                            "16 (80.0%)",
                            "48 (76.2%)",
                            "",
                            ""
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                        [
                            "Moderate-poor",
                            "9 (10.8%)",
                            "3 (15.0%)",
                            "6 (9.5%)",
                            "",
                            ""
                        ],
                        [
                            "Poor",
                            "10 (12.0%)",
                            "1 (5.0%)",
                            "9 (14.3%)",
                            "",
                            ""
                        ],
                        [
                            "Lymph node metastasis",
                            "",
                            "",
                            "",
                            "",
                            "0.35"
                        ],
                        [
                            "Yes",
                            "18 (21.7%)",
                            "6 (30.0%)",
                            "12 (19.0%)",
                            "",
                            ""
                        ],
                        [
                            "No",
                            "65 (78.3%)",
                            "14 (70.0%)",
                            "51 (81.0%)",
                            "",
                            ""
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                        [
                            "AJCC TNM stage",
                            "",
                            "",
                            "",
                            "1.07",
                            "0.30"
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                        [
                            "I/II",
                            "65 (78.3%)",
                            "14 (70.0%)",
                            "51 (81.0%)",
                            "",
                            ""
                        ],
                        [
                            "III/IV",
                            "18 (21.7%)",
                            "6 (30.0%)",
                            "12 (19.0%)",
                            "",
                            ""
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                        [
                            "MVI",
                            "",
                            "",
                            "",
                            "1.60",
                            "0.21"
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                        [
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                            "48 (57.8%)",
                            "14 (70.0%)",
                            "34 (54.0%)",
                            "",
                            ""
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                        [
                            "M1/M2",
                            "35 (42.2%)",
                            "6 (30.0%)",
                            "29 (46.0%)",
                            "",
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                        [
                            "aCA199",
                            "",
                            "",
                            "",
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                        [
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                            "48 (58.2%)",
                            "15 (83.3%)",
                            "33 (54.1%)",
                            "",
                            ""
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                        [
                            "Negative",
                            "31 (41.8%)",
                            "3 (16.7%)",
                            "28 (45.9%)",
                            "",
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                        [
                            "HBV",
                            "",
                            "",
                            "",
                            "2.97",
                            "0.085"
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                        [
                            "Positive",
                            "47 (56.6%)",
                            "8 (40.0%)",
                            "39 (61.9%)",
                            "",
                            ""
                        ],
                        [
                            "Negative",
                            "36 (43.3%)",
                            "12 (60.0%)",
                            "24 (38.1%)",
                            "",
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                        [
                            "Microbiliary invasion",
                            "",
                            "",
                            "",
                            "0.17",
                            "0.68"
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                        [
                            "Yes",
                            "30 (36.1%)",
                            "8 (40.0%)",
                            "22 (34.9%)",
                            "",
                            ""
                        ],
                        [
                            "No",
                            "53 (63.9%)",
                            "12 (60.0%)",
                            "41 (65.1%)",
                            "",
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                        [
                            "Perineural invasion",
                            "",
                            "",
                            "",
                            "0.07",
                            "0.78"
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                        [
                            "Yes",
                            "27 (32.5%)",
                            "7 (35.0%)",
                            "20 (31.7%)",
                            "",
                            ""
                        ],
                        [
                            "No",
                            "56 (67.5%)",
                            "13 (65.0%)",
                            "43 (68.3%)",
                            "",
                            ""
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                        [
                            "Cirrhosis",
                            "",
                            "",
                            "",
                            "",
                            "0.43"
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                        [
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                            "10 (12.0%)",
                            "1 (5.0%)",
                            "9 (14.3%)",
                            "",
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                        [
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                            "73 (88.0%)",
                            "19 (95.0%)",
                            "54 (85.7%)",
                            "",
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                        [
                            "aCEA",
                            "",
                            "",
                            "",
                            "0.96",
                            "0.76"
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                        [
                            "Positive",
                            "24 (30.4%)",
                            "6 (33.3%)",
                            "18 (29.5%)",
                            "",
                            ""
                        ],
                        [
                            "Negative",
                            "55 (69.6%)",
                            "12 (66.7%)",
                            "43 (70.5%)",
                            "",
                            ""
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                        [
                            "a AFP",
                            "",
                            "",
                            "",
                            "",
                            "0.66"
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                        [
                            "Positive",
                            "7 (8.9%)",
                            "2 (11.1%)",
                            "5 (8.2%)",
                            "",
                            ""
                        ],
                        [
                            "Negative",
                            "72 (91.1%)",
                            "16 (88.9%)",
                            "56 (91.8%)",
                            "",
                            ""
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                        [
                            "Recurrence",
                            "",
                            "",
                            "",
                            "",
                            "0.018*"
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                        [
                            "Yes",
                            "57 (68.7%)",
                            "18 (90.0%)",
                            "39 (61.9%)",
                            "",
                            ""
                        ],
                        [
                            "No",
                            "26 (31.3%)",
                            "2 (10.0%)",
                            "24 (38.1%)",
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                    "caption": "Univariate analysis of prognostic factors(OS) for ICC.",
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                            "Parameters",
                            "HR",
                            "95% CI",
                            "P value"
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                            "Age (years) (> 65 vs. ≤ 65)",
                            "0.690",
                            "0.369-1.291",
                            "0.246"
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                            "Sex (male vs. female)",
                            "0.805",
                            "0.445-1.455",
                            "0.472"
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                            "HBV",
                            "1.079",
                            "0.609-1.915",
                            "0.794"
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                            "CA199",
                            "3.487",
                            "1.710-7.110",
                            "0.001*"
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                        [
                            "CEA",
                            "1.638",
                            "0.885-3.032",
                            "0.116"
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                        [
                            "TNM stage (III/IV vs. I/II)",
                            "2.165",
                            "1.129-4.151",
                            "0.020*"
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                        [
                            "Histological grade",
                            "",
                            "",
                            "0.010*"
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                        [
                            "(Moderate-poor vs. poor)",
                            "0.376",
                            "0.124-1.138",
                            "0.083"
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                        [
                            "(Well-Moderate vs. poor)",
                            "0.312",
                            "0.147-0.660",
                            "0.002*"
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                        [
                            "MVI (M1/M2 vs. M0)",
                            "2.600",
                            "1.459-4.635",
                            "0.001*"
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                        [
                            "Lymph node metastasis",
                            "2.165",
                            "1.129-4.151",
                            "0.020*"
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                        [
                            "Bile duct invasion",
                            "1.372",
                            "0.766-2.458",
                            "0.288"
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                        [
                            "Perineural invasion",
                            "1.542",
                            "0.858-2.773",
                            "0.148"
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                        [
                            "Tumor number (≥ 2 vs. 1)",
                            "0.885",
                            "0.396-1.977",
                            "0.766"
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                        [
                            "Tumor size(cm) (> 5 vs. ≤ 5)",
                            "1.594",
                            "0.904-2.811",
                            "0.107"
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                        [
                            "Cirrhosis",
                            "0.739",
                            "0.292-1.868",
                            "0.522"
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                            "Claudin18.2",
                            "2.545",
                            "1.383-4.682",
                            "0.003*"
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                "note": "Cox regression analyses of disease-free survival for ICC.",
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                            "",
                            "Univariable analysis",
                            "Multivariable analysis"
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                            "Parameters",
                            "HR (95% CI)",
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                            "HR (95% CI)",
                            "P value"
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                            "CA199",
                            "2.350 (1.311-4.213)",
                            "0.004*",
                            "1.517 (0.789-2.920)",
                            "0.212"
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                            "2.594 (1.419-4.742)",
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                            "2.612 (1.313-5.197)",
                            "0.006*"
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                            "",
                            "0.049*",
                            "",
                            "0.409"
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                            "0.637 (0.237-1.716)",
                            "0.373",
                            "0.606 (0.199-1.844)",
                            "0.378"
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                            "0.414 (0.199-0.860)",
                            "0.018*",
                            "0.549 (0.228-1.323)",
                            "0.181"
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                            "2.358 (1.384-4.019)",
                            "0.002*",
                            "2.086 (1.157-3.761)",
                            "0.014*"
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                            "2.594 (1.419-4.742)",
                            "0.002*",
                            "2.612 (1.313-5.197)",
                            "0.006*"
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                            "1.865 (1.053-3.304)",
                            "0.033*",
                            "2.229 (1.125-4.415)",
                            "0.022*"
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                            "1.832 (1.087-3.087)",
                            "0.023*",
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                            "0.003*"
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        "gaps": [
            "corpus_record_absent"
        ]
    },
    "review": {
        "state": "absent",
        "machine_critique": null,
        "human_critique": null,
        "stages": [],
        "gaps": [
            "review.absent: this document is a working version. Review and publication are separate actions, and they belong to the Journal."
        ]
    },
    "execution": {
        "state": "complete",
        "status": "run",
        "mode": "computational",
        "runs": [
            {
                "id": "dacfb9f1-47b7-48a3-8d4e-b54006b447f0",
                "record": "fork:pmid:40951359:claudin182-in-intrahepatic-cholangiocarcinoma-figure-reconciliation-93b66ec8",
                "operation": "published_figure_reconciliation",
                "version": "0.1.0",
                "status": "complete",
                "provider": "automated-assays-computational",
                "result_hash": "12917d11b9ab3cd7374a8f749b4fbd2f5fc3e1905b34119f5f78a14332ff157b",
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            {
                "id": "756cfd0b-d63f-499f-9529-0d0baec01d03",
                "record": "pmid:40951359",
                "operation": "published_figure_reconciliation",
                "version": "0.1.0",
                "status": "complete",
                "provider": "automated-assays-computational",
                "result_hash": "12917d11b9ab3cd7374a8f749b4fbd2f5fc3e1905b34119f5f78a14332ff157b",
                "evidence": "9e23c74aee6fe690b8c30cf38abb40dc9a7b67836787dd2d5349caa1966d438a"
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            {
                "id": "70c7f600-6581-44b6-bcd1-878fe9983bfa",
                "record": "pmid:40951359",
                "operation": "published_figure_reconciliation",
                "version": "0.1.0",
                "status": "complete",
                "provider": "automated-assays-computational",
                "result_hash": "12917d11b9ab3cd7374a8f749b4fbd2f5fc3e1905b34119f5f78a14332ff157b",
                "evidence": "b6f3974e63da3a416ef7523755e11f8ffa6e15990713af093607ee14906493d7"
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            {
                "id": "dc4e03f6-1f79-4cb0-9eef-fe6f6b153d53",
                "record": "pmid:40951359",
                "operation": "published_figure_reconciliation",
                "version": "0.1.0",
                "status": "complete",
                "provider": "automated-assays-computational",
                "result_hash": "5b1465b1229ef43fc41c19875420b221f9c828d51354e1a3167fdd16f44da9fd",
                "evidence": "2e852b2b5310f31340717e393cb569b173729c888da993152bd9144db745cfa7"
            },
            {
                "id": "ff8ba881-0ade-4159-8ada-cc2bd12d2f54",
                "record": "pmid:40951359",
                "operation": "published_figure_reconciliation",
                "version": "0.1.0",
                "status": "complete",
                "provider": "automated-assays-computational",
                "result_hash": "5b1465b1229ef43fc41c19875420b221f9c828d51354e1a3167fdd16f44da9fd",
                "evidence": "46c83314a88d4a8a9f9a2fee50924ec4b84872f3790b543ab4640b748de4cf7e"
            }
        ],
        "gaps": []
    },
    "provenance": {
        "entities": [
            {
                "id": "experiment:93b66ec8-4f5c-443f-96b0-596d87d16ecd",
                "type": "experiment",
                "label": "Claudin18.2 in intrahepatic cholangiocarcinoma: figure reconciliation",
                "owner": "automated-assays",
                "version": "0.1.0",
                "digest": null
            },
            {
                "id": "science-record:pmid:40951359",
                "type": "science_record",
                "label": "The Corpus Engine science record this experiment was opened against",
                "owner": "corpus-engine",
                "version": 2,
                "digest": "sha256:253486a70cb3fa8e7f70d7dba9652e49061645eb758f3dd18d190d1bd5b8391c"
            },
            {
                "id": "assay-definition:published-figure-reconciliation@0.1.0",
                "type": "assay_definition",
                "label": "Published figure reconciliation",
                "owner": "automated-assays",
                "version": "0.1.0",
                "digest": "sha256:731b9afcb16e0ede7a5742f40820f09e7e081f10c769f581a4f44300d21c37ea",
                "definition": {
                    "name": "Published figure reconciliation",
                    "slug": "published-figure-reconciliation",
                    "version": "0.1.0",
                    "owner": "automated-assays",
                    "execution_mode": "computational",
                    "purpose": "Assess whether the counts, denominators and percentages a paper prints are mutually consistent, at the precision each was printed at, and report the comparisons and the discrepancies. This is the analysis the DSL calls published_figure_reconciliation, and it is made of the DSL operations percentage_from_counts and published_precision_envelope. This works on the figures as printed. It is not a re-analysis of the paper's data and it is not a re-execution of the paper's experiment.",
                    "operation": "published_figure_reconciliation",
                    "operation_version": "0.1.0",
                    "dsl_family": "published_figure_reconciliation",
                    "dsl_operations": [
                        "published_precision_envelope",
                        "percentage_from_counts"
                    ],
                    "catalogued_by_corpus": true,
                    "catalogue_note": "Both operations are in the DSL. `published_precision_envelope` is in the `diagnostic_evaluation` family of the catalogue and `percentage_from_counts` is in the `published_figure_reconciliation` family of the DSL compiler, which the catalogue does not yet carry. The DSL has no single operation for the comparison, and none is invented here.",
                    "inputs": {
                        "items": {
                            "type": "array",
                            "description": "The printed quantities. Each carries an id, a kind (count, denominator or percentage), the value as printed and the precision it was printed at, which is the number of decimal places.",
                            "required": true
                        },
                        "assertions": {
                            "type": "array",
                            "description": "The checks to make. Each names a kind: percentage_of, count_from_percentage or sum.",
                            "required": true
                        }
                    },
                    "parameters": {},
                    "outputs": {
                        "status": "consistent, or discrepancies_found",
                        "summary": "How many checks were made and how they came out",
                        "assertions": "Each check with its status, the values it compared and the bounds it used",
                        "discrepancies": "The checks that did not agree, in plain words",
                        "interpretation": "What the result is and is not"
                    },
                    "controls": [
                        "Every value checked against the interval its own printed precision allows, never against the digits as exact",
                        "A check that cannot be made is reported as indeterminate",
                        "The figures as printed are the only input; no data is fetched"
                    ],
                    "refusals": {
                        "items_missing": "The request carried no printed quantities",
                        "assertions_missing": "The request carried no checks to make",
                        "precision_mismatch": "A value cannot be printed at the precision it was given"
                    },
                    "procedure": [
                        {
                            "order": 1,
                            "step": "Read each printed quantity and the interval its printed precision allows"
                        },
                        {
                            "order": 2,
                            "step": "Check the percentage a count and a denominator imply against the printed percentage"
                        },
                        {
                            "order": 3,
                            "step": "Check the count a percentage and a denominator imply, and whether any whole number fits"
                        },
                        {
                            "order": 4,
                            "step": "Check that parts add up to a printed total"
                        },
                        {
                            "order": 5,
                            "step": "Report the checks that could not be made as indeterminate rather than as a pass"
                        }
                    ],
                    "execution": {
                        "default_provider": "automated-assays-computational",
                        "provider_rule": "A request may name a provider that supports the exact operation. A provider that does not support it is refused, and is never substituted for one that does.",
                        "request": {
                            "required": {
                                "source_record_id": "The science record the work is about.",
                                "source_content_hash": "The exact version of that record, as sha256:<hex>. The request is refused if the platform does not hold that version.",
                                "operation": "The operation to run.",
                                "operation_version": "The version of that operation.",
                                "inputs": "The inputs the operation takes."
                            },
                            "optional": {
                                "request_id": "The identity of the request. A retry with the same identity and the same request returns the execution that already exists, rather than running the work twice. A retry with the same identity and a different request — a different source, operation, set of inputs, set of parameters or provider — is refused, and the execution that already exists is left unchanged.",
                                "parameters": "The parameters of the run.",
                                "provider": "A provider that supports the exact operation. The default is Automated Assays. A provider that does not support the operation is refused and never substituted for one that does.",
                                "assay_id": "The identity of the assay entry the work concerns, inside the source record. A record of version 1.2 carries an ordered set of assays and every entry has an identity, so a request that names one says exactly which assay of the record the work belongs to. The entry has to be one the record holds and the operation has to be one that entry requires, or the request is refused rather than run against some other assay.",
                                "assay_entry": "The assay entry the work concerns, inside the source record. A science record carries an ordered set of assays, so a record and an operation do not on their own say which of that record's assays the work belongs to. Give definition_id, and definition_version and definition_digest when they are known. When the entry is given and does not match the operation named, the request is refused rather than quietly run against the other entry. This is the earlier form of the same reference and is still accepted; assay_id names the entry by the identity it has inside the record."
                            },
                            "refusals": {
                                "unsupported_operation": "This platform does not run the operation named.",
                                "unsupported_version": "This platform does not run that operation at the version named.",
                                "provider_unknown": "No provider is registered under the name given.",
                                "provider_unsupported": "The provider named does not offer the operation at a version that is available for execution.",
                                "no_provider_available": "The default provider does not offer the operation, and no provider that does something else is substituted for one.",
                                "source_record_missing": "The request did not name the science record the work is about.",
                                "source_hash_missing": "The request did not bind the exact version of the record, as a sha256 content hash.",
                                "source_record_not_held": "This platform holds no science record under that identifier.",
                                "source_hash_mismatch": "The version of the record the platform holds is not the version the request names.",
                                "request_id_conflict": "The request identity has already been answered by a different request. The execution that already exists is unchanged.",
                                "assay_entry_mismatch": "The assay entry named is not one the record holds, or it does not require the operation named, so the request does not say which assay of the record the work concerns."
                            },
                            "endpoint": {
                                "method": "POST",
                                "path": "/api/v1/executions",
                                "authentication": "A bearer token, checked by the paper-assay-api middleware.",
                                "responses": {
                                    "201": "The work ran, or the answer to this request had already been given.",
                                    "202": "The work is already under way under this identity. The execution is named in the response and can be read back.",
                                    "409": "The request identity has already been answered by a different request. The execution that already exists is unchanged.",
                                    "422": "The request was refused. The code and the reason are in the response."
                                }
                            }
                        },
                        "result": {
                            "request_id": "The identity of the request.",
                            "execution_id": "The identity of the execution.",
                            "status": "complete, refused or failed.",
                            "provider": "The provider that actually ran it, with the capability key and version.",
                            "source": "The record and the exact version it was bound to.",
                            "input_hash": "The canonical hash of the request inputs and parameters.",
                            "result_hash": "The canonical hash of the result.",
                            "evidence_hash": "The canonical hash of the evidence manifest.",
                            "finding": "What was found, in bounded words.",
                            "result": "The full result, in the shape the operation defines."
                        }
                    }
                }
            }
        ],
        "activities": [
            {
                "id": "activity:fork:pmid:40951359",
                "type": "fork",
                "label": "Opened from fork:pmid:40951359:claudin182-in-intrahepatic-cholangiocarcinoma-figure-reconciliation-93b66ec8 at version sha256:166ec67c5406055f1fab245b60f439808767532b2376edf8834c377dda279c72",
                "used": [
                    "fork:pmid:40951359:claudin182-in-intrahepatic-cholangiocarcinoma-figure-reconciliation-93b66ec8"
                ],
                "agent": "agent:user:0195616cec89"
            },
            {
                "id": "activity:request-contract:published_figure_reconciliation",
                "type": "assay_request_contract",
                "label": "The request and result contract for this assay",
                "used": [
                    "assay-definition:published-figure-reconciliation@0.1.0"
                ],
                "agent": "agent:automated-assays",
                "request": {
                    "required": {
                        "source_record_id": "The science record the work is about.",
                        "source_content_hash": "The exact version of that record, as sha256:<hex>. The request is refused if the platform does not hold that version.",
                        "operation": "The operation to run.",
                        "operation_version": "The version of that operation.",
                        "inputs": "The inputs the operation takes."
                    },
                    "optional": {
                        "request_id": "The identity of the request. A retry with the same identity and the same request returns the execution that already exists, rather than running the work twice. A retry with the same identity and a different request — a different source, operation, set of inputs, set of parameters or provider — is refused, and the execution that already exists is left unchanged.",
                        "parameters": "The parameters of the run.",
                        "provider": "A provider that supports the exact operation. The default is Automated Assays. A provider that does not support the operation is refused and never substituted for one that does.",
                        "assay_id": "The identity of the assay entry the work concerns, inside the source record. A record of version 1.2 carries an ordered set of assays and every entry has an identity, so a request that names one says exactly which assay of the record the work belongs to. The entry has to be one the record holds and the operation has to be one that entry requires, or the request is refused rather than run against some other assay.",
                        "assay_entry": "The assay entry the work concerns, inside the source record. A science record carries an ordered set of assays, so a record and an operation do not on their own say which of that record's assays the work belongs to. Give definition_id, and definition_version and definition_digest when they are known. When the entry is given and does not match the operation named, the request is refused rather than quietly run against the other entry. This is the earlier form of the same reference and is still accepted; assay_id names the entry by the identity it has inside the record."
                    },
                    "refusals": {
                        "unsupported_operation": "This platform does not run the operation named.",
                        "unsupported_version": "This platform does not run that operation at the version named.",
                        "provider_unknown": "No provider is registered under the name given.",
                        "provider_unsupported": "The provider named does not offer the operation at a version that is available for execution.",
                        "no_provider_available": "The default provider does not offer the operation, and no provider that does something else is substituted for one.",
                        "source_record_missing": "The request did not name the science record the work is about.",
                        "source_hash_missing": "The request did not bind the exact version of the record, as a sha256 content hash.",
                        "source_record_not_held": "This platform holds no science record under that identifier.",
                        "source_hash_mismatch": "The version of the record the platform holds is not the version the request names.",
                        "request_id_conflict": "The request identity has already been answered by a different request. The execution that already exists is unchanged.",
                        "assay_entry_mismatch": "The assay entry named is not one the record holds, or it does not require the operation named, so the request does not say which assay of the record the work concerns."
                    },
                    "endpoint": {
                        "method": "POST",
                        "path": "/api/v1/executions",
                        "authentication": "A bearer token, checked by the paper-assay-api middleware.",
                        "responses": {
                            "201": "The work ran, or the answer to this request had already been given.",
                            "202": "The work is already under way under this identity. The execution is named in the response and can be read back.",
                            "409": "The request identity has already been answered by a different request. The execution that already exists is unchanged.",
                            "422": "The request was refused. The code and the reason are in the response."
                        }
                    }
                },
                "result": {
                    "request_id": "The identity of the request.",
                    "execution_id": "The identity of the execution.",
                    "status": "complete, refused or failed.",
                    "provider": "The provider that actually ran it, with the capability key and version.",
                    "source": "The record and the exact version it was bound to.",
                    "input_hash": "The canonical hash of the request inputs and parameters.",
                    "result_hash": "The canonical hash of the result.",
                    "evidence_hash": "The canonical hash of the evidence manifest.",
                    "finding": "What was found, in bounded words.",
                    "result": "The full result, in the shape the operation defines."
                }
            }
        ],
        "agents": [
            {
                "id": "agent:user:0195616cec89",
                "type": "person",
                "label": "Automated Assays Administrator",
                "identity": "admin@automated-assays.local",
                "role": "author"
            },
            {
                "id": "agent:automated-assays",
                "type": "software",
                "label": "Automated Assays"
            }
        ],
        "source_run_id": "assays-session-93b66ec8-4f5c-443f-96b0-596d87d16ecd",
        "dsl_catalogue_fingerprint": null,
        "capability_table_fingerprint": null,
        "snapshot_id": null
    },
    "lineage": {
        "parent_id": "fork:pmid:40951359:claudin182-in-intrahepatic-cholangiocarcinoma-figure-reconciliation-93b66ec8",
        "parent_hash": "sha256:166ec67c5406055f1fab245b60f439808767532b2376edf8834c377dda279c72",
        "fork_of": "pmid:40951359",
        "generation": 5
    },
    "gaps": [],
    "assays": [
        {
            "id": "assay:1",
            "role": "primary",
            "order_basis": "platform_plan_order:0",
            "definition_id": "published-figure-reconciliation",
            "definition_version": "0.1.0",
            "definition_digest": "sha256:731b9afcb16e0ede7a5742f40820f09e7e081f10c769f581a4f44300d21c37ea",
            "required_operations": [
                "published_figure_reconciliation",
                "published_precision_envelope",
                "percentage_from_counts"
            ],
            "support_state": "supported",
            "source_hashes": {
                "assay_definition": "sha256:731b9afcb16e0ede7a5742f40820f09e7e081f10c769f581a4f44300d21c37ea",
                "science_record": "sha256:253486a70cb3fa8e7f70d7dba9652e49061645eb758f3dd18d190d1bd5b8391c"
            },
            "definition": {
                "definition_id": "published-figure-reconciliation",
                "definition_version": "0.1.0",
                "definition_digest": "sha256:731b9afcb16e0ede7a5742f40820f09e7e081f10c769f581a4f44300d21c37ea",
                "required_operations": [
                    "published_precision_envelope",
                    "percentage_from_counts"
                ],
                "support_state": "supported",
                "input_contract": {
                    "items": {
                        "type": "array",
                        "description": "The printed quantities. Each carries an id, a kind (count, denominator or percentage), the value as printed and the precision it was printed at, which is the number of decimal places.",
                        "required": true
                    },
                    "assertions": {
                        "type": "array",
                        "description": "The checks to make. Each names a kind: percentage_of, count_from_percentage or sum.",
                        "required": true
                    }
                },
                "parameter_contract": {},
                "output_contract": {
                    "status": "consistent, or discrepancies_found",
                    "summary": "How many checks were made and how they came out",
                    "assertions": "Each check with its status, the values it compared and the bounds it used",
                    "discrepancies": "The checks that did not agree, in plain words",
                    "interpretation": "What the result is and is not"
                }
            },
            "request": {
                "assay_id": "assay:1",
                "source_record_id": "fork:pmid:40951359:claudin182-in-intrahepatic-cholangiocarcinoma-figure-reconciliation-93b66ec8",
                "source_content_hash": "sha256:9b18d33a18f874d761a784428a339b58a4142d9e363c1f82ff132423d7bb06f9",
                "operation": "published_figure_reconciliation",
                "operation_version": "0.1.0",
                "inputs": [
                    {
                        "id": "printed_percentage",
                        "kind": "percentage",
                        "value": 24.1,
                        "precision": 1,
                        "label": "the percentage the paper prints",
                        "quote": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.",
                        "locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"
                    },
                    {
                        "id": "printed_count",
                        "kind": "count",
                        "value": 20,
                        "precision": 0,
                        "label": "the count the paper prints beside the percentage",
                        "quote": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.",
                        "locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"
                    },
                    {
                        "id": "printed_denominator",
                        "kind": "denominator",
                        "value": 83,
                        "precision": 0,
                        "label": "the denominator the paper prints beside the percentage",
                        "quote": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.",
                        "locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"
                    }
                ],
                "parameters": {},
                "request_id": "aa-fork-pmid40951359-figure-reconciliation-v1",
                "provider": "automated-assays-computational"
            },
            "result": {
                "assay_id": "assay:1",
                "provider": "automated-assays-computational",
                "execution_id": "dacfb9f1-47b7-48a3-8d4e-b54006b447f0",
                "input_hash": "sha256:012d7daf644cbee995f7b048ec45d10160843eb464a80764daf1072783129860",
                "result_hash": "12917d11b9ab3cd7374a8f749b4fbd2f5fc3e1905b34119f5f78a14332ff157b",
                "evidence_hash": "d302cf5ee6285e7cab5cf4d427788b830ba506a8dc65681da0facaf158ae802d",
                "status": "complete",
                "finding": "assertions=1 consistent=1 inconsistent=0 indeterminate=0",
                "result": {
                    "status": "consistent",
                    "summary": {
                        "assertions": 1,
                        "consistent": 1,
                        "inconsistent": 0,
                        "indeterminate": 0
                    },
                    "assertions": [
                        {
                            "id": "percentage_of_count",
                            "label": "the printed percentage is the printed count out of the printed denominator",
                            "kind": "percentage_of",
                            "status": "consistent",
                            "inputs": {
                                "numerator": {
                                    "id": "printed_count",
                                    "value": 20
                                },
                                "denominator": {
                                    "id": "printed_denominator",
                                    "value": 83
                                },
                                "percentage": {
                                    "id": "printed_percentage",
                                    "value": 24.1,
                                    "precision": 1
                                }
                            },
                            "implied": {
                                "percentage": 24.096385542168676
                            },
                            "bounds": {
                                "published": {
                                    "lower": 24.05,
                                    "upper": 24.15,
                                    "precision": 1,
                                    "printed": 24.1
                                }
                            },
                            "dsl": {
                                "published_precision_envelope": {
                                    "value": 24.1,
                                    "half_width": 0.049999999999998934,
                                    "lower": 24.05,
                                    "upper": 24.15,
                                    "method": "printed_precision",
                                    "deterministic": true
                                },
                                "percentage_from_counts": {
                                    "value": 24.096385542168676,
                                    "unit": "percentage_points",
                                    "deterministic": true,
                                    "proportion": 0.24096385542168675,
                                    "count": 20,
                                    "denominator": 83
                                }
                            },
                            "difference": -0.003614457831325524,
                            "excess": 0,
                            "detail": "The count 20 over the denominator 83 is 24.0964%, which is inside the 24.0500% to 24.1500% that the printed 24.1% stands for."
                        }
                    ],
                    "discrepancies": [],
                    "provenance": {
                        "items": [
                            {
                                "id": "printed_percentage",
                                "kind": "percentage",
                                "published_value": 24.1,
                                "precision": 1,
                                "label": "the percentage the paper prints",
                                "quote": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.",
                                "locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"
                            },
                            {
                                "id": "printed_count",
                                "kind": "count",
                                "published_value": 20,
                                "precision": 0,
                                "label": "the count the paper prints beside the percentage",
                                "quote": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.",
                                "locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"
                            },
                            {
                                "id": "printed_denominator",
                                "kind": "denominator",
                                "published_value": 83,
                                "precision": 0,
                                "label": "the denominator the paper prints beside the percentage",
                                "quote": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.",
                                "locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"
                            }
                        ],
                        "assertions": [
                            {
                                "id": "percentage_of_count",
                                "kind": "percentage_of",
                                "label": "the printed percentage is the printed count out of the printed denominator"
                            }
                        ],
                        "rounding": "Each printed percentage is treated as the interval its printed precision allows, not as the exact number printed.",
                        "definitions": {
                            "percentage_of": "The percentage a count and a denominator imply, against the percentage the paper printed.",
                            "count_from_percentage": "The count a percentage and a denominator imply, against the count the paper printed, and whether any whole number is consistent at all.",
                            "sum": "Parts that add up to a total."
                        }
                    },
                    "interpretation": "This is a check of the figures as printed against each other, at the precision each was printed at. It is not a re-analysis of the paper's data and it is not a re-execution of the paper's experiment."
                }
            }
        }
    ]
}