← All .science files
pmid:35875153
Prognostic Significance of the Systemic Immune-Inflammation Index in Patients With Cholangiocarcinoma: A Meta-Analysis
Frontiers in Oncology · 2022 doi:10.3389/fonc.2022.938549
Paper
partial
Experiment
partial
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
generator object · 3 fields
paper object · 10 fields
claims array · 1 item
[0] object · 6 fields
target object · 4 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 2 items
experiment object · 8 fields
steps array · 4 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[3] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 0 items
instruments array · 0 items
reagents array · 0 items
materials array · 2 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 3 items
data object · 3 fields
assets array · 7 items
[0] object · 15 fields
structure object · 1 field
[1] object · 15 fields
structure object · 2 fields
[2] object · 15 fields
structure object · 2 fields
[3] object · 15 fields
structure object · 2 fields
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 6 items
[0] array · 10 items
[1] array · 10 items
[2] array · 10 items
[3] array · 10 items
[4] array · 10 items
[5] array · 10 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 10 items
[0] array · 6 items
[1] array · 7 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 7 items
[6] array · 7 items
[7] array · 6 items
[8] array · 6 items
[9] array · 7 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 25 items
[0] array · 4 items
[1] array · 7 items
[2] array · 7 items
[3] array · 1 item
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 1 item
[8] array · 7 items
[9] array · 7 items
[10] array · 1 item
[11] array · 7 items
[12] array · 7 items
[13] array · 1 item
[14] array · 7 items
[15] array · 7 items
[16] array · 1 item
[17] array · 7 items
[18] array · 7 items
[19] array · 1 item
[20] array · 7 items
[21] array · 7 items
[22] array · 1 item
[23] array · 7 items
[24] array · 7 items
gaps array · 4 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
targets array · 1 item
gaps array · 2 items
capability object · 3 fields
requirements array · 2 items
[0] object · 6 fields
assay_families array · 9 items
[1] object · 6 fields
assay_families array · 19 items
gaps array · 1 item
readiness object · 8 fields
axes object · 3 fields
method object · 4 fields
detail object · 3 fields
capability object · 4 fields
detail object · 3 fields
families array · 0 items
data object · 4 fields
detail object · 3 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 2 items
capabilities array · 1 item
data_gaps array · 4 items
gaps array · 1 item
review object · 5 fields
machine_critique object · 7 fields
providers array · 1 item
[0] object · 7 fields
target_providers array · 2 items
[0] object · 8 fields
reading object · 6 fields
[1] object · 8 fields
reading object · 6 fields
disagreements array · 0 items
agreement_basis object · 3 fields
decisive_fields array · 4 items
advisory_fields array · 0 items
human_critique object · 5 fields
stages array · 7 items
[0] object · 4 fields
[1] object · 4 fields
evidence object · 1 field
provider_errors array · 1 item
[0] object · 3 fields
[2] object · 4 fields
[3] object · 4 fields
[4] object · 4 fields
[5] object · 4 fields
[6] object · 4 fields
gaps array · 2 items
provenance object · 7 fields
entities array · 1 item
activities array · 1 item
agents array · 2 items
lineage object · 4 fields
gaps array · 16 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35875153", "kind": "science-record", "revision": 2, "content_hash": "sha256:414dc50878bf6cd16447e75c54502d989622ce9ba213a3a4d8eae93d74ff3670", "created_at": "2026-11-01T10:25:48Z", "updated_at": "2026-11-01T14:01:31Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Prognostic Significance of the Systemic Immune-Inflammation Index in Patients With Cholangiocarcinoma: A Meta-Analysis", "doi": "10.3389/fonc.2022.938549", "pmid": "35875153", "authors": null, "journal": "Frontiers in Oncology", "year": 2022, "abstract": null, "claims": [{"id": "claim-1", "statement": "the pooled hazard ratio for overall survival in cholangiocarcinoma patients with a high preoperative systemic immune-inflammation index", "kind": "quantitative", "state": "complete", "target": {"value": 1.916, "unit": "hazard ratio", "tolerance": null, "source": "chars 899-1066 of source sha256 dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d"}, "evidence": [{"asset": "source:pmid:35875153", "locator": "chars 899-1066 of source sha256 dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d", "quote": "The results showed that a higher SII was associated with poor OS in patients with CCA who underwent invasive surgery (HR=1.916; 95% CI, 1.566–2.343; Z=6.329; P<0.001)."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the pooled hazard ratio for overall survival in cholangiocarcinoma patients with a high preoperative systemic immune-inflammation index", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35875153"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "method:epidemiological_modelling_incidence_rate", "description": "Re-run the paper's analysis on the source data and produce the registered result.", "duration_hours": null, "parameters": {}, "inputs": ["materials:the analysis programme that recomputes the published estimate"], "outputs": ["the registered result"], "instruments": [], "reagents": []}, {"id": "provide_capability_bench_workcell", "order": 4, "name": "Provide General bench workcell (liquid transfer, plate handling, incubation)", "kind": "computational", "state": "blocked", "blocked_on": "instrument not yet purchased", "description": "Make this capability available to the experiment: amplicon_seq, animal_model, apoptosis_assay, cell_culture, cell_imaging, chip_seq, clinical_cohort, clinical_trial, elisa, flow_cytometry, ihc, image_quantification, mass_spectrometry, methylation_array, microarray, qpcr, rna_seq, transfection, western_blot", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": [], "instruments": [], "reagents": []}], "materials": ["the source data behind pmid:35875153, which the paper says are available from the authors on request", "the analysis programme that recomputes the published estimate"], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent", "step:provide_capability_bench_workcell blocked on instrument not yet purchased", "step:run_analysis blocked on method:epidemiological_modelling_incidence_rate"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35875153", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2022.938549", "sha256": "sha256:dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2022.938549", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "materials:the source data behind pmid:35875153, which the paper says are available from the authors on request", "role": "raw", "format": "unknown", "media_type": "application/octet-stream", "uri": null, "sha256": null, "bytes": null, "access": "restricted", "state": "declared", "reader": null, "reader_status": "unknown", "identifier": null, "version": null, "note": "the source data behind pmid:35875153, which the paper says are available from the authors on request", "structure": {"material_kind": "dataset", "access_state": "restricted"}}, {"id": "materials:the analysis programme that recomputes the published estimate", "role": "code", "format": "unknown", "media_type": "application/octet-stream", "uri": null, "sha256": null, "bytes": null, "access": "unknown", "state": "unavailable", "reader": null, "reader_status": "unknown", "identifier": null, "version": null, "note": "the analysis programme that recomputes the published estimate", "structure": {"material_kind": "code", "access_state": "absent"}}, {"id": "data:availability", "role": "raw", "format": "unknown", "media_type": "application/octet-stream", "uri": null, "sha256": null, "bytes": null, "access": "unknown", "state": "declared", "reader": null, "reader_status": "unknown", "identifier": null, "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "structure": {"access_route": "request_on_author", "location": "section [data-availability-statement]: Data Availability Statement"}}, {"id": "asset:table:pmid:35875153:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dde8fb953b5488e988cf9bf4d2ac317c2909f9145af44754940d8a505e82642c", "bytes": 997, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "Main characteristic of the included studies.", "structure": {"pmcid": "PMC9300870", "section_index": 9, "section_title": "Results", "row_count": 6, "column_count": 10}, "table": {"label": "Table 1", "caption": "Main characteristic of the included studies.", "rows": [["Author", "Year", "Study duration", "Study design", "Sample size", "Treatment", "SII cutoff values", "Outcome", "NOS", "HR (95%CI)"], ["Tsilimigras DI (20)", "2020", "2020–2017", "Cohort", "688", "Radical surgery", "1150", "OSCSS", "8", "OS: 1.70 (1.23–2.34)CSS: 1.55(1.09–2.21)"], ["Hui Li (21)", "2020", "2009–2017", "Cohort", "530", "Radical surgery", "450", "OSRFS", "9", "OS: 1.774 (1.245-2.528)RFS: 1.385 (1.005-1.909)"], ["Zeyu Zhang (22)", "2020", "2013–2017", "Cohort", "128", "Radical surgery", "1027", "OSRFS", "8", "OS: 2.454 (1.278-4.712)RFS: 2.368 (1.279-4.386)"], ["Fumihiro Terasaki (23)", "2020", "2002–2015", "Cohort", "140", "Radical surgery", "1450", "OS", "9", "OS: 2.05 (1.03-4.06)"], ["Jian LI (24)", "2021", "2012–2016", "Cohort", "181", "Radical surgery or palliative surgery", "412.6", "OS", "9", "OS: 2.887(2.256-7.903)"]], "row_count": 6, "column_count": 10, "numeric_cells": 36, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:35875153:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:af2d5d268637b2330cc6071e9945025ab75ca912a3101c497f0bf534ce0fec8c", "bytes": 1032, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#T2", "version": null, "note": "Items of NOS of included studies in the meta-analysis.", "structure": {"pmcid": "PMC9300870", "section_index": 9, "section_title": "Results", "row_count": 10, "column_count": 7}, "table": {"label": "Table 2", "caption": "Items of NOS of included studies in the meta-analysis.", "rows": [["Study (author year)", "Tsilimigras DI 2020", "Hui Li 2020", "Zeyu Zhang 2020", "Fumihiro Terasaki 2020", "Jian Li 2021"], ["Selection", "Representativeness of the exposed cohort", "●", "●", "●", "●", "●"], ["Selection of the non-exposed cohort", "●", "●", "●", "●", "●"], ["Ascertainment of exposure", "●", "●", "●", "●", "●"], ["Demonstration that the outcome of interest was not present at the start of the study", "●", "●", "●", "●", "●"], ["Comparability", "Comparability of cohorts based on the design or analysis", "●○", "●●", "●○", "●●", "●●"], ["Outcome", "Assessment of outcome", "●", "●", "●", "●", "●"], ["Was follow-up long enough for outcomes to occur", "●", "●", "●", "●", "●"], ["Adequacy of follow-up of cohorts", "●", "●", "●", "●", "●"], ["Total score", "", "8", "9", "8", "9", "9"]], "row_count": 10, "column_count": 7, "numeric_cells": 10, "header_rows": 1, "locator": "section[9]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:35875153:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1866315024b1918ec2dba5794470340a8a91a2c87269e30ce24ba534b286c7e9", "bytes": 1470, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T3", "version": null, "note": "Subgroup analysis for OS.", "structure": {"pmcid": "PMC9300870", "section_index": 11, "section_title": "Subgroup Analysis and Metaregression Analysis", "row_count": 25, "column_count": 7}, "table": {"label": "Table 3", "caption": "Subgroup analysis for OS.", "rows": [["Subgroups", "No. of studies", "Heterogeneity", "Fixed-effects model"], ["", "", "I2(%)", "P", "HR (95%CI)", "Z", "P"], ["Total", "5", "0.0%", "0.567", "1.92 (1.57–2.34)", "6.329", "<0.001"], ["Country"], ["China", "3", "3.5%", "0.355", "2.07 (1.57–2.74)", "5.124", "<0.001"], ["America", "1", "–", "–", "1.70 (1.23–2.34)", "3.234", "<0.001"], ["Japan", "1", "–", "–", "2.05 (1.03–4.07)", "2.051", "0.040"], ["Age (years)"], ["≥60", "2", "0.0%", "0.567", "2.47 (1.56–3.92)", "3.831", "<0.001"], ["<60", "3", "0.0%", "0.608", "1.81 (1.44–2.26)", "5.177", "<0.001"], ["Sample size"], ["<150", "2", "0.0%", "0.710", "2.25 (1.40–3.61)", "3.368", "<0.001"], [">150", "3", "11.3%", "0.324", "1.85 (1.48–2.31)", "5.409", "<0.001"], ["Cutoff value"], ["<500", "2", "43.1%", "0.185", "2.00 (1.47–2.72)", "4.393", "<0.001"], [">500", "3", "0.0%", "0.585", "1.86 (1.43–2.42)", "4.568", "<0.001"], ["Treatment"], ["Radical surgery", "4", "0.0%", "0.774", "1.83 (1.48-2.26)", "5.558", "<0.001"], ["Radical/palliative surgery", "1", "–", "–", "2.89 (1.54–5.40)", "3.315", "0.001"], ["Chemotherapy"], ["Excluded", "3", "3.5%", "0.539", "2.07 (1.57–2.74)", "5.124", "<0.001"], ["Included", "2", "0.0%", "0.628", "1.76 (1.31–2.35)", "3.799", "<0.001"], ["NOS"], ["8", "2", "0.0%", "0.323", "1.83 (1.37–2.44)", "4.093", "<0.001"], ["9", "3", "0.0%", "0.414", "2.00 (1.51–2.66)", "4.848", "<0.001"]], "row_count": 25, "column_count": 7, "numeric_cells": 99, "header_rows": 2, "locator": "section[11]/table-wrap[1]#T3"}}], "gaps": ["asset:data:availability not verified", "asset:materials:the analysis programme that recomputes the published estimate not verified", "asset:materials:the source data behind pmid:35875153, which the paper says are available from the authors on request not verified", "asset:source:pmid:35875153 not verified"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "meta_analysis", "specific": "meta-analysis", "label": "", "dsl_operations": [], "missing_operations": [], "expressible": false, "parameters": {}, "data_shapes": [], "evidence": {"score": 0.0, "band": "low", "quote": "This meta-analysis was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines (15). Ethical approval was not required for this meta-analysis because the data were extracted from published studies."}}], "targets": [{"id": "target-1", "claim_id": "claim-1", "operation": null, "expected_value": 1.916, "unit": "hazard ratio", "tolerance": null, "state": "complete"}], "gaps": ["method.corpus_not_determined", "method.operations"]}, "capability": {"state": "partial", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["differential_expression", "gwas", "machine_learning", "meta_analysis", "molecular_docking", "network_analysis", "pca", "statistical_regression", "survival_analysis"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}, {"capability_id": "capability:bench_workcell", "label": "General bench workcell (liquid transfer, plate handling, incubation)", "assay_families": ["amplicon_seq", "animal_model", "apoptosis_assay", "cell_culture", "cell_imaging", "chip_seq", "clinical_cohort", "clinical_trial", "elisa", "flow_cytometry", "ihc", "image_quantification", "mass_spectrometry", "methylation_array", "microarray", "qpcr", "rna_seq", "transfection", "western_blot"], "availability_state": "purchasable", "tier_unlocked": "R3", "candidate": "Supplier-neutral 96/384-well liquid handler"}], "gaps": ["capability:capability:bench_workcell purchasable"]}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"axis": "method", "tier": "R4", "blocker": "method:not_determinable", "detail": {"outcome": "not_determinable", "reason": "No specific statistical method is stated in recognised wording. Full methods review is required.", "basis": "The title, abstract and methods text do not carry the method, so a person has to read the paper before it can be programmed."}}, "capability": {"axis": "capability", "tier": "R1", "blocker": null, "detail": {"families": [], "applies": false, "basis": "This paper needs no bench capability: it computes on data it already has."}}, "data": {"axis": "data", "tier": "R4", "blocker": "data:accession_absent", "detail": {"applies": true, "reachable": false, "basis": "The record names no repository accession and no data-availability statement, so the source data has to be requested from the authors."}}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35875153", "asset:table:pmid:35875153:1", "asset:table:pmid:35875153:2", "asset:table:pmid:35875153:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["unknown", "xml"], "capabilities": ["capability:bench_workcell"], "data_gaps": ["source:pmid:35875153", "materials:the source data behind pmid:35875153, which the paper says are available from the authors on request", "materials:the analysis programme that recomputes the published estimate", "data:availability"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax-m3-1-flash", "model": "MiniMax-M3.1-Flash", "prompt_version": "peer-review-reading-v1", "prompt_hash": "410df12e74cd37da4819cc6ac3a5c7dcc6698c1ddf23e31a87eaae14425483b1", "source_hash": "dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d", "raw_response_sha256": "sha256:b80fed4203c94d20f2fb84b27a68d7c3413fbe4d1048eb3a7a73a69da653a580", "raw_response_chars": 1775}], "target_providers": [{"provider": "minimax-m3-1-flash", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "721989aa7bc7135209933e4e15129d1c1cfa80461518d17231f096b134fb3118", "source_hash": "dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d", "raw_response": "{\"parent_value\":1.916,\"unit\":\"hazard ratio\",\"evidence\":\"The results showed that a higher SII was associated with poor OS in patients with CCA who underwent invasive surgery (HR=1.916; 95% CI, 1.566–2.343; Z=6.329; P<0.001).\",\"target_result\":\"Pooled hazard ratio for overall survival in cholangiocarcinoma patients with a high preoperative systemic immune-inflammation index.\",\"number_stated\":true}", "reading": {"parent_value": 1.916, "unit": "hazard ratio", "evidence": "The results showed that a higher SII was associated with poor OS in patients with CCA who underwent invasive surgery (HR=1.916; 95% CI, 1.566–2.343; Z=6.329; P<0.001).", "target_result": "Pooled hazard ratio for overall survival in cholangiocarcinoma patients with a high preoperative systemic immune-inflammation index.", "number_stated": true, "source_locator": "chars 899-1066 of source sha256 dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d"}, "recorded_at": "2026-10-31T14:38:16.625355+00:00"}, {"provider": "minimax-m3", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "6cd19a5dea7e7fdf65d56fe09111be79e9c795247623005326e844e71bf8f2df", "source_hash": "dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d", "raw_response": "{\"parent_value\":1.916,\"unit\":\"HR\",\"evidence\":\"The results showed that a higher SII was associated with poor OS in patients with CCA who underwent invasive surgery (HR=1.916; 95% CI, 1.566–2.343; Z=6.329; P<0.001).\",\"target_result\":\"Pooled hazard ratio for overall survival: 1.916\",\"number_stated\":true}", "reading": {"parent_value": 1.916, "unit": "HR", "evidence": "The results showed that a higher SII was associated with poor OS in patients with CCA who underwent invasive surgery (HR=1.916; 95% CI, 1.566–2.343; Z=6.329; P<0.001).", "target_result": "Pooled hazard ratio for overall survival: 1.916", "number_stated": true, "source_locator": "chars 899-1066 of source sha256 dd8ba0399541fb275f848046a3dc2c6448dd5df836b18cc03d3ca2b06b48525d"}, "recorded_at": "2026-10-31T14:38:21.921992+00:00"}], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["number_stated", "parent_value", "unit", "work_type"], "advisory_fields": []}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The reading stage and the target extraction did not both return two readings, so the package claims no agreement.", "evidence": {"provider_errors": [{"provider": "minimax-m3", "model": "MiniMax-M3", "reason": "a quoted span is absent from the supplied text"}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:8502a3141103c305050ce64836cf27dd6f8cd0c3387ed2537500152ffefb9edd", "type": "sep_package", "label": "SEP v1 package for pmid:35875153"}], "activities": [{"id": "activity:conversion:pmid:35875153", "type": "conversion", "used": ["package:8502a3141103c305050ce64836cf27dd6f8cd0c3387ed2537500152ffefb9edd"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax-m3-1-flash", "type": "model", "label": "minimax-m3-1-flash"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35875153", "parent_hash": "sha256:dfc47f63b21c615d435877fc837d83ae4527e52632686834a0add57fed498727", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:data:availability not verified", "asset:materials:the analysis programme that recomputes the published estimate not verified", "asset:materials:the source data behind pmid:35875153, which the paper says are available from the authors on request not verified", "asset:source:pmid:35875153 not verified", "authors", "capability:capability:bench_workcell purchasable", "execution.not_run", "method.corpus_not_determined", "method.operations", "method:not_determinable", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:accession_absent", "step:provide_capability_bench_workcell blocked on instrument not yet purchased", "step:run_analysis blocked on method:epidemiological_modelling_incidence_rate"]}