← All .science files
pmid:36013502
Helicobacterpylori Infection-A Risk Factor for Irritable Bowel Syndrome? An Updated Systematic Review and Meta-Analysis.
Medicina (Kaunas, Lithuania) · 2022 doi:10.3390/medicina58081035
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
gaps array · 2 items
experiment object · 8 fields
steps array · 3 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
materials array · 2 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 2 items
data object · 3 fields
assets array · 3 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
gaps array · 3 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
targets array · 1 item
gaps array · 2 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
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 · 0 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 · 0 items
data_gaps array · 3 items
gaps array · 1 item
review object · 5 fields
machine_critique object · 7 fields
providers array · 2 items
[0] object · 7 fields
[1] 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 object · 3 fields
target_result object · 3 fields
analysis_methods object · 3 fields
minimax-m3-1-flash array · 8 items
minimax-m3 array · 5 items
source_claims object · 3 fields
minimax-m3-1-flash array · 4 items
minimax-m3 array · 4 items
agreement_basis object · 3 fields
decisive_fields array · 4 items
advisory_fields array · 3 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 · 0 items
[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 · 3 items
lineage object · 4 fields
gaps array · 13 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36013502", "kind": "science-record", "revision": 1, "content_hash": "sha256:b3f7fa351e67f2889d22b4ca6693752077c543fd56a4f41e72ab5d7aeeadaae8", "created_at": "2026-11-01T10:25:48Z", "updated_at": "2026-11-01T10:25:48Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Helicobacterpylori Infection-A Risk Factor for Irritable Bowel Syndrome? An Updated Systematic Review and Meta-Analysis.", "doi": "10.3390/medicina58081035", "pmid": "36013502", "authors": null, "journal": "Medicina (Kaunas, Lithuania)", "year": 2022, "abstract": null, "claims": [{"id": "claim-1", "statement": "the pooled odds ratio of the association between Helicobacter pylori infection and irritable bowel syndrome", "kind": "quantitative", "state": "complete", "target": {"value": 1.03, "unit": "odds ratio", "tolerance": null, "source": "chars 964-1057 of source sha256 79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71"}, "evidence": [{"asset": "source:pmid:36013502", "locator": "chars 964-1057 of source sha256 79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71", "quote": "The pooled OR of the association between HPI and IBS was 1.03 (95% CI [0.80,1.31]; p = 0.84)."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the pooled odds ratio of the association between Helicobacter pylori infection and irritable bowel syndrome", "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:36013502"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the study data behind the published pooled estimate", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The published estimate cannot be recomputed without the data the review pooled.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the pooled study data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "method:not_determinable", "description": "Re-run the paper's analysis on the source data and produce the registered result.", "duration_hours": null, "parameters": {}, "inputs": ["materials:the study data pooled behind the published estimate in pmid:36013502"], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": ["the study data pooled behind the published estimate in pmid:36013502", "the analysis programme that recomputes the published estimate"], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent", "step:run_analysis blocked on method:not_determinable"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36013502", "role": "manuscript", "format": "txt", "media_type": "text/plain", "uri": "https://doi.org/10.3390/medicina58081035", "sha256": "sha256:79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71", "bytes": null, "access": "unknown", "state": "declared", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/medicina58081035", "version": null, "note": "Source read by the package builder: abstract_only.", "structure": {"access_state": "abstract_only"}}, {"id": "materials:the study data pooled behind the published estimate in pmid:36013502", "role": "raw", "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 study data pooled behind the published estimate in pmid:36013502", "structure": {"material_kind": "dataset", "access_state": "not_identified"}}, {"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"}}], "gaps": ["asset:materials:the analysis programme that recomputes the published estimate not verified", "asset:materials:the study data pooled behind the published estimate in pmid:36013502 not verified", "asset:source:pmid:36013502 not verified"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "meta_analysis", "specific": null, "label": "", "dsl_operations": [], "missing_operations": [], "expressible": false, "parameters": {}, "data_shapes": [], "evidence": {"score": 0.0, "band": "low", "quote": null}}], "targets": [{"id": "target-1", "claim_id": "claim-1", "operation": null, "expected_value": 1.03, "unit": "odds ratio", "tolerance": null, "state": "complete"}], "gaps": ["method.corpus_not_determined", "method.operations"]}, "capability": {"state": "complete", "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"}], "gaps": []}, "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": [], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["txt", "unknown"], "capabilities": [], "data_gaps": ["source:pmid:36013502", "materials:the study data pooled behind the published estimate in pmid:36013502", "materials:the analysis programme that recomputes the published estimate"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax-m3-1-flash", "model": "MiniMax-M3.1-Flash", "prompt_version": "peer-review-reading-v1", "prompt_hash": "dce392794f95a0682cee1039c67a9c50619d5995ad3385646127b853f48af594", "source_hash": "79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71", "raw_response_sha256": "sha256:93c2b9f22827f2a37c8aa753afc3be000c343b03079096d0e6ea528fe72a3c51", "raw_response_chars": 2098}, {"provider": "minimax-m3", "model": "MiniMax-M3", "prompt_version": "peer-review-reading-v1", "prompt_hash": "af84fbdb5922acd05f3f110be080c939e296bff83ed358d2b25dc69147ab9978", "source_hash": "79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71", "raw_response_sha256": "sha256:acdc01b7b20505df8623f7294186936de4388fe991850befb152eefb408beb56", "raw_response_chars": 2089}], "target_providers": [{"provider": "minimax-m3-1-flash", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "a78513e0c65a6e9592f2043d3f1d1a24b666ad9643031b820233442a6e5ae8ec", "source_hash": "79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71", "raw_response": "{\"parent_value\":1.03,\"unit\":\"odds ratio\",\"evidence\":\"The pooled OR of the association between HPI and IBS was 1.03 (95% CI [0.80,1.31]; p = 0.84).\",\"target_result\":\"The pooled odds ratio of the association between Helicobacter pylori infection and irritable bowel syndrome was 1.03.\",\"number_stated\":true}", "reading": {"parent_value": 1.03, "unit": "odds ratio", "evidence": "The pooled OR of the association between HPI and IBS was 1.03 (95% CI [0.80,1.31]; p = 0.84).", "target_result": "The pooled odds ratio of the association between Helicobacter pylori infection and irritable bowel syndrome was 1.03.", "number_stated": true, "source_locator": "chars 964-1057 of source sha256 79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71"}, "recorded_at": "2026-10-31T13:26:17.798546+00:00"}, {"provider": "minimax-m3", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "f471169cb3bec118976b77c7d36f60c73695b0b64936e3a72473f195c2f31871", "source_hash": "79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71", "raw_response": "{\"parent_value\":1.03,\"unit\":\"odds ratio\",\"evidence\":\"The pooled OR of the association between HPI and IBS was 1.03 (95% CI [0.80,1.31]; p = 0.84).\",\"target_result\":\"The pooled OR of the association between HPI and IBS was 1.03.\",\"number_stated\":true}", "reading": {"parent_value": 1.03, "unit": "odds ratio", "evidence": "The pooled OR of the association between HPI and IBS was 1.03 (95% CI [0.80,1.31]; p = 0.84).", "target_result": "The pooled OR of the association between HPI and IBS was 1.03.", "number_stated": true, "source_locator": "chars 964-1057 of source sha256 79cd14f269d840fd0fd01310e3429314a32601e1bc528a4a423be3d882f0bf71"}, "recorded_at": "2026-10-31T13:26:32.805971+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax-m3-1-flash": "Pooled odds ratio (OR) 1.03 (95% CI 0.80–1.31; p = 0.84) for the association between Helicobacter pylori infection and irritable bowel syndrome.", "minimax-m3": "Pooled odds ratio for the association between Helicobacter pylori infection and irritable bowel syndrome: OR 1.03 (95% CI [0.80,1.31]; p = 0.84).", "decisive": false}, "analysis_methods": {"minimax-m3-1-flash": ["Systematic literature search in PubMed, EMBASE, and the Cochrane Library", "Meta-analysis of 13 studies involving 13,173 participants", "Calculation of pooled odds ratios and 95% confidence intervals", "Subgroup analyses", "Funnel-plot assessment of publication bias", "Egger's test", "Begg's test", "Sensitivity analysis"], "minimax-m3": ["Systematic literature search and meta-analysis", "Calculation of pooled odds ratios and 95% confidence intervals", "Subgroup analyses to assess heterogeneity", "Publication-bias assessment using funnel plots, Egger's test, and Begg's test", "Sensitivity analysis"], "decisive": false}, "source_claims": {"minimax-m3-1-flash": ["The pooled OR of the association between HPI and IBS was 1.03 (95% CI [0.80,1.31]; p = 0.84).", "The adjusted OR after excluding studies with team-defined confounding factors was 1.29 (95% CI [1.03,1.62]; p = 0.03).", "A positive association was reported between HPI and IBS-D (OR 1.54; 95% CI [1.22,1.95]; p = 0.0003).", "The overall association between HPI and IBS was not statistically significant."], "minimax-m3": ["Thirteen studies with 13,173 participants were included in the meta-analysis.", "The pooled odds ratio for the association between H. pylori infection and IBS was 1.03, with a 95% confidence interval of 0.80 to 1.31 and p = 0.84.", "After excluding studies with team-defined confounding factors, the adjusted pooled odds ratio was 1.29 (95% CI [1.03,1.62]; p = 0.03).", "A positive association was reported for IBS-D (OR 1.54; 95% CI [1.22,1.95]; p = 0.0003)."], "decisive": false}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["number_stated", "parent_value", "unit", "work_type"], "advisory_fields": ["analysis_methods", "source_claims", "target_result"]}, "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": "passed", "reason": null, "evidence": {"provider_errors": []}}, {"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.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:2dfa0aa0cc800dcc85226f6204cb83835077499c4ddf235608918833444fbf51", "type": "sep_package", "label": "SEP v1 package for pmid:36013502"}], "activities": [{"id": "activity:conversion:pmid:36013502", "type": "conversion", "used": ["package:2dfa0aa0cc800dcc85226f6204cb83835077499c4ddf235608918833444fbf51"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax-m3", "type": "model", "label": "minimax-m3"}, {"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": "af50d357-4f53-4ca7-9969-626b8b47a8e8", "parent_hash": "2dfa0aa0cc800dcc85226f6204cb83835077499c4ddf235608918833444fbf51", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:materials:the analysis programme that recomputes the published estimate not verified", "asset:materials:the study data pooled behind the published estimate in pmid:36013502 not verified", "asset:source:pmid:36013502 not verified", "authors", "execution.not_run", "method.corpus_not_determined", "method.operations", "method:not_determinable", "review.human_critique", "review.machine_critique.passed", "step:obtain_source_data blocked on data:accession_absent", "step:run_analysis blocked on method:not_determinable"]}