Development of a prognostic model based on immunogenic cell death/ferroptosis-related genes and the study of TREX1 effects on prostate cancer cells.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41346575", "kind": "science-record", "revision": 2, "content_hash": "sha256:5863cc130fcc3c62a2b09c6f10b65d84c10e4a1557c770edc0e69dda2ed0c704", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T14:01:51Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Development of a prognostic model based on immunogenic cell death/ferroptosis-related genes and the study of TREX1 effects on prostate cancer cells.", "doi": "10.3389/fimmu.2025.1708437", "pmid": "41346575", "authors": null, "journal": "Frontiers in immunology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "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:41346575"], "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:not_downloaded", "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": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41346575", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41346575' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41346575", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1708437", "sha256": "sha256:1a15ddf8b55815b28b9f5831280dff59a418185ed6451bceb8bfb0648713559a", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1708437", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:41346575:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c00dd2952c9e26115aff63407e34ecbb4e2cd85fb71400f8eb4f596586337d63", "bytes": 385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[33]/table-wrap[1]#T1", "version": null, "note": "Differential expression of TREX1 in prostate cancer and adjacent normal tissues.", "structure": {"pmcid": "PMC12672885", "section_index": 33, "section_title": "TREX1 expression in prostate cancer tissues", "row_count": 4, "column_count": 4}, "table": {"label": "Table 1", "caption": "Differential expression of TREX1 in prostate cancer and adjacent normal tissues.", "rows": [["Tissue type", "Low expression (0-3)", "High expression (4-9)", "Total"], ["Tumor", "15", "45", "60"], ["Adjacent Normal", "33", "24", "57"], ["Total", "48", "69", "117"]], "row_count": 4, "column_count": 4, "numeric_cells": 11, "header_rows": 1, "locator": "section[33]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:41346575:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a80939daf0870324b417115988a605e284d2b606c90f5c30ebd3a382a9448cbc", "bytes": 400, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[33]/table-wrap[2]#T2", "version": null, "note": "Differential expression statistics of TREX1 in prostate cancer and adjacent normal tissues.", "structure": {"pmcid": "PMC12672885", "section_index": 33, "section_title": "TREX1 expression in prostate cancer tissues", "row_count": 4, "column_count": 6}, "table": {"label": "Table 2", "caption": "Differential expression statistics of TREX1 in prostate cancer and adjacent normal tissues.", "rows": [["Tissue type", "Total (n)", "TREX1 expression", "χ² Value", "P value"], ["High", "Low"], ["Tumor", "60", "45", "15", "13.08", "0.0003"], ["Adjacent Normal", "57", "24", "33"]], "row_count": 4, "column_count": 6, "numeric_cells": 8, "header_rows": 2, "locator": "section[33]/table-wrap[2]#T2"}}], "gaps": ["asset:source:pmid:41346575 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41346575", "asset:table:pmid:41346575:1", "asset:table:pmid:41346575:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41346575"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "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 independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"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", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:756b023b87f14e66a06c5dc3dde5899562b0823ebecf6a09d86dfc2114e18613", "type": "sep_package", "label": "SEP v1 package for pmid:41346575"}], "activities": [{"id": "activity:conversion:pmid:41346575", "type": "conversion", "used": ["package:756b023b87f14e66a06c5dc3dde5899562b0823ebecf6a09d86dfc2114e18613"], "agent": "agent:corpus-assay-engine"}], "agents": [{"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:41346575", "parent_hash": "sha256:5a50d1e647e35846cc583611164ed03e52e03b6bccd579debcface48ce3df024", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:41346575 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41346575' does not resolve to a declared asset", "targets"]}