Construction of a novel CD8T cell-related index for predicting clinical outcomes and immune landscape in ovarian cancer by combined single-cell and RNA-sequencing analysis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40354001", "kind": "science-record", "revision": 2, "content_hash": "sha256:a0fc72fff4b46189a0f3742944e1bd20a6c0e63efb11da3f195e5766d77e3b26", "created_at": "2026-11-01T10:25:50Z", "updated_at": "2026-11-01T14:01:40Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Construction of a novel CD8T cell-related index for predicting clinical outcomes and immune landscape in ovarian cancer by combined single-cell and RNA-sequencing analysis.", "doi": "10.1007/s12672-025-02582-4", "pmid": "40354001", "authors": null, "journal": "Discover oncology", "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:40354001"], "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:40354001", "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:40354001' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40354001", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-025-02582-4", "sha256": "sha256:0585bbbaffcc22780cadffd9c4417baa8d24e013083a987f29788cb39eb6889e", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-025-02582-4", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40354001:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:93aed1ed33e921e888f20dfd1539af3f16aad1170ee572bb8f7409ec4ed78a72", "bytes": 870, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Clinicopathological indicators in TCGA-OV cohort", "structure": {"pmcid": "PMC12069775", "section_index": 3, "section_title": "Data sources", "row_count": 19, "column_count": 3}, "table": {"label": "Table 1", "caption": "Clinicopathological indicators in TCGA-OV cohort", "rows": [["Clinicopathological indicators", "Type", "TCGA-OV cohort (n = 587)"], ["Age", "≤60", "326 (55.54%)"], [">60", "261 (44.46%)"], ["Grade", "G1", "6 (1.02%)"], ["G2", "69 (11.76%)"], ["G3", "495 (84.33%)"], ["Not available", "17 (2.89%)"], ["TNM-Stage", "Stage I", "17 (2.89%)"], ["Stage II", "30 (5.11%)"], ["Stage III", "446 (76.00%)"], ["Stage IV", "89 (15.16%)"], ["Not available", "5 (0.85%)"], ["Survival status", "Alive", "236 (40.20%)"], ["Deceased", "350 (59.62%)"], ["Not available", "1 (0.17%)"], ["Pathological type", "Serous cystadenocarcinoma", "578 (98.47%)"], ["Serous surface papillary carcinoma", "2 (0.34%)"], ["Papillary serous cystadenocarcinoma", "4 (0.68%)"], ["Not available", "3 (0.51%)"]], "row_count": 19, "column_count": 3, "numeric_cells": 21, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:40354001:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e97ea60767a201abce1b76b16b564174dc3105db1180dd8192eb3b601cc15a8d", "bytes": 982, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab2", "version": null, "note": "Cox regression analysis of IRGs differentially expressed in CD8 T cells", "structure": {"pmcid": "PMC12069775", "section_index": 15, "section_title": "Construction of the CCAI", "row_count": 18, "column_count": 5}, "table": {"label": "Table 2", "caption": "Cox regression analysis of IRGs differentially expressed in CD8 T cells", "rows": [["Gene", "Hazard ratio (HR)", "HR.95L", "HR.95H", "P-value"], ["HLA-F", "0.894", "0.803", "0.994", "0.039"], ["TAP1", "0.898", "0.820", "0.985", "0.022"], ["ISG20", "0.845", "0.754", "0.946", "0.004"], ["LRP1", "1.163", "1.027", "1.317", "0.017"], ["CXCR4", "0.883", "0.793", "0.984", "0.025"], ["IGKC", "0.962", "0.927", "0.997", "0.035"], ["PLAUR", "1.141", "1.005", "1.295", "0.041"], ["OGN", "1.114", "1.028", "1.207", "0.008"], ["IL2RG", "0.869", "0.789", "0.956", "0.004"], ["LCK", "0.864", "0.755", "0.989", "0.034"], ["SH2D1A", "0.769", "0.608", "0.973", "0.028"], ["GZMB", "0.892", "0.811", "0.982", "0.020"], ["CD3D", "0.885", "0.805", "0.974", "0.012"], ["CD3E", "0.905", "0.820", "0.998", "0.046"], ["CD3G", "0.768", "0.640", "0.920", "0.004"], ["TRAC", "0.911", "0.839", "0.989", "0.026"], ["TRBC1", "0.907", "0.840", "0.979", "0.013"]], "row_count": 18, "column_count": 5, "numeric_cells": 71, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:40354001:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bb565eff9acdb6541647ebb78f95900c28e297d4ba94ea8aeca3c37e12267270", "bytes": 774, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#Tab3", "version": null, "note": "CD8T cell-related index for ovarian cancer", "structure": {"pmcid": "PMC12069775", "section_index": 15, "section_title": "Construction of the CCAI", "row_count": 10, "column_count": 3}, "table": {"label": "Table 3", "caption": "CD8T cell-related index for ovarian cancer", "rows": [["Index factor", "Coefficient", "Association with outcome"], ["TAP1", "−0.004648235", "Associated with better outcome"], ["ISG20", "−0.107240807", "Associated with better outcome"], ["LRP1", "0.015253703", "Associated with poorer outcome"], ["CXCR4", "−0.094351506", "Associated with better outcome"], ["PLAUR", "0.189890158", "Associated with poorer outcome"], ["OGN", "0.041441964", "Associated with poorer outcome"], ["IL2RG", "−0.10531695", "Associated with better outcome"], ["LCK", "−0.004777555", "Associated with better outcome"], ["CD3G", "−0.072098181", "Associated with better outcome"]], "row_count": 10, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[15]/table-wrap[2]#Tab3"}}], "gaps": ["asset:source:pmid:40354001 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:40354001", "asset:table:pmid:40354001:1", "asset:table:pmid:40354001:2", "asset:table:pmid:40354001:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40354001"]}, "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:8255c8e18c28e84a2f4e805241fa4baa30e740955a2874a22cd7da6f7d999f57", "type": "sep_package", "label": "SEP v1 package for pmid:40354001"}], "activities": [{"id": "activity:conversion:pmid:40354001", "type": "conversion", "used": ["package:8255c8e18c28e84a2f4e805241fa4baa30e740955a2874a22cd7da6f7d999f57"], "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:40354001", "parent_hash": "sha256:dfd78d336fe8aad20a980031bc9fce5d1844766f056c4c0a977e13efc9374dc7", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40354001 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:40354001' does not resolve to a declared asset", "targets"]}