A novel stemness-related lncRNA signature predicts prognosis, immune infiltration and drug sensitivity of clear cell renal cell carcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40016772", "kind": "science-record", "revision": 1, "content_hash": "sha256:14183710cacc4afe4779993af3868c50bf37d1acdaac2b74c51a03d863215908", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T10:25:49Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "A novel stemness-related lncRNA signature predicts prognosis, immune infiltration and drug sensitivity of clear cell renal cell carcinoma.", "doi": "10.1186/s12967-025-06251-6", "pmid": "40016772", "authors": null, "journal": "Journal of translational medicine", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 6.0, "unit": "srlncrnas", "tolerance": null, 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"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:40016772", "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:40016772' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40016772", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-025-06251-6", "sha256": "sha256:03026cbe679b4a1f7eb958185e9d13783ffd626c7e0277a99bf21fd7fc123f39", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12967-025-06251-6", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40016772 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:40016772"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40016772"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "3060074df26371c8eabf61fd4ab39d366740588ffd4bc4f2a808cb6d3906140d", "source_hash": "03026cbe679b4a1f7eb958185e9d13783ffd626c7e0277a99bf21fd7fc123f39", "raw_response_sha256": "sha256:d51da2192d2a2e6da4c32bf70f8cc48a6565aa6676b367c5e020891e76f10831", "raw_response_chars": 54477}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "775adb2bdebb8c6c3c5b4d7377453bbcd7bca8ac784bff75cfebebeb9e4da684", "source_hash": "03026cbe679b4a1f7eb958185e9d13783ffd626c7e0277a99bf21fd7fc123f39", "raw_response": "{\"parent_value\":6,\"unit\":\"SRlncRNAs\",\"evidence\":\"Six SRlncRNAs were used to construct the prognostic signature.\",\"target_result\":\"The paper states that six SRlncRNAs were used to construct the prognostic signature.\",\"number_stated\":true}", "reading": {"parent_value": 6, "unit": "SRlncRNAs", "evidence": "Six SRlncRNAs were used to construct the prognostic signature.", "target_result": "The paper states that six SRlncRNAs were used to construct the prognostic signature.", "number_stated": true, "source_locator": "chars 2117-2179 of source sha256 03026cbe679b4a1f7eb958185e9d13783ffd626c7e0277a99bf21fd7fc123f39"}, "recorded_at": "2026-10-31T15:31:51.563582+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "45e2805271f290ff2287e6ab50ebbd62d43c09865ce986f7bc2382d60f20b5e6", "source_hash": "03026cbe679b4a1f7eb958185e9d13783ffd626c7e0277a99bf21fd7fc123f39", "raw_response": "<think>We need answer JSON only, claims from source. Need identify single numerical result headline main finding registered target. Source has six SRlncRNAs signature, perhaps number stated is Six. Need determine \"headline numerical result paper states for its main finding\", likely signature comprised of 6 SRlncRNAs. The question expects extraction. Need exact contiguous quote containing number and attribution. Sentence: \"Six SRlncRNAs were used to construct the prognostic signature.\" Headline numerical result maybe six lncRNAs. Need parent_value number 6, unit perhaps \"SRlncRNAs\" (paper prints? It doesn't print \"6 SRlncRNAs\", but \"Six SRlncRNAs\"). Unit must be unit paper prints. Could use \"SRlncRNAs\". Evidence exact quote. target_result perhaps \"Six SRlncRNAs were used to construct the prognostic signature.\" number_stated true.\n\nBut need inspect wording: Registered target = \"the headline numerical result the paper states for its main finding.\" Main finding is novel stemness-related lncRNA signature. Numerical result in supplied source: Six SRlncRNAs used. Also 787 DEGs etc ancillary. The single headline likely six. Need report headline number only perhaps target_result should concise result perhaps \"Six SRlncRNAs were used to construct the prognostic signature.\" They demand \"Report headline number only\" but schema target_result string. Perhaps set target_result \"Six SRlncRNAs\". Evidence full clause. unit \"SRlncRNAs\". Ensure exact quote. Parent value 6.\n\nCould there be actual headline result elsewhere omitted? Source appears abstract/results but detailed signature results absent. The numerical result likely number of genes (six). Need not overthink. Output valid JSON no markdown.</think>\n\n{\"parent_value\":6,\"unit\":\"SRlncRNAs\",\"evidence\":\"Six SRlncRNAs were used to construct the prognostic signature.\",\"target_result\":\"Six SRlncRNAs were used to construct the prognostic signature.\",\"number_stated\":true}", "reading": {"parent_value": 6, "unit": "SRlncRNAs", "evidence": "Six SRlncRNAs were used to construct the prognostic signature.", "target_result": "Six SRlncRNAs were used to construct the prognostic signature.", "number_stated": true, "source_locator": "chars 2117-2179 of source sha256 03026cbe679b4a1f7eb958185e9d13783ffd626c7e0277a99bf21fd7fc123f39"}, "recorded_at": "2026-10-31T15:31:52.861157+00:00"}], "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": "MiniMax-M3.1-Flash", "reason": "a repository quotation is absent from the supplied text", "raw_response": "{\n  \"target_result\": \"Six SRlncRNAs were used to construct the prognostic signature.\",\n  \"work_type\": \"analysis_plus_physical_validation\",\n  \"physical_methods\": [\n    \"single-cell RNA-seq (scRNA-seq)\",\n    \"RT-qPCR\",\n    \"in vitro experiments\",\n    \"in vivo experiments\"\n  ],\n  \"analysis_methods\": [\n    \"RNA stemness scores (RNAss)\",\n    \"weighted correlation network analysis (WGCNA)\",\n    \"least absolute shrinkage and selection operator (LASSO)\",\n    \"multivariate Cox regression\",\n    \"gene set enrichment analysis (GSEA)\",\n    \"immune infiltration assessment\",\n    \"drug sensitivity prediction\",\n    \"mutation landscape analysis\",\n    \"Student's t-test\",\n    \"Mann–Whitney U test\",\n    \"limma\"\n  ],\n  \"statistical_method\": \"The least absolute shrinkage and selection operator (LASSO) in combination with multivariate Cox regression was selected as the optimal approach.\",\n  \"method_evidence\": \"The least absolute shrinkage and selection operator (LASSO) in combination with multivariate Cox regression was selected as the optimal approach.\",\n  \"repositories\": [\n    {\n      \"repository\": \"The Cancer Genome Atlas (TCGA)\",\n      \"accession\": \"TCGA-KIRC\",\n      \"data_description\": \"Gene-expression and clinical data for the TCGA-KIRC training cohort, which was used to construct and assess the prognostic signature.\",\n      \"evidence\": \"Gene-expression and clinical data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Samples from TCGA-KIRC and GSE29609 cohorts were designated as the training and validation cohorts, respectively.\",\n      \"publicly_downloadable\": true\n    },\n    {\n      \"repository\": \"Gene Expression Omnibus (GEO)\",\n      \"accession\": \"GSE29609\",\n      \"data_description\": \"Gene-expression and clinical data for the GSE29609 validation cohort, which was used to validate the prognostic signature.\",\n      \"evidence\": \"Gene-expression and clinical data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Samples from TCGA-KIRC and GSE29609 cohorts were designated as the training and validation cohorts, respectively.\",\n      \"publicly_downloadable\": true\n    }\n  ],\n  \"availability_statement\": \"The original data presented in this study are included within the article or its accompanying Supplementary Materials. Essential scripts and codes used for analysis are available on the Github website (https://github.com/pengdubjcancer/kirc_SRlncRNAs). For any further inquiries, please feel free to contact the corresponding author.\",\n  \"data_on_request\": true,\n  \"source_claims\": [\n    \"The study developed a prognostic signature consisting of six SRlncRNAs.\",\n    \"LASSO combined with multivariate Cox regression was selected as the optimal modeling approach.\",\n    \"TCGA-KIRC and GSE29609 were designated as the training and validation cohorts, respectively.\",\n    \"The paper reports in vitro and in vivo validation of the findings.\"\n  ],\n  \"missing_information\": [\n    \"The supplied text does not state a quantitative performance result for the prognostic signature, such as a hazard ratio, concordance index, AUC, or survival difference.\",\n    \"The names of all six SRlncRNAs in the signature are not provided; only EMX2OS and LINC00944 are explicitly discussed.\",\n    \"The regression coefficients and risk-score formula for the six-SRlncRNA signature are not provided.\",\n    \"The paper does not explicitly state that TCGA-KIRC or GSE29609 can be accessed without an application, embargo, or request; public availability is inferred only from the statement that the data were downloaded from the named databases.\",\n    \"The numerical criteria used to identify the signature's six SRlncRNAs are not reported in the supplied text.\"\n  ],\n  \"evidence_spans\": [\n    \"Six SRlncRNAs were used to construct the prognostic signature.\",\n    \"The least absolute shrinkage and selection operator (LASSO) in combination with multivariate Cox regression was selected as the optimal approach.\",\n    \"Gene-expression and clinical data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases.\",\n    \"Samples from TCGA-KIRC and GSE29609 cohorts were designated as the training and validation cohorts, respectively.\",\n    \"Expression and effects of SRlncRNAs in ccRCC were further corroborated through the utilization of single-cell RNA-seq (scRNA-seq), as well as in vitro and in vivo experiments.\",\n    \"ScRNA-seq and RT-qPCR demonstrated the differential expression of SRlncRNAs between ccRCC tumors and normal tissues.\",\n    \"In vitro and in vivo experiments demonstrated that downregulation of EMX2OS and LINC00944 affected the proliferation, migration, invasion, apoptosis, and metastasis of ccRCC cells.\",\n    \"The original data presented in this study are included within the article or its accompanying Supplementary Materials. Essential scripts and codes used for analysis are available on the Github website (https://github.com/pengdubjcancer/kirc_SRlncRNAs). For any further inquiries, please feel free to contact the corresponding author.\"\n  ]\n}"}]}}, {"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:53c07dd8eccc1336442a84e59b71fd88ecb6191cec853cb3e27939e0d7adf44c", "type": "sep_package", "label": "SEP v1 package for pmid:40016772"}], "activities": [{"id": "activity:conversion:pmid:40016772", "type": "conversion", "used": ["package:53c07dd8eccc1336442a84e59b71fd88ecb6191cec853cb3e27939e0d7adf44c"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"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": "f3e8e2b9-6830-4a8d-a26a-00846e8574dc", "parent_hash": "53c07dd8eccc1336442a84e59b71fd88ecb6191cec853cb3e27939e0d7adf44c", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40016772 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "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:40016772' does not resolve to a declared asset", "targets"]}