{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37426414", "kind": "science-record", "revision": 3, "content_hash": "sha256:72e1b4ae7c339ae2110e20f8b3daa73d2e093028a0a6c7017687d824b911bdf0", "created_at": "2026-11-01T19:02:11Z", "updated_at": "2026-11-01T21:31:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of a circHIPK3-based ceRNA network and identification of mRNA signature in breast cancer patients harboring BRCA mutation.", "doi": "10.7717/peerj.15572", "pmid": "37426414", "authors": ["Qi-Xin Lian", "Yang Song", "Lili Han", "Zunxian Wang", "Yinhui Song"], "journal": "PeerJ", "year": 2023, "abstract": "Background: Exploring the regulatory network of competing endogenous RNAs (ceRNAs) as hallmarks for breast cancer development has great significance and could provide therapeutic targets. An mRNA signature predictive of prognosis and therapy response in BRCA carriers was developed according to circular RNA homeodomain-interacting protein kinase 3 (circHIPK3)-based ceRNA network.\nMethod: We constructed a circHIPK3-based ceRNA network based on GSE173766 dataset and identified potential mRNAs that were associated with BRCA mutation patients within this ceRNA network. A total of 11 prognostic mRNAs and a risk model were identified and developed by univariate Cox regression analysis and the LASSO regression analysis as well as stepAIC method. Genomic landscape was treated by mutect2 and fisher. Immune characteristics was analyzed by ESTIMATE, MCP-counter. TIDE analysis was conducted to predict immunotherapy. The clinical treatment outcomes of BRCA mutation patients were assessed using a nomogram. The proliferation, migration and invasion in breast cancer cell lines were examined using CCK8 assay and transwell assay.\nResult: We found 241 mRNAs within the circHIPK3-based ceRNA network. An 11 mRNA-based signature was identified for prognostic model construction. High risk patients exhibited dismal prognosis, low response to immunotherapy, less immune cell infiltration and tumor mutation burden (TMB). High-risk patients were sensitive to six anti-tumor drugs, while low-risk patient were sensitive to 47 drugs. The risk score was the most effective on evaluating patients' survival. The robustness and good prediction performance were validated in The Cancer Genome Atlas (TCGA) dataset and immunotherapy datasets, respectively. In addition, circHIPK3 mRNA level was upregulated, and promoted cell viability, migration and invasion in breast cancer cell lines.\nConclusion: The current study could improve the understanding of mRNAs in relation to BRCA mutation and pave the way to develop mRNA-based therapeutic targets for breast cancer patients with BRCA mutation.", "claims": [{"id": "claim-method", "statement": "Through univariate Cox regression analysis, 40 mRNAs associated with prognosis were screened in the Train dataset (Fig. S2A). LASSO Cox regression analysis was employ to further refine the model. Independent variable coefficients that are progressively heading to zero rose as lambda was steadily increased (Fig. S2B). Figure S2C displays the confidence interval under each lambda from 10-fold cross-validation. 21 mRNAs were found when lambda = 0.0182. With stepwise multivariate regression analysis and stepAIC, a total of 11 mRNAs were identified, including four risk mRNAs and seven protective mRNAs (Fig. S2D).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37426414", "locator": "sections[20] \"Development and verification of mRNA prognostic model\" paragraph 2", "quote": "Through univariate Cox regression analysis, 40 mRNAs associated with prognosis were screened in the Train dataset (Fig. S2A). LASSO Cox regression analysis was employ to further refine the model. Independent variable coefficients that are progressively heading to zero rose as lambda was steadily increased (Fig. S2B). Figure S2C displays the confidence interval under each lambda from 10-fold cross-validation. 21 mRNAs were found when lambda = 0.0182. With stepwise multivariate regression analysis and stepAIC, a total of 11 mRNAs were identified, including four risk mRNAs and seven protective mRNAs (Fig. S2D)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe data is available at OSF: Song, Yinhui. 2023. “Data Source.” OSF. May 22. doi: 10.17605/OSF.IO/DS6TA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37426414", "locator": "sections[41] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThe data is available at OSF: Song, Yinhui. 2023. “Data Source.” OSF. May 22. doi: 10.17605/OSF.IO/DS6TA."}], "state": "complete"}, {"id": "claim-target-result", "statement": "An 11 mRNA-based signature was identified for prognostic model construction.", "kind": "quantitative", "target": {"value": 0.0001, "unit": "p-value", "tolerance": null, "source": "Survival analysis showed high risk patients exhibited poor prognosis compared with low risk patients (P < 0.0001) with 1-year AUC of 0.67, 3-year AUC of 0.75, 5-year AUC of 0.77 and 7-year AUC of 0.77 in the Train dataset (Fig. 2B)."}, "evidence": [{"asset": "source:pmid:37426414", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "An 11 mRNA-based signature was identified for prognostic model construction."}, {"asset": "source:pmid:37426414", "locator": "sections[20] \"Development and verification of mRNA prognostic model\" paragraph 3", "quote": "Survival analysis showed high risk patients exhibited poor prognosis compared with low risk patients (P < 0.0001) with 1-year AUC of 0.67, 3-year AUC of 0.75, 5-year AUC of 0.77 and 7-year AUC of 0.77 in the Train dataset (Fig. 2B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "An 11 mRNA-based signature was identified for prognostic model construction.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37426414"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE103091"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE103091"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37426414", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.15572", "sha256": "sha256:7c8dc678fd862f22f0aa9a74c5277eab56665fd165d1e5f3c17e9053988101ff", "bytes": 50057, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.15572", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10329424", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE103091", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103091", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE103091", "version": null, "note": "The following information was supplied regarding data availability:\nThe data is available at OSF: Song, Yinhui. 2023. “Data Source.” OSF. 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May 22. doi: 10.17605/OSF.IO/DS6TA.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe data is available at OSF: Song, Yinhui. 2023. “Data Source.” OSF. May 22. doi: 10.17605/OSF.IO/DS6TA.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1176873", "GSM1176874", "GSM1176875", "GSM1176876", "GSM1176877", "GSM1176878", "GSM1176879", "GSM1176880", "GSM1176881", "GSM1176882", "GSM1176883", "GSM1176884", "GSM1176885", "GSM1176886", "GSM1176887", "GSM1176888", "GSM1176889", "GSM1176890", "GSM1176891", "GSM1176892", "GSM1176893", "GSM1176894", "GSM1176895", "GSM1176896", "GSM1176897", "GSM1176898", "GSM1176899", "GSM1176900", "GSM1176901", "GSM1176902", "GSM1176903", "GSM1176904", "GSM1176905", "GSM1176906", "GSM1176907", "GSM1176908", "GSM1176909", "GSM1176910", "GSM1176911", "GSM1176912", "GSM1176913", "GSM1176914", "GSM1176915", "GSM1176916", "GSM1176917", "GSM1176918", "GSM1176919", "GSM1176920", "GSM1176921", "GSM1176922", "GSM1176923", "GSM1176924", "GSM1176925", "GSM1176926", "GSM1176927", "GSM1176928", "GSM1176929", "GSM1176930", "GSM1176931", "GSM1176932", "GSM1176933", "GSM1176934", "GSM1176935", "GSM1176936", "GSM1176937", "GSM1176938", "GSM1176939", "GSM1176940", "GSM1176941", "GSM1176942", "GSM1176943", "GSM1176944", "GSM1176945", "GSM1176946", "GSM1176947", "GSM1176948", "GSM1176949", "GSM1176950", "GSM1176951", "GSM1176952", "GSM1176953"], "sample_count": 81, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Concurrent Gene Signatures for Han Chinese Breast Cancers [Affymetrix]", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE78220", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78220", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE78220", "version": null, "note": "The following information was supplied regarding data availability:\nThe data is available at OSF: Song, Yinhui. 2023. “Data Source.” OSF. May 22. doi: 10.17605/OSF.IO/DS6TA.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe data is available at OSF: Song, Yinhui. 2023. “Data Source.” OSF. May 22. doi: 10.17605/OSF.IO/DS6TA.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2069823", "GSM2069824", "GSM2069825", "GSM2069826", "GSM2069827", "GSM2069828", "GSM2069829", "GSM2069830", "GSM2069831", "GSM2069832", "GSM2069833", "GSM2069834", "GSM2069835", "GSM2069836", "GSM2069837", "GSM2069838", "GSM2069839", "GSM2069840", "GSM2069841", "GSM2069842", "GSM2069843", "GSM2069844", "GSM2069845", "GSM2069846", "GSM2069847", "GSM2069848", "GSM2069849", "GSM2069850"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE103091 not downloaded", "asset:data:geo:GSE103091 licence not read", "asset:data:geo:GSE135222 not downloaded", "asset:data:geo:GSE135222 licence not read", "asset:data:geo:GSE16446 not downloaded", "asset:data:geo:GSE16446 licence not read", "asset:data:geo:GSE173766 not downloaded", "asset:data:geo:GSE173766 licence not read", "asset:data:geo:GSE20685 not downloaded", "asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE20713 not downloaded", "asset:data:geo:GSE20713 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE48390 not downloaded", "asset:data:geo:GSE48390 licence not read", "asset:data:geo:GSE78220 not downloaded", "asset:data:geo:GSE78220 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Through univariate Cox regression analysis, 40 mRNAs associated with prognosis were screened in the Train dataset (Fig. S2A). LASSO Cox regression analysis was employ to further refine the model. Independent variable coefficients that are progressively heading to zero rose as lambda was steadily increased (Fig. S2B). Figure S2C displays the confidence interval under each lambda from 10-fold cross-validation. 21 mRNAs were found when lambda = 0.0182. With stepwise multivariate regression analysis and stepAIC, a total of 11 mRNAs were identified, including four risk mRNAs and seven protective mRNAs (Fig. S2D)."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 0.0001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE173766", "GSE103091", "GSE16446", "GSE20685", "GSE20713", "GSE42568", "GSE48390", "GSE135222", "GSE78220"], "resolved_accessions": ["GSE173766", "GSE103091", "GSE16446", "GSE20685", "GSE20713", "GSE42568", "GSE48390", "GSE135222", "GSE78220"], "statements": ["The following information was supplied regarding data availability:\nThe data is available at OSF: Song, Yinhui. 2023. “Data Source.” OSF. May 22. doi: 10.17605/OSF.IO/DS6TA."], "basis": "The paper names GSE173766, GSE103091, GSE16446, GSE20685, GSE20713, GSE42568, GSE48390, GSE135222, GSE78220 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:37426414", "data:geo:GSE103091"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE103091"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:46:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15320, "completion_tokens": 3689, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37426414", "type": "paper", "label": "pmid:37426414"}, {"id": "source:pmid:37426414", "type": "manuscript", "label": "PMID 37426414 full text"}, {"id": "data:geo:GSE103091", "type": "dataset", "label": "GEO GSE103091"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37426414", "type": "paper", "label": "pmid:37426414"}, {"id": "source:pmid:37426414", "type": "manuscript", "label": "PMID 37426414 full text"}, {"id": "data:geo:GSE103091", "type": "dataset", "label": "GEO GSE103091"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37426414", "type": "extraction", "used": ["source:pmid:37426414"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE103091", "type": "accession_resolution", "used": ["data:geo:GSE103091"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37426414", "parent_hash": "sha256:7d92e02f0ab79eba80e6284bc26f5ec7309b3de444cbf9283e4a69119c835b33", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE103091 licence not read", "asset:data:geo:GSE103091 not downloaded", "asset:data:geo:GSE135222 licence not read", "asset:data:geo:GSE135222 not downloaded", "asset:data:geo:GSE16446 licence not read", "asset:data:geo:GSE16446 not downloaded", "asset:data:geo:GSE173766 licence not read", "asset:data:geo:GSE173766 not downloaded", "asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE20685 not downloaded", "asset:data:geo:GSE20713 licence not read", "asset:data:geo:GSE20713 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE48390 licence not read", "asset:data:geo:GSE48390 not downloaded", "asset:data:geo:GSE78220 licence not read", "asset:data:geo:GSE78220 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["breast cancer cell lines were examined using CCK8 assay and transwell assay. Result: We found"], "order_basis": "paper_text_order:1187", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["roup differences. Cell culture and transient transfection MCF-10A, MDA-MB-231, MCF-7 cells were commer", "3 siRNA (Invitrogen, Carlsbad, CA, USA) were transfected into the cells utilizing Lipofectamine 2000", "SA). The negative control (NC) and circHIPK3 siRNA (Invitrogen, Carlsbad, CA, USA) were transfe"], "order_basis": "paper_text_order:3090", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ht from ATCC (Manassas, USA). The cells were cultured in Gibco DEME F-12 medium (Thermo Fisher, Scien", "transient transfection MCF-10A, MDA-MB-231, MCF-7 cells were commercially bought from ATCC (Ma"], "order_basis": "paper_text_order:3125", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Through univariate Cox regression analysis, 40 mRNAs associated with prognosis were screened in the Train dataset (Fig. S2A). LASSO Cox regression analysis was employ to further refine the model. Independent variable coefficients that are progressively heading to zero rose as lambda was steadily increased (Fig. S2B). Figure S2C displays the confidence interval under each lambda from 10-fold cross-validation. 21 mRNAs were found when lambda = 0.0182. With stepwise multivariate regression analysis and stepAIC, a total of 11 mRNAs were identified, including four risk mRNAs and seven protective mRNAs (Fig. S2D)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:32:50+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}