{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29296238", "kind": "science-record", "revision": 8, "content_hash": "sha256:b9bbc780afb7f36e654c9c2d51aaeb62210c03e4abe53323663dce9b20d299d8", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T21:59:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The implication from RAS/RAF/ERK signaling pathway increased activation in epirubicin treated triple negative breast cancer.", "doi": "10.18632/oncotarget.22604", "pmid": "29296238", "authors": ["Jianbo Huang", "Qingqing Luo", "Yun Xiao", "Hongyuan Li", "Lingquan Kong", "Guosheng Ren"], "journal": "Oncotarget", "year": 2017, "abstract": "BACKGROUND: Triple negative breast cancer (TNBC) is not sensitive to RAS/RAF/ERK signaling pathway (ERK pathway) targeting therapy, due to the absence of excessive activation of ERK pathway. However, the kinase cascades might be activated after chemotherapy in TNBC. Here we aimed to predict whether ERK pathway targeting therapy could be used as an adjuvant therapy in TNBC.\nMETHODS: Within online GEO datasets (GSE43816 and GSE54326), gene set enrichment analysis (GSEA) was performed to detect molecular changes in epirubicin treated TNBC samples and cells, ERK pathway components and regulation genes changes were included.\nRESULTS: In epirubicin treated TNBC samples and cells, we found ERK pathway components (eg. MAPK13, MAP3K1, MAPK12, MAPK11 and MAPKAPK3) were obviously enriched, also, expression of ERK pathway positive regulation genes significantly increased (P<0.05) and negative regulation genes decreased (P<0.05) in epirubicin resistant cells. Moreover, phosphorylated ERK levels were significantly elevated in MDA-MB-231 cells after epirubicin treatment.\nCONCLUSION: ERK signaling pathway was more activated in epirubicin treated TNBC, possibly contributing to the epirubicin resistance in TNBC, it implicated that ERK pathway could be used as an novel candidate for targeting therapy in refractory and relapse TNBC.", "claims": [{"id": "claim-method", "statement": "GEO datasets GSE43816 and GSE54326 were downloaded from website (https://www.ncbi.nlm.nih.gov/), GSEA, enrichment map analysis and heat map were performed with R software. Statistical analysis was done using Student's t-test, variance analysis and/or non-parametric tests. For all the tests, P<0.05 was considered as statistical significance. All statistics were calculated by SPSS 13.0 or R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29296238", "locator": "sections[9] \"GEO datasets, GSEA, enrichment map analysis and heatmap\" paragraph 2", "quote": "GEO datasets GSE43816 and GSE54326 were downloaded from website (https://www.ncbi.nlm.nih.gov/), GSEA, enrichment map analysis and heat map were performed with R software."}, {"asset": "source:pmid:29296238", "locator": "sections[13] \"Statistics\" paragraph 2", "quote": "Statistical analysis was done using Student's t-test, variance analysis and/or non-parametric tests."}, {"asset": "source:pmid:29296238", "locator": "sections[13] \"Statistics\" paragraph 2", "quote": "For all the tests, P<0.05 was considered as statistical significance."}, {"asset": "source:pmid:29296238", "locator": "sections[13] \"Statistics\" paragraph 2", "quote": "All statistics were calculated by SPSS 13.0 or R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here we applied an online GEO dataset (GSE43816) for GSEA to discuss the molecular changes in epirubicin treated TNBC. This cohort study of 7 women with primary invasive TNBC were collected for tumor specimen before and after 4 cycles of NAC with epirubicine and cyclophosphamide, followed by 4 cycles of taxanes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29296238", "locator": "sections[4] \"ERK pathway activation elevated in epirubicin treated TNBC samples\" paragraph 2", "quote": "Here we applied an online GEO dataset (GSE43816) for GSEA to discuss the molecular changes in epirubicin treated TNBC. This cohort study of 7 women with primary invasive TNBC were collected for tumor specimen before and after 4 cycles of NAC with epirubicine and cyclophosphamide, followed by 4 cycles of taxanes."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using gene set enrichment analysis of the online GEO datasets GSE43816 and GSE54326, the study found that ERK signaling became more activated in epirubicin-treated TNBC, with positive-regulation gene expression increased and negative-regulation gene expression decreased at P<0.05, suggesting a possible role in epirubicin resistance.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "In epirubicin treated TNBC samples and cells, we found ERK pathway components (eg. MAPK13, MAP3K1, MAPK12, MAPK11 and MAPKAPK3) were obviously enriched, also, expression of ERK pathway positive regulation genes significantly increased (P<0.05) and negative regulation genes decreased (P<0.05) in epirubicin resistant cells."}, "evidence": [{"asset": "source:pmid:29296238", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Within online GEO datasets (GSE43816 and GSE54326), gene set enrichment analysis (GSEA) was performed to detect molecular changes in epirubicin treated TNBC samples and cells, ERK pathway components and regulation genes changes were included."}, {"asset": "source:pmid:29296238", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In epirubicin treated TNBC samples and cells, we found ERK pathway components (eg. MAPK13, MAP3K1, MAPK12, MAPK11 and MAPKAPK3) were obviously enriched, also, expression of ERK pathway positive regulation genes significantly increased (P<0.05) and negative regulation genes decreased (P<0.05) in epirubicin resistant cells."}, {"asset": "source:pmid:29296238", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "ERK signaling pathway was more activated in epirubicin treated TNBC, possibly contributing to the epirubicin resistance in TNBC, it implicated that ERK pathway could be used as an novel candidate for targeting therapy in refractory and relapse TNBC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using gene set enrichment analysis of the online GEO datasets GSE43816 and GSE54326, the study found that ERK signaling became more activated in epirubicin-treated TNBC, with positive-regulation gene expression increased and negative-regulation gene expression decreased at P<0.05, suggesting a possible role in epirubicin resistance.", "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:29296238"], "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. 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(July, 2017)", "structure": {"pmcid": "PMC5746140", "section_index": 3, "section_title": "A retrospective overview of ERK pathway inhibitors in cancer treatment", "row_count": 19, "column_count": 6}, "table": {"label": "Table 1", "caption": "Clinical trials evaluating RAS/RAF/ERK inhibitors, according to Clinical Trials.gov. (July, 2017)", "rows": [["Compound", "Combination", "Phase", "Tumor", "Results", "Author, Year"], ["Selumetinib (MEK1/2 inhibitor)", "-", "II", "Myeloma (36)", "The response rate (CR + PR) was 5.6% with a mean duration of response of 4.95 months and median progression-free survival time of 3.52 months. One patient had a very good partial response, 1 patient had a partial response, 17 patients had stable disease, 13 patients had progressive disease.", "Holkova B, 2016"], ["Vemurafenib (BRAF inhibitor)", "-", "II", "Leukemia (54)", "The overall response rates were 96% (25 of 26 patients who could be evaluated) after a median of 8 weeks in the Italian study and 100% (24 of 24) after a median of 12 weeks in the U.S. study. The rates of complete response were 35% (9 of 26 patients) and 42% (10 of 24) in the two trials, respectively.", "Tiacci E, 2015"], ["Selumetinib (MEK1/2 inhibitor)", "dacarbazine", "III", "Uveal melanoma (estimated 128)", "Ongoing", "Carvajal RD, 2015"], ["Trametinib (MEK1/2 inhibitor)", "-", "II", "NSCLC (86)", "10 (12%) patients had partial responses", "Blumenschein GR Jr, 2015"], ["Selumetinib (MEK1/2 inhibitor)", "irinotecan", "II", "Colorectal (31)", "3 patients (9.7 %) had partial response. 16 patients (51.6 %) had stable disease for ≥4 weeks, including three >1 year.", "Hochster HS, 2015"], ["Vemurafenib (BRAF inhibitor)", "", "II", "Papillary thyroid cancer (51)", "Partial responses were recorded in ten of 26 patients in cohort 1.", "Brose MS, 2016"], ["Trametinib (MEK inhibitor)", "Dabrafenib", "II", "Melanoma (23)", "Disease control rate was 45%, and median PFS was 13 weeks.", "Chen G, 2016"], ["Selumetinib (MEK1/2 inhibitor)", "", "II", "Endometrial cancer (54)", "Three (6%) patients had objective response (1 CR, 2 PR); 13 had SD as best response. The proportion of patients with 6-month EFS was 12%. Median EFS, progression-free and overall survival was 2.1, 2.3, and 8.5months, respectively.", "Coleman RL, 2015"], ["Trametinib (MEK inhibitor)", "Dabrafenib", "II", "colorectal cancer (43)", "Five (12%) achieved a partial response or better, including one (2%) complete response, with duration of response > 36 months; 24 patients (56%) achieved stable disease as best confirmed response.", "Corcoran RB, 2015"], ["Binimetinib (MEK inhibitor)", "", "III", "Melanoma (402)", "Median progression-free survival was 2·8 months in the binimetinib group and 1·5 months in the dacarbazine group.", "Dummer R, 2017"], ["Selumetinib (MEK inhibitor)", "temsirolimus", "II", "Soft-tissue sarcomas (71)", "There was no difference in PFS between the two arms for the overall cohort; an improved median PFS was observed in the combination arm (N = 11) over single agent (N = 10) in the prespecified leiomyosarcoma stratum. Four-month PFS rate was 50% with the combination vs 0% with selumetinib alone in the leiomyosarcoma cohort.", "Eroglu Z, 2015"], ["Selumetinib (MEK1/2 inhibitor)", "Erlotinib", "II", "Pancreatic Adenocarcinoma (46)", "Although no objective responses were observed, 19 patients (41%) showed evidence of stable disease for ≥6 weeks, and 13 of 34 patients (38%) had a CA19-9 decline ≥50%. Median progression-free survival was 1.9 months, with a median overall survival of 7.3 months.", "Ko AH, 2016"], ["Vemurafenib (BRAF inhibitor)", "II", "", "Colorectal (21)", "Of the 21 patients treated, one patient had a confirmed partial response and seven other patients had stable disease by RECIST criteria. Median progression- free survival was 2.1 months.", "Kopetz S, 2015"], ["Trametinib (MEK1/MEK2 inhibitor)", "", "III", "Melanoma (322)", "The intent-to-treat (ITT) analysis estimated a 28% reduction in the hazard of death with trametinib treatment for patients in the primary efficacy population. Adjustment analyses deemed plausible provided OS HR point estimates ranging from 0.48 to 0.53. Similar reductions in the HR were estimated for the first-line metastatic subgroup. Treatment with trametinib, compared with chemotherapy, significantly reduced the risk of death and risk of disease progression in patients with BRAF V600E/K mutation-positive advanced melanoma or MM.", "Latimer NR, 2016"], ["Trametinib (MEK inhibitors) Dabrafenib (BRAF inhibitor)", "", "II", "NSCLC(57)", "Thirty-six patients (63·2%) achieved an investigator-assessed overall response", "Planchard D, 2016"], ["Dabrafenib (BRAF inhibitor)", "", "II", "NSCLC(84)", "Twenty-six of the 78 previously treated patients achieved an investigator-assessed overall response (33%). Four of the six previously untreated patients had an objective response.", "Planchard D, 2016"], ["Dabrafenib (BRAF inhibitor) and Trametinib (MEK inhibitor)", "", "III", "Melanoma(704)", "The overall survival rate at 12 months was 72% in the combination-therapy group and 65% in the vemurafenib group. The prespecified interim stopping boundary was crossed, and the study was stopped for efficacy. Median progression-free survival was 11.4 months in the combination-therapy group and 7.3 months in the vemurafenib group. The objective response rate was 64% in the combination-therapy group and 51% in the vemurafenib group.", "Robert C, 2015"], ["Selumetinib (MEK 1/2 inhibitor)", "Fulvestrant", "II", "Breast(46)", "Recruitment was interrupted because the selumetinib-fulvestrant arm did not reach the pre-specified DCR. DCR was 23% in the selumetinib arm and 50%in the placebo arm. Median progression-free survival was 3.7months in the selumetinib arm and 5.6months in the placebo arm. Median time to treatment failure was 5.1 and 5.6 months, respectively.", "Zaman K, 2015"]], "row_count": 19, "column_count": 6, "numeric_cells": 60, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:29296238:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0660b91d729d83dfec017089f710b4647e199c3d5df497ff248156524db95f90", "bytes": 857, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T2", "version": null, "note": "MAPK family gene enriched in ERKsignaling pathway after neoadjuvant chemotherapy", "structure": {"pmcid": "PMC5746140", "section_index": 4, "section_title": "ERK pathway activation elevated in epirubicin treated TNBC samples", "row_count": 9, "column_count": 5}, "table": {"label": "Table 2", "caption": "MAPK family gene enriched in ERKsignaling pathway after neoadjuvant chemotherapy", "rows": [["Probe", "Gene title", "Rank metric score", "Running ES", "Core enrichment"], ["KEGG_ MAPK signaling pathway"], ["MAPK10", "mitogen-activated protein kinase 10", "0.203", "0.1633", "Yes"], ["MAPK13", "mitogen-activated protein kinase 13", "0.113", "0.2426", "Yes"], ["MAPK11", "mitogen-activated protein kinase 11", "0.082", "0.2517", "Yes"], ["MAPKAPK3", "mitogen-activated protein kinase-activated protein kinase 3", "0.056", "0.2966", "Yes"], ["REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES"], ["MAPK10", "mitogen-activated protein kinase 10", "0.203", "0.4514", "Yes"], ["MAPK11", "mitogen-activated protein kinase 11", "0.082", "0.5460", "Yes"]], "row_count": 9, "column_count": 5, "numeric_cells": 23, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:29296238:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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protein kinase kinasekinase 14", "1.502", "0.1608", "Yes"], ["MAP3K1", "mitogen-activated protein kinase kinasekinase 1", "1.151", "0.2085", "Yes"], ["MAPKAPK3", "mitogen-activated protein kinase-activated protein kinase 3", "1.055", "0.2247", "Yes"], ["MAPK3", "mitogen-activated protein kinase 3", "1.039", "0.2289", "Yes"], ["MAPK12", "mitogen-activated protein kinase 12", "1.038", "0.2352", "Yes"], ["MAP4K2", "mitogen-activated protein kinase kinasekinasekinase 2", "1.006", "0.2440", "Yes"], ["MAP4K3", "mitogen-activated protein kinase kinasekinasekinase 3", "0.916", "0.2595", "Yes"], ["MAP2K6", "mitogen-activated protein kinase kinase 6", "0.909", "0.2636", "Yes"], ["MAPK11", "mitogen-activated protein kinase 11", "0.850", "0.2689", "Yes"], ["MAP3K8", "mitogen-activated protein kinase kinasekinase 8", "0.569", "0.2737", "Yes"], ["MAP2K3", "mitogen-activated protein kinase kinase 3", "0.499", "0.2806", "Yes"], ["REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION"], ["MAPKAPK3", 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Statistical analysis was done using Student's t-test, variance analysis and/or non-parametric tests. For all the tests, P<0.05 was considered as statistical significance. All statistics were calculated by SPSS 13.0 or R software."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "student_t", "expected_value": 0.05, "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": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE43816", "GSE54326"], "resolved_accessions": ["GSE43816", "GSE54326"], "statements": ["Here we applied an online GEO dataset (GSE43816) for GSEA to discuss the molecular changes in epirubicin treated TNBC. This cohort study of 7 women with primary invasive TNBC were collected for tumor specimen before and after 4 cycles of NAC with epirubicine and cyclophosphamide, followed by 4 cycles of taxanes."], "basis": "The paper names GSE43816, GSE54326 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:29296238", "data:geo:GSE43816", "asset:table:pmid:29296238:1", "asset:table:pmid:29296238:2", "asset:table:pmid:29296238:3"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE43816"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:22Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 51405, "completion_tokens": 4191, "cached_tokens": 7456}}, "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:29296238", "type": "paper", "label": "pmid:29296238"}, {"id": "source:pmid:29296238", "type": "manuscript", "label": "PMID 29296238 full text"}, {"id": "data:geo:GSE43816", "type": "dataset", "label": "GEO GSE43816"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29296238", "type": "paper", "label": "pmid:29296238"}, {"id": "source:pmid:29296238", "type": "manuscript", "label": "PMID 29296238 full text"}, {"id": "data:geo:GSE43816", "type": "dataset", "label": "GEO GSE43816"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29296238", "type": "extraction", "used": ["source:pmid:29296238"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE43816", "type": "accession_resolution", "used": ["data:geo:GSE43816"], "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:29296238", "parent_hash": "sha256:8d8d410b7694c019851468abe995a4b3d71dc9174b25714c1ef7172d5ec2d399", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE43816 licence not read", "asset:data:geo:GSE43816 not downloaded", "asset:data:geo:GSE54326 licence not read", "asset:data:geo:GSE54326 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["the whole transcriptome was quantified with Affymetrix HuGene 1.1 ST. Among top 20 enriched pathway"], "order_basis": "paper_text_order:2185", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["GEO datasets GSE43816 and GSE54326 were downloaded from website (https://www.ncbi.nlm.nih.gov/), GSEA, enrichment map analysis and heat map were performed with R software. Statistical analysis was done using Student's t-test, variance analysis and/or non-parametric tests. For all the tests, P<0.05 was considered as statistical significance. All statistics were calculated by SPSS 13.0 or R software."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T03:34:12+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}}}