{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35207629", "kind": "science-record", "revision": 4, "content_hash": "sha256:1b003f1329f9939e1670e4796b33f046ae49c9314e40a70248c4322d587f7c03", "created_at": "2026-11-01T17:36:58Z", "updated_at": "2026-11-01T22:48:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High Expression of Interferon Pathway Genes CXCL10 and STAT2 Is Associated with Activated T-Cell Signature and Better Outcome of Oral Cancer Patients.", "doi": "10.3390/jpm12020140", "pmid": "35207629", "authors": ["Yun-Cian Huang", "Jau-Ling Huang", "Lu-Chia Tseng", "Ping-Hung Yu", "Si-Yun Chen", "Chang-Shen Lin"], "journal": "Journal of personalized medicine", "year": 2022, "abstract": "To improve the survival rate of cancer patients, biomarkers for both early diagnosis and patient stratification for appropriate therapeutics play crucial roles in precision oncology. Investigation of altered gene expression and the relevant molecular pathways in cancer cells are helpful for discovering such biomarkers. In this study, we explore the potential prognostic biomarkers for oral cancer patients through systematically analyzing five oral cancer transcriptomic data sets (TCGA, GSE23558, GSE30784, GSE37991, and GSE138206). Gene Set Enrichment Analysis (GSEA) was individually applied to each data set and the upregulated Hallmark molecular pathways of each data set were intersected to generate 13 common pathways including interferon-α/γ pathways. Among the 5 oral cancer data sets, 43 interferon pathway genes were commonly upregulated and 17 genes exhibited prognostic values in TCGA cohort. After validating in another oral cancer cohort (GSE65858), high expressions of C-X-C motif chemokine ligand 10 (CXCL10) and Signal transducer and activator of transcription 2 (STAT2) were confirmed to be good prognostic biomarkers. GSEA of oral cancers stratified by CXCL10/STAT2 expression showed that activation of T-cell pathways and increased tumor infiltration scores of Type 1 T helper (Th1) and CD8+ T cells were associated with high CXCL10/STAT2 expression. These results suggest that high CXCL10/STAT2 expression can predict a favorable outcome in oral cancer patients.", "claims": [{"id": "claim-method", "statement": "The patient overall survival (OS) in TCGA and GSE65858 oral cancer cohorts was analyzed by the web-based tools Kaplan-Meier plotter (http://kmplot.com/analysis/ accessed between 15 November 2020 and 4 April 2021) with “best cut-off” setting [19]. The IBM SPSS Statistics (version 22, Armonk, NY, USA) was used to compute hazard ratio (HR) of patient OS according to variables of CXCL10/STAT2 expression (HH versus LL), T-stage (T3–4 versus T1–2), N-stage (N1–3 versus N0), gender (male versus female), and age (>60-yr vs. <60-yr) by Cox model analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35207629", "locator": "sections[7] \"2.3. Kaplan-Meier Survival and Statistical Analyses\" paragraph 2", "quote": "The patient overall survival (OS) in TCGA and GSE65858 oral cancer cohorts was analyzed by the web-based tools Kaplan-Meier plotter (http://kmplot.com/analysis/ accessed between 15 November 2020 and 4 April 2021) with “best cut-off” setting [19]. The IBM SPSS Statistics (version 22, Armonk, NY, USA) was used to compute hazard ratio (HR) of patient OS according to variables of CXCL10/STAT2 expression (HH versus LL), T-stage (T3–4 versus T1–2), N-stage (N1–3 versus N0), gender (male versus female), and age (>60-yr vs. <60-yr) by Cox model analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data supporting reported results can be found through requesting the corresponding author. The TCGA and GEO oral cancer data sets can be accessed at https://portal.gdc.cancer.gov and https://www.ncbi.nlm.nih.gov/geo/ (data accessed on 15 July 2020), respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35207629", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "All data supporting reported results can be found through requesting the corresponding author. The TCGA and GEO oral cancer data sets can be accessed at https://portal.gdc.cancer.gov and https://www.ncbi.nlm.nih.gov/geo/ (data accessed on 15 July 2020), respectively."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using Kaplan-Meier and Cox analyses of the TCGA and GSE65858 oral cancer cohorts, coordinated high CXCL10/STAT2 expression predicted favorable overall survival, with univariate HH-versus-LL hazard ratios of 0.568 in TCGA and 0.225 in GSE65858.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35207629", "locator": "sections[12] \"3.3. High Expressions of CXCL10 and STAT2 Were Good Prognostic Factors\" paragraph 2", "quote": "The results of Kaplan-Meier survival analysis demonstrated that both the HH patient subgroups in TCGA (Figure 5C) and GSE65858 (Figure 5D) cohorts exhibited good prognosis. The hazard ratio (HR, HH versus LL) was 0.568 (p = 0.003) in TCGA and was 0.225 (p = 0.010) in GSE65858 in univariate Cox model analysis (Table 3)."}, {"asset": "source:pmid:35207629", "locator": "sections[5] \"2.1.2. Validation Data Sets\" paragraph 2", "quote": "The gene expression and clinical data of 83 oral cancers were extracted from GSE65858 (Germany) data set to validate the prognostic roles of interferon pathway genes discovered in TCGA oral cancer data set."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using Kaplan-Meier and Cox analyses of the TCGA and GSE65858 oral cancer cohorts, coordinated high CXCL10/STAT2 expression predicted favorable overall survival, with univariate HH-versus-LL hazard ratios of 0.568 in TCGA and 0.225 in GSE65858.", "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:35207629"], "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:GSE138206"], "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:GSE138206"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35207629", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/jpm12020140", "sha256": "sha256:92ecf36ebdd3c2f1d709e7ab1dba3603da489a11cb7976ed0e6f43c4c19d4a87", "bytes": 42745, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/jpm12020140", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8877377", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE138206", "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=GSE138206", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE138206", "version": null, "note": "All data supporting reported results can be found through requesting the corresponding author. The TCGA and GEO oral cancer data sets can be accessed at https://portal.gdc.cancer.gov and https://www.ncbi.nlm.nih.gov/geo/ (data accessed on 15 July 2020), respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data supporting reported results can be found through requesting the corresponding author. The TCGA and GEO oral cancer data sets can be accessed at https://portal.gdc.cancer.gov and https://www.ncbi.nlm.nih.gov/geo/ (data accessed on 15 July 2020), respectively.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4101925", "GSM4101926", "GSM4101927", "GSM4101928", "GSM4101929", "GSM4101930", "GSM4101931", "GSM4101932", "GSM4101933", "GSM4101934", "GSM4101935", "GSM4101936", "GSM4101937", "GSM4101938", "GSM4101939", "GSM4101940", "GSM4101941", "GSM4101942"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA expression data from oral squamous cell carcinoma patients", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE23558", "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=GSE23558", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23558", "version": null, "note": "All data supporting reported results can be found through requesting the corresponding author. 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The TCGA and GEO oral cancer data sets can be accessed at https://portal.gdc.cancer.gov and https://www.ncbi.nlm.nih.gov/geo/ (data accessed on 15 July 2020), respectively.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM577914", "GSM577915", "GSM577916", "GSM577917", "GSM577918", "GSM577919", "GSM577920", "GSM577921", "GSM577922", "GSM577923", "GSM577924", "GSM577925", "GSM577926", "GSM577927", "GSM577928", "GSM577929", "GSM577930", "GSM577931", "GSM577932", "GSM577933", "GSM577934", "GSM577935", "GSM577936", "GSM577937", "GSM577938", "GSM577939", "GSM577940", "GSM577941", "GSM577942", "GSM577943", "GSM577944", "GSM577945"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Oral Squamous Cell Carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE30784", "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=GSE30784", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30784", "version": null, "note": "All data supporting reported results can be found through requesting the corresponding author. 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"GSM1607879", "GSM1607880", "GSM1607881", "GSM1607882", "GSM1607883", "GSM1607884", "GSM1607885", "GSM1607886", "GSM1607887", "GSM1607888", "GSM1607889", "GSM1607890", "GSM1607891", "GSM1607892", "GSM1607893", "GSM1607894", "GSM1607895", "GSM1607896", "GSM1607897", "GSM1607898", "GSM1607899", "GSM1607900", "GSM1607901", "GSM1607902", "GSM1607903", "GSM1607904", "GSM1607905", "GSM1607906", "GSM1607907", "GSM1607908", "GSM1607909", "GSM1607910", "GSM1607911", "GSM1607912", "GSM1607913", "GSM1607914", "GSM1607915", "GSM1607916", "GSM1607917", "GSM1607918", "GSM1607919", "GSM1607920", "GSM1607921", "GSM1607922", "GSM1607923", "GSM1607924", "GSM1607925", "GSM1607926", "GSM1607927", "GSM1607928", "GSM1607929", "GSM1607930", "GSM1607931", "GSM1607932", "GSM1607933", "GSM1607934", "GSM1607935", "GSM1607936", "GSM1607937", "GSM1607938", "GSM1607939", "GSM1607940", "GSM1607941", "GSM1607942", "GSM1607943", "GSM1607944", "GSM1607945", "GSM1607946", "GSM1607947", "GSM1607948", "GSM1607949", "GSM1607950", "GSM1607951", "GSM1607952", "GSM1607953"], "sample_count": 270, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck cancer", "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:GSE138206 not downloaded", "asset:data:geo:GSE138206 licence not read", "asset:data:geo:GSE23558 not downloaded", "asset:data:geo:GSE23558 licence not read", "asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE37991 not downloaded", "asset:data:geo:GSE37991 licence not read", "asset:data:geo:GSE65858 not downloaded", "asset:data:geo:GSE65858 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The patient overall survival (OS) in TCGA and GSE65858 oral cancer cohorts was analyzed by the web-based tools Kaplan-Meier plotter (http://kmplot.com/analysis/ accessed between 15 November 2020 and 4 April 2021) with “best cut-off” setting [19]. The IBM SPSS Statistics (version 22, Armonk, NY, USA) was used to compute hazard ratio (HR) of patient OS according to variables of CXCL10/STAT2 expression (HH versus LL), T-stage (T3–4 versus T1–2), N-stage (N1–3 versus N0), gender (male versus female), and age (>60-yr vs. <60-yr) by Cox model analysis."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Cox model"}}], "targets": [], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE23558", "GSE30784", "GSE37991", "GSE138206", "GSE65858"], "resolved_accessions": ["GSE23558", "GSE30784", "GSE37991", "GSE138206", "GSE65858"], "statements": ["All data supporting reported results can be found through requesting the corresponding author. The TCGA and GEO oral cancer data sets can be accessed at https://portal.gdc.cancer.gov and https://www.ncbi.nlm.nih.gov/geo/ (data accessed on 15 July 2020), respectively."], "basis": "The paper names GSE23558, GSE30784, GSE37991, GSE138206, GSE65858 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:35207629", "data:geo:GSE138206"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE138206"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:35:47Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13701, "completion_tokens": 2955, "cached_tokens": 264}}, "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:35207629", "type": "paper", "label": "pmid:35207629"}, {"id": "source:pmid:35207629", "type": "manuscript", "label": "PMID 35207629 full text"}, {"id": "data:geo:GSE138206", "type": "dataset", "label": "GEO GSE138206"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35207629", "type": "paper", "label": "pmid:35207629"}, {"id": "source:pmid:35207629", "type": "manuscript", "label": "PMID 35207629 full text"}, {"id": "data:geo:GSE138206", "type": "dataset", "label": "GEO GSE138206"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35207629", "type": "extraction", "used": ["source:pmid:35207629"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE138206", "type": "accession_resolution", "used": ["data:geo:GSE138206"], "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:35207629", "parent_hash": "sha256:e38368247d7af3637df3effa3b727fb32e101e91bd1adbe9c41e5e5c57d29825", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE138206 licence not read", "asset:data:geo:GSE138206 not downloaded", "asset:data:geo:GSE23558 licence not read", "asset:data:geo:GSE23558 not downloaded", "asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE37991 licence not read", "asset:data:geo:GSE37991 not downloaded", "asset:data:geo:GSE65858 licence not read", "asset:data:geo:GSE65858 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The patient overall survival (OS) in TCGA and GSE65858 oral cancer cohorts was analyzed by the web-based tools Kaplan-Meier plotter (http://kmplot.com/analysis/ accessed between 15 November 2020 and 4 April 2021) with “best cut-off” setting [19]. The IBM SPSS Statistics (version 22, Armonk, NY, USA) was used to compute hazard ratio (HR) of patient OS according to variables of CXCL10/STAT2 expression (HH versus LL), T-stage (T3–4 versus T1–2), N-stage (N1–3 versus N0), gender (male versus female), and age (>60-yr vs. <60-yr) by Cox model analysis."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T03:35:09+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}}}