{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39456526", "kind": "science-record", "revision": 4, "content_hash": "sha256:5c4e8a00ea91f518b4e303ae7f59533ea595fc87dc7f15d9f52571426a2454f6", "created_at": "2026-11-01T20:29:43Z", "updated_at": "2026-11-01T22:55:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative Human Genetic and Cellular Analysis of the Pathophysiological Roles of AnxA2 in Alzheimer's Disease.", "doi": "10.3390/antiox13101274", "pmid": "39456526", "authors": ["Lianmeng Ye", "Jiazheng Zhao", "Zhengpan Xiao", "Wenyu Gu", "Xiaoxuan Liu", "Nuela Manka'a Che Ajuyo", "Yi Min", "Yechun Pei", "Dayong Wang"], "journal": "Antioxidants (Basel, Switzerland)", "year": 2024, "abstract": "Alzheimer's disease (AD) is an intractable and progressive neurodegenerative disease. Amyloid beta (Aβ) aggregation is the hallmark of AD. Aβ induces neurotoxicity through a variety of mechanisms, including interacting with membrane receptors to alter downstream signaling, damaging cellular or organelle membranes, interfering with protein degradation and synthesis, and inducing an excessive immune-inflammatory response, all of which lead to neuronal death and other pathological changes associated with AD. In this study, we extracted gene expression profiles from the GSE5281 and GSE97760 microarray datasets in the GEO (Gene Expression Omnibus) database, as well as from the Human Gene Database. We identified differentially expressed genes in the brain tissues of AD patients and healthy persons. Through GO, KEGG, and ROC analyses, annexin A2 (AnxA2) was identified as a putative target gene. Notably, accumulating evidence suggests that intracellular AnxA2 is a key regulator in various biological processes, including endocytosis, transmembrane transport, neuroinflammation, and apoptosis. Thus, we conducted a series of cell biology experiments to explore the biological function of AnxA2 in AD. The results indicate that AnxA2 gene knockdown primarily affects oxidative phosphorylation, cell cycle, AD, protein processing in the endoplasmic reticulum, SNARE interactions in vesicular transport, and autophagy. In SH-SY5Y cells secreting Aβ42, AnxA2 gene knockdown exacerbated Aβ42-induced cytotoxicity, including cell death, intracellular ROS levels, and neuronal senescence, altered cell cycle, and reduced ATP levels, suggesting its critical role in mitochondrial function maintenance. AnxA2 gene knockdown also exacerbated the inhibitory effect of Aβ42 on cell migration. AnxA2 overexpression reduced the inflammatory response induced by Aβ42, while its absence increased pro-inflammatory and decreased anti-inflammatory responses. Furthermore, AnxA2 gene knockdown facilitated apoptosis and decreased autophagy. These results indicated potential pathophysiological roles of AnxA2 in AD.", "claims": [{"id": "claim-data-access", "statement": "Data Availability StatementThe datasets generated and/or analyzed during the current study are available in the following public repositories: Gene expression profiles (GSE5281 and GSE97760) were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 26 August 2022). The gene-related information used in this study was retrieved from GeneCard: The Human Gene Database (https://www.genecards.org/, accessed on 26 August 2022). All relevant datasets are publicly accessible.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39456526", "locator": "sections[40] \"notes\" paragraph 1", "quote": "Data Availability StatementThe datasets generated and/or analyzed during the current study are available in the following public repositories: Gene expression profiles (GSE5281 and GSE97760) were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 26 August 2022). The gene-related information used in this study was retrieved from GeneCard: The Human Gene Database (https://www.genecards.org/, accessed on 26 August 2022). All relevant datasets are publicly accessible."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Through GO, KEGG, and ROC analyses, annexin A2 (AnxA2) was identified as a putative target gene.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39456526", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Through GO, KEGG, and ROC analyses, annexin A2 (AnxA2) was identified as a putative target gene."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Through GO, KEGG, and ROC analyses, annexin A2 (AnxA2) was identified as a putative target gene.", "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:39456526"], "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:GSE5281"], "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:GSE5281"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39456526", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/antiox13101274", "sha256": "sha256:243414003a5a96662e991019992bdff7bf052ef48bde3fabbaa1cf2afe1f39b7", "bytes": 56296, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/antiox13101274", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11504888", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE5281", "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=GSE5281", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE5281", "version": null, "note": "Data Availability StatementThe datasets generated and/or analyzed during the current study are available in the following public repositories: Gene expression profiles (GSE5281 and GSE97760) were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 26 August 2022). The gene-related information used in this study was retrieved from GeneCard: The Human Gene Database (https://www.genecards.org/, accessed on 26 August 2022). All relevant datasets are publicly accessible.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability StatementThe datasets generated and/or analyzed during the current study are available in the following public repositories: Gene expression profiles (GSE5281 and GSE97760) were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 26 August 2022). The gene-related information used in this study was retrieved from GeneCard: The Human Gene Database (https://www.genecards.org/, accessed on 26 August 2022). All relevant datasets are publicly accessible.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM119615", "GSM119616", "GSM119617", "GSM119618", "GSM119619", "GSM119620", "GSM119621", "GSM119622", "GSM119623", "GSM119624", "GSM119625", "GSM119626", "GSM119627", "GSM119628", "GSM119629", "GSM119630", "GSM119631", "GSM119632", "GSM119633", "GSM119634", "GSM119635", "GSM119636", "GSM119637", "GSM119638", "GSM119639", "GSM119640", "GSM119641", "GSM119642", "GSM119643", "GSM119644", "GSM119645", "GSM119646", "GSM119647", "GSM119648", "GSM119649", "GSM119650", "GSM119651", "GSM119652", "GSM119653", "GSM119654", "GSM119655", "GSM119656", "GSM119657", "GSM119658", "GSM119659", "GSM119660", "GSM119661", "GSM119662", "GSM119663", "GSM119664", "GSM119665", "GSM119666", "GSM119667", "GSM119668", "GSM119669", "GSM119670", "GSM119671", "GSM119672", "GSM119673", "GSM119674", "GSM119675", "GSM119676", "GSM119677", "GSM119678", "GSM119679", "GSM119680", "GSM119681", "GSM119682", "GSM119683", "GSM119684", "GSM119685", "GSM119686", "GSM119687", "GSM119688", "GSM238763", "GSM238790", "GSM238791", "GSM238792", "GSM238793", "GSM238794", "GSM238795", "GSM238796", "GSM238797", "GSM238798", "GSM238799", "GSM238800", "GSM238801", "GSM238802", "GSM238803", "GSM238804", "GSM238805", "GSM238806", "GSM238807", "GSM238808", "GSM238809", "GSM238810", "GSM238811", "GSM238812", "GSM238813", "GSM238815", "GSM238816", "GSM238817", "GSM238818", "GSM238819", "GSM238820", "GSM238821", "GSM238822", "GSM238823", "GSM238824", "GSM238825", "GSM238826", "GSM238827", "GSM238834", "GSM238835", "GSM238837", "GSM238838", "GSM238839", "GSM238840", "GSM238841", "GSM238842", "GSM238843", "GSM238844", "GSM238845", "GSM238846", "GSM238847", "GSM238848", "GSM238851", "GSM238854", "GSM238855", "GSM238856", "GSM238857", "GSM238858", "GSM238860", "GSM238861", "GSM238862", "GSM238863", "GSM238864", "GSM238865", "GSM238867", "GSM238868", "GSM238870", "GSM238871", "GSM238872", "GSM238873", "GSM238874", "GSM238875", "GSM238877", "GSM238941", "GSM238942", "GSM238943", "GSM238944", "GSM238945", "GSM238946", "GSM238947", "GSM238948", "GSM238949", "GSM238951", "GSM238952", "GSM238953", "GSM238955", "GSM238963"], "sample_count": 161, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Alzheimer's disease and the normal aged brain (steph-affy-human-433773)", "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:GSE97760", "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=GSE97760", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97760", "version": null, "note": "Data Availability StatementThe datasets generated and/or analyzed during the current study are available in the following public repositories: Gene expression profiles (GSE5281 and GSE97760) were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 26 August 2022). The gene-related information used in this study was retrieved from GeneCard: The Human Gene Database (https://www.genecards.org/, accessed on 26 August 2022). All relevant datasets are publicly accessible.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability StatementThe datasets generated and/or analyzed during the current study are available in the following public repositories: Gene expression profiles (GSE5281 and GSE97760) were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 26 August 2022). The gene-related information used in this study was retrieved from GeneCard: The Human Gene Database (https://www.genecards.org/, accessed on 26 August 2022). All relevant datasets are publicly accessible.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2577046", "GSM2577047", "GSM2577048", "GSM2577049", "GSM2577050", "GSM2577051", "GSM2577052", "GSM2577053", "GSM2577054", "GSM2577055", "GSM2577056", "GSM2577057", "GSM2577058", "GSM2577059", "GSM2577060", "GSM2577061", "GSM2577062", "GSM2577063", "GSM2577064"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Blood genome-wide gene expression microarray profiles in female patients with advanced Alzheimer's Disease and healthy controls", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE5281 not downloaded", "asset:data:geo:GSE5281 licence not read", "asset:data:geo:GSE97760 not downloaded", "asset:data:geo:GSE97760 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Bioconductor linear models for the microarray data package (http://www.bioconductor.org/packages/release/bioc/html/limma.html, accessed on 26 August 2022) were used to identify DEGs by comparing the expression values between AD and the control tissues."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE5281", "GSE97760"], "resolved_accessions": ["GSE5281", "GSE97760"], "statements": ["Data Availability StatementThe datasets generated and/or analyzed during the current study are available in the following public repositories: Gene expression profiles (GSE5281 and GSE97760) were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 26 August 2022). The gene-related information used in this study was retrieved from GeneCard: The Human Gene Database (https://www.genecards.org/, accessed on 26 August 2022). All relevant datasets are publicly accessible."], "basis": "The paper names GSE5281, GSE97760 in GEO (Gene Expression Omnibus) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:39456526", "data:geo:GSE5281"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE5281"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:36:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16082, "completion_tokens": 2419, "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:39456526", "type": "paper", "label": "pmid:39456526"}, {"id": "source:pmid:39456526", "type": "manuscript", "label": "PMID 39456526 full text"}, {"id": "data:geo:GSE5281", "type": "dataset", "label": "GEO GSE5281"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39456526", "type": "paper", "label": "pmid:39456526"}, {"id": "source:pmid:39456526", "type": "manuscript", "label": "PMID 39456526 full text"}, {"id": "data:geo:GSE5281", "type": "dataset", "label": "GEO GSE5281"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39456526", "type": "extraction", "used": ["source:pmid:39456526"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE5281", "type": "accession_resolution", "used": ["data:geo:GSE5281"], "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:39456526", "parent_hash": "sha256:b87c2f326fd29611b43f6aeb3f157ff205a6df91ada88e722767920a774e8f3b", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE5281 licence not read", "asset:data:geo:GSE5281 not downloaded", "asset:data:geo:GSE97760 licence not read", "asset:data:geo:GSE97760 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": ["nsmembrane transport, neuroinflammation, and apoptosis. Thus, we conducted a series of cell biology", "urthermore, AnxA2 gene knockdown facilitated apoptosis and decreased autophagy. These results indic"], "order_basis": "paper_text_order:1157", "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": ["in AD. The results indicate that AnxA2 gene knockdown primarily affects oxidative phosphorylation,", "In SH-SY5Y cells secreting Aβ42, AnxA2 gene knockdown exacerbated Aβ42-induced cytotoxicity, inclu", "tochondrial function maintenance. AnxA2 gene knockdown also exacerbated the inhibitory effect of Aβ", "lammatory responses. Furthermore, AnxA2 gene knockdown facilitated apoptosis and decreased autophag"], "order_basis": "paper_text_order:1313", "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": ["ns in vesicular transport, and autophagy. In SH-SY5Y cells secreting Aβ42, AnxA2 gene knockdown e", "elatin made from deep-sea fish skin and then cultured in a CO2 incubator at 37 °C. When the cultured", "ltured in a CO2 incubator at 37 °C. When the cultured cells reached 80% confluency, they were used", "statistically significant. 2.9. Cell Culture SH-SY5Y and HMC3 cells taken out from the liquid nit"], "order_basis": "paper_text_order:1493", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["cells secreting Aβ42 (Figure 2), followed by Western blotting and transcriptome sequencing. Interestingly,"], "order_basis": "paper_text_order:3695", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Bioconductor linear models for the microarray data package (http://www.bioconductor.org/packages/release/bioc/html/limma.html, accessed on 26 August 2022) were used to identify DEGs by comparing the expression values between AD and the control tissues."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T01:33:53+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}}}