{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:20440302", "kind": "science-record", "revision": 6, "content_hash": "sha256:1a0efe44db8cfd3ecae37a2da78c71d1f17acb2fb5223ed24313fe4c2711287a", "created_at": "2026-11-01T15:14:34Z", "updated_at": "2026-11-01T18:46:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq.", "doi": "10.1038/cr.2010.64", "pmid": "20440302", "authors": ["Qiang Gan", "Iouri Chepelev", "Gang Wei", "Lama Tarayrah", "Kairong Cui", "Keji Zhao", "Xin Chen"], "journal": "Cell research", "year": 2010, "abstract": "Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. We identified a set of genes that have sex-specific isoforms in wild-type (WT) gonads, including several transcription factors. We found that differentiation of sperms from undifferentiated germ cells induced a dramatic downregulation of RNA splicing factors. Our data confirmed that RNA splicing events are significantly more frequent in the undifferentiated cell-enriched bag of marbles (bam) mutant testis, but downregulated upon differentiation in WT testis. Consistent with this, we showed that genes required for meiosis and terminal differentiation in WT testis were mainly regulated at the transcriptional level, but not by alternative splicing. Unexpectedly, we observed an increase in expression of all families of chromatin remodeling factors and histone modifying enzymes in the undifferentiated cell-enriched bam testis. More interestingly, chromatin regulators and histone modifying enzymes with opposite enzymatic activities are coenriched in undifferentiated cells in testis, suggesting that these cells may possess dynamic chromatin architecture. Finally, our data revealed many new features of the Drosophila gonadal transcriptomes, and will lead to a more comprehensive understanding of how differential gene expression and splicing regulate gametogenesis in Drosophila. Our data provided a foundation for the systematic study of gene expression and alternative splicing in many interesting areas of germ cell biology in Drosophila, such as the molecular basis for sexual dimorphism and the regulation of the proliferation vs terminal differentiation programs in germline stem cell lineages. The GEO accession number for the raw and analyzed RNA-seq data is GSE16960.", "claims": [{"id": "claim-target-result", "statement": "The paper identified sex-specific isoforms in wild-type Drosophila gonads and compared its RNA-seq data with published microarray data using RMA normalization in limma and P≤0.05 plus ≥2-fold-change cutoffs; the microarray CEL files were obtained from NCBI GEO.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:20440302", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We identified a set of genes that have sex-specific isoforms in wild-type (wt) gonads, including several transcription factors."}, {"asset": "source:pmid:20440302", "locator": "sections[26] \"Comparison of RNA-seq data with published microarray data\" paragraph 2", "quote": "We first downloaded the CEL files generated by Parisi et al 22 and Chintapalli et al 96 from NCBI GEO database."}, {"asset": "source:pmid:20440302", "locator": "sections[26] \"Comparison of RNA-seq data with published microarray data\" paragraph 2", "quote": "We then extracted and normalized microarray signals with RMA function embedded in the limma package [downloaded from Bioconductor R packages (http://www.bioconductor.org)]."}, {"asset": "source:pmid:20440302", "locator": "sections[26] \"Comparison of RNA-seq data with published microarray data\" paragraph 2", "quote": "Differentially expressed genes were identified using the combination of P-value (P≤0.05) and fold change (≥2) cutoffs, followed by comparison with their expression level using the RNA-seq data."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper identified sex-specific isoforms in wild-type Drosophila gonads and compared its RNA-seq data with published microarray data using RMA normalization in limma and P≤0.05 plus ≥2-fold-change cutoffs; the microarray CEL files were obtained from NCBI GEO.", "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:20440302"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:20440302", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/cr.2010.64", "sha256": "sha256:0f2b3c4de94b48a771af1017565252b957a29090f49ffe48b368b7332d200848", "bytes": 75474, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/cr.2010.64", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC2919574", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:20440302:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:66e34f09d768b5d54f840611481315ffeedb8d85362462c448a5e09926e5dd09", "bytes": 1865, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[39]/table-wrap[1]#T1", "version": null, "note": "Summary of the Drosophila RNA-seq results.", "structure": {"pmcid": "PMC2919574", "section_index": 39, "section_title": "Figures and Tables", "row_count": 22, "column_count": 5}, "table": {"label": "Table 1", "caption": "Summary of the Drosophila RNA-seq results.", "rows": [["Mapping summary", "bam testis", "wt testis", "bam ovary", "wt ovary"], ["Total reads", "41730579", "30013546", "32806238", "29736261"], ["Low-quality and no matched reads", "14736702", "8645118", "14287662", "8220597"], ["Reads with multiple matches (>1 hits)", "6952842", "2667877", "1862272", "1094363"], ["Uniquely mapped reads (genomic+junction)", "20041035", "18700551", "16656304", "20421301"], ["Uniquely mapped non-redundant reads (genomic+junction)", "13028364", "10853191", "11765719", "11206968"], ["Uniquely mapped non-redundant reads ( genomic+junction) subsample", "10163916", "10163916", "10163916", "10163916"], ["Uniquely mapped non-redundant reads (genomic)", "9780037", "9827900", "9763089", "9774561"], ["Uniquely mapped non-redundant reads (junction)", "383879", "336016", "400827", "389355"], ["Unique and non-redundant reads mapping to annotated exons", "9311716", "9416811", "9216015", "9444989"], ["Unique and non-redundant reads mapping to annotated introns", "208725", "174567", "274958", "152291"], ["Unique and non-redundant reads mapping to intergenic region", "259596", "236522", "272116", "177281"], ["ENSEMBL genes with at least 1RPKM", "9383", "10735", "9486", "8434"], ["ENSEMBL genes with at least 5RPKM", "7777", "8233", "7828", "7147"], ["Alternatively spliced genes", "989", "805", "988", "879"], ["Total CFTRs", "2123", "2455", "2487", "1500"], ["CFTRs in intron*", "719", "922", "959", "501"], ["CFTRs in intergenic regions", "1404", "1533", "1528", "999"], ["CFTRs supported by mRNA or EST", "1402", "1149", "1727", "1241"], ["CFTRs predicted by N-SCAN or CONTRAST", "332", "370", "408", "304"], ["CFTRs hit to NCBI non-redundant protein sequence", "227", "378", "223", "150"], ["Average length of CFTRs (bp)", "419", "348", "417", "415"]], "row_count": 22, "column_count": 5, "numeric_cells": 87, "header_rows": 1, "locator": "section[39]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:20440302:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8281f21bd670e7567e5bd65ab722be69309021141b9d015e2387554c313947d7", "bytes": 3542, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[39]/table-wrap[2]#T2", "version": null, "note": "Chromatin regulators are enriched in bam testis compared to wt testisThe chromatin remodeling factors were retrieved from http://web.wi.mit.edu/young/pub/chromatin_remodeling.html; the histone modifying enzymes were from 99–107 (All chromatin remodeling factors and histone modifying enzymes listed here are supported by published research papers.). For each chromatin regulator, the fold change in bam/wt gonads is listed, as well as the RPKM values in bam and wt gonads, respectively. Red numbers indicate enrichment in bam gonads, and blue numbers indicate enrichment in wt gonads. Most of the chromatin regulators have high expression in bam testis (RPKM> 10), therefore the down-regulation in wt testis is significant.", "structure": {"pmcid": "PMC2919574", "section_index": 39, "section_title": "Figures and Tables", "row_count": 22, "column_count": 16}, "table": {"label": "Table 2", "caption": "Chromatin regulators are enriched in bam testis compared to wt testisThe chromatin remodeling factors were retrieved from http://web.wi.mit.edu/young/pub/chromatin_remodeling.html; the histone modifying enzymes were from 99–107 (All chromatin remodeling factors and histone modifying enzymes listed here are supported by published research papers.). For each chromatin regulator, the fold change in bam/wt gonads is listed, as well as the RPKM values in bam and wt gonads, respectively. Red numbers indicate enrichment in bam gonads, and blue numbers indicate enrichment in wt gonads. Most of the chromatin regulators have high expression in bam testis (RPKM> 10), therefore the down-regulation in wt testis is significant.", "rows": [["Gene Name", "bam/wt testis", "bam testis (RPKM)", "wt testis (RPKM)", "Gene Name", "bam/wt testis", "bam testis (RPKM)", "wt testis (RPKM)", "Gene Name", "bam/wt testis", "bam testis (RPKM)", "wt testis (RPKM)", "Gene Name", "bam/wt ovary", "bam ovary (RPKM)", "wt ovary (RPKM)"], ["Rpd3", "15.35", "158.02", "10.29", "CG11033", "4.70", "43.67", "9.30", "trr", "3.05", "26.58", "8.72", "tna", "2.81", "48.70", "17.31"], ["ph-p", "13.46", "17.27", "1.28", "Suv4-20", "4.56", "78.75", "17.25", "mof", "2.90", "34.20", "11.80", "Iswi", "2.29", "122.00", "53.20"], ["Art4", "11.92", "43.10", "3.62", "kis", "4.45", "120.73", "27.16", "tlk", "2.89", "80.46", "27.86", "SuUR", "0.29", "8.37", "28.63"], ["CG3654", "8.45", "48.74", "5.77", "Mi-2", "4.30", "138.92", "32.32", "Snr1", "2.82", "59.58", "21.12", "Art4", "0.36", "26.46", "73.45"], ["tara", "8.38", "17.31", "2.07", "osa", "4.20", "174.52", "41.54", "Su(var)3-9", "2.74", "85.46", "31.20", "Ada2b", "0.37", "28.12", "75.50"], ["mod", "8.24", "127.82", "15.52", "CG13902", "4.19", "22.48", "5.36", "Su(var)2-HP2", "2.58", "37.82", "14.65", "Sgf11", "0.48", "14.46", "30.38"], ["egg", "6.77", "76.40", "11.29", "ial", "4.11", "56.06", "13.62", "CG2982", "2.52", "72.24", "28.65", "borr", "0.48", "28.40", "59.37"], ["MED21", "6.53", "14.72", "2.25", "E(z)", "4.06", "51.80", "12.75", "wda", "2.48", "18.39", "7.42", "z", "0.50", "22.94", "46.21"], ["Psc", "6.31", "15.90", "2.52", "not", "4.02", "66.83", "16.62", "Hcf", "2.32", "43.82", "18.91", "Scm", "0.49", "23.64", "48.50"], ["Rpb4", "6.19", "20.81", "3.36", "Bre1", "3.96", "52.01", "13.13", "Su(var)3-3", "2.27", "28.13", "12.39", "Set2", "0.50", "29.84", "60.13"], ["BAP60", "6.12", "69.93", "11.43", "CG12879", "3.90", "15.40", "3.95", "Sce", "2.17", "47.07", "21.73", "", "", "", ""], ["esc", "6.03", "51.57", "8.55", "CG8165", "3.87", "10.56", "2.73", "Invadolysin", "2.14", "50.45", "23.56", "", "", "", ""], ["BAP55", "5.77", "87.57", "15.17", "phol", "3.77", "68.00", "18.03", "Su(var)205", "2.14", "101.00", "47.23", "", "", "", ""], ["lid", "5.56", "149.49", "26.87", "pr-set7", "3.52", "44.45", "12.64", "Taf1", "2.05", "46.89", "22.86", "", "", "", ""], ["Hdac3", "5.56", "68.80", "12.38", "Nurf-38", "3.39", "191.34", "56.43", "ash1", "0.49", "18.95", "38.48", "", "", "", ""], ["Art1", "5.53", "140.78", "25.47", "Sir2", "3.37", "39.03", "11.58", "Mst35Ba", "0.49", "0.00", "84.60", "", "", "", ""], ["mor", "5.39", "103.02", "19.12", "trx", "3.28", "29.73", "9.07", "Kdm4B", "0.49", "54.43", "111.24", "", "", "", ""], ["Dp1", "5.37", "157.07", "29.24", "Pc", "3.28", "12.13", "3.70", "tna", "0.21", "42.48", "205.15", "", "", "", ""], ["Elp3", "5.30", "57.39", "10.83", "Nurf55", "3.21", "123.73", "38.50", "Mst35Bb", "0.01", "0.00", "135.32", "", "", "", ""], ["Acf1", "4.97", "55.55", "11.17", "HDAC4", "3.16", "31.95", "10.12", "CG31281", "0.00", "0.00", "282.35", "", "", "", ""], ["Pcaf", "4.86", "50.72", "10.44", "Su(z)12", "3.10", "75.43", "24.30", "", "", "", "", "", "", "", ""]], "row_count": 22, "column_count": 16, "numeric_cells": 238, "header_rows": 1, "locator": "section[39]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:20440302:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ab9e479c77ea1cf546a0b3ba2b7f8fef0743ebe9999eb2e9eae623af04dbda1f", "bytes": 2884, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[39]/table-wrap[3]#T3", "version": null, "note": "Genes that exhibit sex-specific or sex-biased isoforms in bam and wt gonadsGenes that encode transcription factors or putative transcription factors were highlighted in red. Genes that encode splicing factors or putative splicing factors were highlighted in yellow.", "structure": {"pmcid": "PMC2919574", "section_index": 39, "section_title": "Figures and Tables", "row_count": 25, "column_count": 3}, "table": {"label": "Table 3", "caption": "Genes that exhibit sex-specific or sex-biased isoforms in bam and wt gonadsGenes that encode transcription factors or putative transcription factors were highlighted in red. Genes that encode splicing factors or putative splicing factors were highlighted in yellow.", "rows": [["bam testis vs. bam ovary", "wt testis vs. wt ovary", "wt testis vs. wt ovary"], ["CG18812 (unknown)", "CG6151 (unknown)", "mge (transmembrane transporter activit)"], ["Jbug (actin binding)", "CG6767 (ribose phosphate diphosphokinase activity)", "Mlf (unknown)"], ["ltd (GTPase activity)", "CG6921 (unknown)", "mud (protein binding)"], ["Mctp (unknown)", "CG8709 (unknown)", "Pabp (mRNA 3’-UTR binding)"], ["PRL-1 tyrosine phosphatase activity)", "cnn (microtubule binding)", "Pfk (6-phosphofructokinase ac)"], ["wt testis vs. wt ovary", "CoRest (chromatin binding)", "PhKgamma (phosphorylase kinase activity)"], ["Alh (transcription factor activity)", "Cpr (NADPH-hemoprotein reductase activity)", "Picot (high affinity inorganic phosphate:sodium symporter activity)"], ["aop (protein binding)", "CycB (cyclin-dependent protein kinase regulator activity)", "qua (actin binding)"], ["aret (RNA binding)", "eIF-4E (translation initiation factor activity)", "Rab14 (GTPase activity)"], ["BicC (protein binding)", "exu (RNA localization)", "rdx (protein binding)"], ["bun (protein homodimerization activity)", "fs(2)ltoPP43 (unknown)", "Rpn6 (endopeptidase activity)"], ["capu (microtubule binding)", "garz (guanyl-nucleotide exchange factor activity)", "Rtnl1 (unknown)"], ["Cbl (ligase activity)", "granny-smith (aminopeptidase activity)", "sgg (protein kinase activity)"], ["CG12360 (unknown)", "Hmgcr (NADPH activity)", "sle (unknown)"], ["CG1244 (ATPase activity)", "I-2 (phosphoprotein phosphatase inhibitor activity)", "smg (translation repressor activity)"], ["CG14619 (ubiquitin-specific protease", "Imp (mRNA bindin)", "SPoCk (manganese-transporting ATPase activity)"], ["CG1640 (L-alanine:2-oxoglutarate aminotransferase activity)", "p53 (transcription factor activity)", "SRPK (protein kinase activity)"], ["CG17034 (ATPase activity)", "jog (unknown)", "ssh (protein phosphatase activity)"], ["CG18135 (protein binding)", "kdn (citrate synthase activity)", "tamo (protein binding)"], ["CG1882 (catalytic activity)", "kis (ATP-dependent helicase activity)", "toc (protein kinase binding)"], ["CG3074 (endopeptidase activity)", "klar (protein binding)", "Tpi (triose-phosphate isomerase activity)"], ["CG33523 (structural molecule activity)", "Lk6 (protein kinase activity)", "Tpr2 (heat shock protein binding)"], ["CG3994 (zinc ion transmembrane transporter activity)", "lola (transcription factor activity)", "vig (mRNA binding)"], ["CG4238 (ubiquitin-protein ligase activity)", "ltd (GTPase activity)", "CG5315 (hormone binding)"]], "row_count": 25, "column_count": 3, "numeric_cells": 25, "header_rows": 1, "locator": "section[39]/table-wrap[3]#T3"}}], "gaps": []}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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There are 11,893 genes in the FlyGEM microarray, 11,341 of them have the same gene ID used f"], "order_basis": "paper_text_order:3210", "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":"2026-11-04T03:14:18+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}}}