{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35147192", "kind": "science-record", "revision": 6, "content_hash": "sha256:0c545a3e8770ea7677da1b243d097e971cefc50ac340ed0cee0fadc7402dc1fb", "created_at": "2026-11-01T17:36:53Z", "updated_at": "2026-11-01T22:48:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure.", "doi": "10.1093/humrep/deac019", "pmid": "35147192", "authors": ["Carolina von Grothusen", "Caroline Frisendahl", "Vijayachitra Modhukur", "Parameswaran Grace Lalitkumar", "Maire Peters", "Omid R Faridani", "Andres Salumets", "Nageswara Rao Boggavarapu", "Kristina Gemzell-Danielsson"], "journal": "Human reproduction (Oxford, England)", "year": 2022, "abstract": "STUDY QUESTION: Is the composition of microRNAs (miRNAs) in uterine fluid (UF) of women with recurrent implantation failure (RIF) different from that of healthy fertile women?\nSUMMARY ANSWER: The composition of miRNAs in UF of women with RIF is different from that of healthy fertile women and the dysregulated miRNAs are associated with impaired endometrial receptivity and embryo implantation.\nWHAT IS KNOWN ALREADY: It has previously been demonstrated that the miRNAs secreted from endometrial cells into the UF contribute to the achievement of endometrial receptivity. Endometrial miRNAs are dysregulated in women with RIF.\nSTUDY DESIGN, SIZE, DURATION: In this descriptive laboratory case-control study, miRNA abundancy was compared between UF collected during implantation phase from healthy fertile women (n = 17) and women with RIF (n = 34), which was defined as three failed IVF cycles with high-quality embryos.\nPARTICIPANTS/MATERIALS, SETTING, METHODS: Recruitment of study subjects and sampling of UF were performed at two university clinics in Stockholm, Sweden and Tartu, Estonia. The study participants monitored their menstrual cycles using an LH test kit. The UF samples were collected on Day LH + 7-9 by flushing with saline. Samples were processed for small RNA sequencing and mapped for miRNAs. The differential abundance of miRNAs in UF was compared between the two groups using differential expression analysis (DESeq2). Further downstream analyses, including miRNA target gene prediction (miRTarBase), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (g:Profiler) and external validation using relevant published data, were performed on the dysregulated miRNAs. Two miRNAs were technically validated with quantitative real-time PCR (RT-PCR).\nMAIN RESULTS AND THE ROLE OF CHANCE: After processing of the sequencing data, there were 15 samples in the healthy fertile group and 33 samples in the RIF group. We found 61 differentially abundant UF miRNAs (34 upregulated and 27 downregulated) in RIF compared to healthy women with a false discovery rate of <0.05 and a fold change (FC) of ≤-2 or ≥2. When analyzed with published literature, we found that several of the differentially abundant miRNAs are expressed in endometrial epithelial cells and have been reported in endometrial extracellular vesicles and in association with endometrial receptivity and RIF. Their predicted target genes were further expressed both in the trophectodermal cells of blastocyst-stage embryos and endometrial mid-secretory epithelial cells, as assessed by publicly available single-cell transcriptome-sequencing studies. Pathway analysis further revealed that 25 pathways, having key roles in endometrial receptivity and implantation, were significantly enriched. Hsa-miR-486-5p (FC -20.32; P-value = 0.004) and hsa-miR-92b-3p (FC -9.72; P-value = 0.004) were successfully technically validated with RT-PCR.\nLARGE SCALE DATA: The data are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/ with GEO accession number: GSE173289.\nLIMITATIONS, REASONS FOR CAUTION: This is a descriptive study with a limited number of study participants. Moreover, the identified differentially abundant miRNAs should be validated in a larger study cohort, and the predicted miRNA target genes and enriched pathways in RIF need to be confirmed and further explored in vitro.\nWIDER IMPLICATIONS OF THE FINDINGS: RIF is a major challenge in the current IVF setting with no diagnostic markers nor effective treatment options at hand. For the first time, total miRNAs have been extensively mapped in receptive phase UF of both healthy women with proven fertility and women diagnosed with RIF. Our observations shed further light on the molecular mechanisms behind RIF, with possible implications in future biomarker and clinical treatment studies.\nSTUDY FUNDING/COMPETING INTEREST(S): This work was financially supported by the Swedish Research Council (2017-00932), a joint grant from Region Stockholm and Karolinska Institutet (ALF Medicine 2020, FoUI-954072), Estonian Research Council (PRG1076), Horizon 2020 innovation (ERIN, EU952516) and European Commission and Enterprise Estonia (EU48695). The authors have no competing interests to declare for the current study.", "claims": [{"id": "claim-method", "statement": "The differential abundance of miRNAs in UF was compared between the two groups using differential expression analysis (DESeq2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35147192", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "The differential abundance of miRNAs in UF was compared between the two groups using differential expression analysis (DESeq2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data underlying this article are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/ and can be accessed with GEO accession number: GSE173289.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35147192", "locator": "sections[26] \"Data availability\" paragraph 2", "quote": "The data underlying this article are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/ and can be accessed with GEO accession number: GSE173289."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We found 61 differentially abundant UF miRNAs (34 upregulated and 27 downregulated) in RIF compared to healthy women with a false discovery rate of <0.05 and a fold change (FC) of ≤−2 or ≥2.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35147192", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "We found 61 differentially abundant UF miRNAs (34 upregulated and 27 downregulated) in RIF compared to healthy women with a false discovery rate of <0.05 and a fold change (FC) of ≤−2 or ≥2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We found 61 differentially abundant UF miRNAs (34 upregulated and 27 downregulated) in RIF compared to healthy women with a false discovery rate of <0.05 and a fold change (FC) of ≤−2 or ≥2.", "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:35147192"], "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:GSE111976"], "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:GSE111976"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35147192", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/humrep/deac019", "sha256": 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"GSM3047318", "GSM3047319", "GSM3047320", "GSM3047321", "GSM3047322", "GSM3047323", "GSM3047324", "GSM3047325", "GSM3047326", "GSM3047327", "GSM3047328", "GSM3047329", "GSM3047330", "GSM3047331", "GSM3047332", "GSM3047333", "GSM3047334", "GSM3047335", "GSM3047336", "GSM3047337", "GSM3047338", "GSM3047339", "GSM3047340", "GSM3047341", "GSM3047342", "GSM3047343", "GSM3047344", "GSM3047345", "GSM3047346", "GSM3047347", "GSM3047348", "GSM3047349", "GSM3047350", "GSM3047351", "GSM3047352", "GSM3047353", "GSM3047354", "GSM3047355", "GSM3047356", "GSM3047357", "GSM3047358", "GSM3047359", "GSM3047360", "GSM3047361", "GSM3047362", "GSM3047363", "GSM3047364", "GSM3047365", "GSM3047366", "GSM3047367", "GSM3047368", "GSM3047369", "GSM3047370", "GSM3047371", "GSM3047372", "GSM3047373", "GSM3047374", "GSM3047375", "GSM3047376", "GSM3047377", "GSM3047378", "GSM3047379", "GSM3047380", "GSM3047381", "GSM3047382", "GSM3047383", "GSM3047384", "GSM3047385", "GSM3047386", "GSM3047387", "GSM3047388", "GSM3047389", "GSM3047390", "GSM3047391", "GSM3047392", "GSM3047393", "GSM3047394", "GSM3047395", "GSM3047396", "GSM3047397", "GSM3047398", "GSM3047399", "GSM3047400", "GSM3047401", "GSM3047402", "GSM3047403", "GSM3047404", "GSM3047405", "GSM3047406", "GSM3047407", "GSM3047408", "GSM3047409", "GSM3047410", "GSM3047411", "GSM3047412", "GSM3047413", "GSM3047414", "GSM3047415", "GSM3047416", "GSM3047417", "GSM3047418", "GSM3047419", "GSM3047420", "GSM3047421", "GSM3047422", "GSM3047423", "GSM3047424", "GSM3047425", "GSM3047426", "GSM3047427", "GSM3047428", "GSM3047429", "GSM3047430", "GSM3047431", "GSM3047432", "GSM3047433", "GSM3047434", "GSM3047435", "GSM3047436", "GSM3047437", "GSM3047438", "GSM3047439", "GSM3047440", "GSM3047441", "GSM3047442", "GSM3047443", "GSM3047444", "GSM3047445", "GSM3047446", "GSM3047447", "GSM3047448", "GSM3047449", "GSM3047450", "GSM3047451", "GSM3047452", "GSM3047453", "GSM3047454", "GSM3047455", "GSM3047456", "GSM3047457", "GSM3047458", "GSM3047459", "GSM3047460", "GSM3047461", "GSM3047462", "GSM3047463", "GSM3047464", "GSM3047465", "GSM3047466", "GSM3047467", "GSM3047468", "GSM3047469", "GSM3047470", "GSM3047471", "GSM3047472", "GSM3047473", "GSM3047474", "GSM3047475", "GSM3047476", "GSM3047477", "GSM3047478", "GSM3047479", "GSM3047480", "GSM3047481", "GSM3047482", "GSM3047483", "GSM3047484", "GSM3047485", "GSM3047486", "GSM3047487", "GSM3047488", "GSM3047489", "GSM3047490", "GSM3047491", "GSM3047492", "GSM3047493", "GSM3047494", "GSM3047495", "GSM3047496", "GSM3047497", "GSM3047498", "GSM3047499", "GSM3047500", "GSM3047501", "GSM3047502", "GSM3047503", "GSM3047504", "GSM3047505", "GSM3047506", "GSM3047507", "GSM3047508", "GSM3047509", "GSM3047510", "GSM3047511", "GSM3047512", "GSM3047513", "GSM3047514", "GSM3047515", "GSM3047516", "GSM3047517", "GSM3047518", "GSM3047519", "GSM3047520", "GSM3047521", "GSM3047522", "GSM3047523", "GSM3047524", "GSM3047525", "GSM3047526", "GSM3047527", "GSM3047528", "GSM3047529", "GSM3047530", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE173289", "GSE111976"], "resolved_accessions": ["GSE173289", "GSE111976"], "statements": ["The data underlying this article are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/ and can be accessed with GEO accession number: GSE173289."], "basis": "The paper names GSE173289, GSE111976 in Gene Expression Omnibus (GEO) 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:35147192", "data:geo:GSE111976"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE111976"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:33:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14987, "completion_tokens": 1131, "cached_tokens": 128}}, "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:35147192", "type": "paper", "label": "pmid:35147192"}, {"id": "source:pmid:35147192", "type": "manuscript", "label": "PMID 35147192 full text"}, {"id": "data:geo:GSE111976", "type": "dataset", "label": "GEO GSE111976"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35147192", "type": "paper", "label": "pmid:35147192"}, {"id": "source:pmid:35147192", "type": "manuscript", "label": "PMID 35147192 full text"}, {"id": "data:geo:GSE111976", "type": "dataset", "label": "GEO GSE111976"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35147192", "type": "extraction", "used": ["source:pmid:35147192"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE111976", "type": "accession_resolution", "used": ["data:geo:GSE111976"], "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:35147192", "parent_hash": "sha256:8cafb6982ac62c295e1bb3ea3cf4d912baa8daab0d246611e6457d9c9facc85a", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE111976 licence not read", "asset:data:geo:GSE111976 not downloaded", "asset:data:geo:GSE173289 licence not read", "asset:data:geo:GSE173289 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ith saline. Samples were processed for small RNA sequencing and mapped for miRNAs. The differential abun", "s assessed by publicly available single-cell transcriptome-sequencing studies. Pathway analysis further"], "order_basis": "paper_text_order:1319", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["were technically validated with quantitative real-time PCR (RT-PCR). MAIN RESULTS AND THE ROLE OF CHANC"], "order_basis": "paper_text_order:1798", "id": "assay:2"}, {"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 differential abundance of miRNAs in UF was compared between the two groups using differential expression analysis (DESeq2)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T03:01:36+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}}}