{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38114921", "kind": "science-record", "revision": 3, "content_hash": "sha256:77048774656906b5e3bb24a3a126e61365188721d09ec157d3c0d8277f8f75ef", "created_at": "2026-11-01T19:20:03Z", "updated_at": "2026-11-01T22:10:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.", "doi": "10.1186/s12859-023-05613-5", "pmid": "38114921", "authors": ["Kateřina Faltejsková", "Jiří Vondrášek"], "journal": "BMC bioinformatics", "year": 2023, "abstract": "BACKGROUND: The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the binding site. In this work, we present a novel heuristic algorithm that can reconstruct the unique binding sites captured in a sequencing experiment without using the reference genome.\nRESULTS: We present PAPerFly, the Partial Assembly-based Peak Finder, a tool for the binding site and binding context reconstruction from the sequencing data without any prior knowledge. This tool operates without the need to know the reference genome of the respective organism. We employ algorithmic approaches that are used during genome assembly. The proposed algorithm constructs a de Bruijn graph from the sequencing data. Based on this graph, sequences and their enrichment are reconstructed using a novel heuristic algorithm. The reconstructed sequences are aligned and the peaks in the sequence enrichment are identified. Our approach was tested by processing several ChIP-seq experiments available in the ENCODE database and comparing the results of Paperfly and standard methods.\nCONCLUSIONS: We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available at https://github.com/Caeph/paperfly/ or on Zenodo ( https://doi.org/10.5281/zenodo.7116424 ).", "claims": [{"id": "claim-method", "statement": "Subsequently, we compare the segment in the array of abundances corresponding to a treatment replicate with the segment in the respective control abundances array segment using a Mann–Whitney U test [29] with Bonferroni correction [30].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38114921", "locator": "sections[8] \"Peak calling\" paragraph 5", "quote": "Subsequently, we compare the segment in the array of abundances corresponding to a treatment replicate with the segment in the respective control abundances array segment using a Mann–Whitney U test [29] with Bonferroni correction [30]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38114921", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PAPerFly yields better results than an aggregation of ChIP-seq agnostic tools.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38114921", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PAPerFly yields better results than an aggregation of ChIP-seq agnostic tools.", "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:38114921"], "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:GSE11431"], "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:GSE11431"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38114921", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12859-023-05613-5", "sha256": "sha256:3cd3631a542dd4597c6e1b9f44241c121672ebd9bfd364d6258ad8bf2fac9404", "bytes": 37758, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12859-023-05613-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10731698", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11431", "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=GSE11431", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11431", "version": null, "note": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM288345", "GSM288346", "GSM288347", "GSM288348", "GSM288349", "GSM288350", "GSM288351", "GSM288352", "GSM288353", "GSM288354", "GSM288355", "GSM288356", "GSM288357", "GSM288358", "GSM288359", "GSM288360"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "9185", "taxon": "Mus musculus", "title": "Mapping of transcription factor binding sites in mouse embryonic stem cells", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE11431 not downloaded", "asset:data:geo:GSE11431 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "Blast"}}, {"id": "method-2", "family": null, "specific": null, "label": "Mann–Whitney U test with Bonferroni correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Subsequently, we compare the segment in the array of abundances corresponding to a treatment replicate with the segment in the respective control abundances array segment using a Mann–Whitney U test [29] with Bonferroni correction [30]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "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": ["GSE11431"], "resolved_accessions": ["GSE11431"], "statements": ["The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none."], "basis": "The paper names GSE11431 in SRA and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:38114921", "data:geo:GSE11431"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE11431"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:03:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10942, "completion_tokens": 2741, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38114921", "type": "paper", "label": "pmid:38114921"}, {"id": "source:pmid:38114921", "type": "manuscript", "label": "PMID 38114921 full text"}, {"id": "data:geo:GSE11431", "type": "dataset", "label": "GEO GSE11431"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38114921", "type": "paper", "label": "pmid:38114921"}, {"id": "source:pmid:38114921", "type": "manuscript", "label": "PMID 38114921 full text"}, {"id": "data:geo:GSE11431", "type": "dataset", "label": "GEO GSE11431"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38114921", "type": "extraction", "used": ["source:pmid:38114921"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE11431", "type": "accession_resolution", "used": ["data:geo:GSE11431"], "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:38114921", "parent_hash": "sha256:7b458b31e715aaeb9e5c3498512ae1c6c1c1f07afe2cf09b086d9b67bf3b00bc", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE11431 licence not read", "asset:data:geo:GSE11431 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "chip_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ur approach was tested by processing several ChIP-seq experiments available in the ENCODE database", "yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available", "APerFly takes in raw sequencing reads from a ChIP-seq experiment (or similar; our workflow does no", "assumptions about the particularities of the ChIP-seq experiment design) and the size of k-mer (th"], "order_basis": "paper_text_order:1141", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["espective significance. Method comparison on mouse embryonic stem cells (ESC) To compare our to", "ed their analysis on a ChIP-seq dataset from mouse embryonic stem cells (GSE11431) [31]. First,", "we mapped the results of our analysis to the mouse reference genome (mm8, to be consistent with", "ed with mapping the PAPerFly chiptigs to the mouse genome. Then, we checked whether the PAPerFl"], "order_basis": "paper_text_order:1911", "id": "assay:2"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Blast"], "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":"2026-11-04T00:47:27+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}}}