{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32415162", "kind": "science-record", "revision": 4, "content_hash": "sha256:7a2bbe2f674c261b85e6a92e3f19116251a0ea99e88b5722359618bfb71a6495", "created_at": "2026-11-01T15:41:01Z", "updated_at": "2026-11-01T21:23:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Large database for the analysis and prediction of spliced and non-spliced peptide generation by proteasomes.", "doi": "10.1038/s41597-020-0487-6", "pmid": "32415162", "authors": ["Gerd Specht", "Hanna P Roetschke", "Artem Mansurkhodzhaev", "Petra Henklein", "Kathrin Textoris-Taube", "Henning Urlaub", "Michele Mishto", "Juliane Liepe"], "journal": "Scientific data", "year": 2020, "abstract": "Proteasomes are the main producers of antigenic peptides presented to CD8+ T cells. They can cut proteins and release their fragments or recombine non-contiguous fragments thereby generating novel sequences, i.e. spliced peptides. Understanding which are the driving forces and the sequence preferences of both reactions can streamline target discovery in immunotherapies against cancer, infection and autoimmunity. Here, we present a large database of spliced and non-spliced peptides generated by proteasomes in vitro, which is available as simple CSV file and as a MySQL database. To generate the database, we performed in vitro digestions of 55 unique synthetic polypeptide substrates with different proteasome isoforms and experimental conditions. We measured the samples using three mass spectrometers, filtered and validated putative peptides, identified 22,333 peptide product sequences (15,028 spliced and 7,305 non-spliced product sequences). Our database and datasets have been deposited to the Mendeley (doi:10.17632/nr7cs764rc.1) and PRIDE (PXD016782) repositories. We anticipate that this unique database can be a valuable source for predictors of proteasome-catalyzed peptide hydrolysis and splicing, with various future translational applications.", "claims": [{"id": "claim-method", "statement": "Differences in distributions have been tested using the Kolmogorov-Smirnov test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32415162", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "Differences in distributions have been tested using the Kolmogorov-Smirnov test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The algorithm generating all possible cis and trans spliced peptides was originally described by Liepe et al.56. Scripts for MySQL database setup have been deposited in the MySQL database dump to the Mendeley repository with the dataset access doi:10.17632/nr7cs764rc.158.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32415162", "locator": "sections[16] \"Code availability\" paragraph 2", "quote": "The algorithm generating all possible cis and trans spliced peptides was originally described by Liepe et al.56. Scripts for MySQL database setup have been deposited in the MySQL database dump to the Mendeley repository with the dataset access doi:10.17632/nr7cs764rc.158."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:32415162"], "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:32415162", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41597-020-0487-6", "sha256": 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"section_title": "Database", "row_count": 24, "column_count": 2}, "table": {"label": "Table 1", "caption": "Database description.", "rows": [["Column name", "Description"], ["sampleID", "Unique identifier for every sample"], ["sampleName", "Sample Name used during experiment"], ["runID", "Technical replicate number"], ["protIsotype", "proteasome isoform used for digestion"], ["digestTime", "Elapsed digestion time (hours) at time of measurement"], ["species", "species origin for used proteasome"], ["sampleDate", "Sample date"], ["instrument", "Instrument used for measurement"], ["fragmentation", "Fragmentation method used for measurement"], ["substrateOrigin", "Biological origin of substrate"], ["location", "Measurement location"], ["substrateSeq", "Amino acid sequence of substrate"], ["substrateID", "Unique identifier for a substrate sequence"], ["pepSeq", "Amino acid sequence of peptide products"], ["scanNum", "Scan Number listed in the RAW file"], ["rankMS", "Peptide rank assigned by Mascot Server"], ["ionScore", "Ion Score assigned by Mascot Server"], ["qValue", "Q-Value assigned by Mascot Server"], ["productType", "PCP: non-spliced peptide; PSP: spliced peptide"], ["spliceType", "PSP: cis, reverse cis or trans spliced peptides"], ["positions", "Peptide sequence described as amino acid positions in the substrate sequence"], ["charge", "Ion charge"], ["PTM", "Post-translational modifications"]], "row_count": 24, "column_count": 2, "numeric_cells": 0, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32415162:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:34ec29fc77820ca060dddb1fa9066ee9ea213961f845c92a4c887033ec61ea0a", "bytes": 3111, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab2", "version": null, "note": "Tests for statistical differences between characteristics of identified peptides.", "structure": {"pmcid": "PMC7228940", "section_index": 12, "section_title": "Spliced and non-spliced peptide analysis and further validations", "row_count": 41, "column_count": 3}, "table": {"label": "Table 2", "caption": "Tests for statistical differences between characteristics of identified peptides.", "rows": [["Group 1", "Group2", "p-value"], ["Peptide length"], ["Non-spliced products", "Non-spliced synthesis artifacts", "<2e-16"], ["Non-spliced products", "Non-spliced random control", "<2e-16"], ["Non-spliced synthesis artifacts", "Non-spliced random control", "<2e-16"], ["cis spliced products", "cis spliced synthesis artifacts", "<2e-16"], ["cis spliced products", "cis spliced random control", "<2e-16"], ["cis spliced synthesis artifacts", "cis spliced random control", "<2e-16"], ["trans spliced products", "trans spliced synthesis artifacts", "<2e-16"], ["trans spliced products", "trans spliced random control", "<2e-16"], ["trans spliced synthesis artifacts", "trans spliced random control", "<2e-16"], ["Non-spliced products", "cis spliced products", "<2e-16"], ["cis spliced products", "trans spliced products", "<2e-16"], ["Non-spliced products", "trans spliced products", "<2e-16"], ["Splice-reactant length: SR1"], ["Normal cis spliced products", "Normal cis spliced synthesis artifacts", "<2e-16"], ["Normal cis spliced products", "Normal cis spliced random control", "<2e-16"], ["Normal cis spliced synthesis artifacts", "Normal cis spliced random control", "<2e-16"], ["Reverse cis spliced products", "Reverse cis spliced synthesis artifacts", "<2e-16"], ["Reverse cis spliced products", "Reverse cis spliced random control", "6.3e-16"], ["Reverse cis spliced synthesis artifacts", "Reverse cis spliced random control", "7.9e-13"], ["trans spliced products", "trans spliced synthesis artifacts", "<2e-16"], ["trans spliced products", "trans spliced random control", "<2e-16"], ["trans spliced synthesis artifacts", "trans spliced random control", "1.8e-11"], ["Splice-reactant length: SR2"], ["Normal cis spliced products", "Normal cis spliced synthesis artifacts", "<2e-16"], ["Normal cis spliced products", "Normal cis spliced random control", "0.055"], ["Normal cis spliced synthesis artifacts", "Normal cis spliced random control", "<2e-16"], ["Reverse cis spliced products", "Reverse cis spliced synthesis artifacts", "<2e-16"], ["Reverse cis spliced products", "Reverse cis spliced random control", "<2e-16"], ["Reverse cis spliced synthesis artifacts", "Reverse cis spliced random control", "<2e-16"], ["trans spliced products", "trans spliced synthesis artifacts", "<2e-16"], ["trans spliced products", "trans spliced random control", "<2e-16"], ["trans spliced synthesis artifacts", "trans spliced random control", "<2e-16"], ["Intervening sequence length"], ["Normal cis spliced products", "Normal cis spliced synthesis artifacts", "0.013"], ["Normal cis spliced products", "Normal cis spliced random control", "<2e-16"], ["Normal cis spliced synthesis artifacts", "Normal cis spliced random control", "<2e-16"], ["Reverse cis spliced products", "Reverse cis spliced synthesis artifacts", "0.042"], ["Reverse cis spliced products", "Reverse cis spliced random control", "0.014"], ["Reverse cis spliced synthesis artifacts", "Reverse cis spliced random control", "0.14"]], "row_count": 41, "column_count": 3, "numeric_cells": 37, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab2"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Kolmogorov-Smirnov test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differences in distributions have been tested using the Kolmogorov-Smirnov test."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": 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analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The algorithm generating all possible cis and trans spliced peptides was originally described by Liepe et al.56. Scripts for MySQL database setup have been deposited in the MySQL database dump to the Mendeley repository with the dataset access doi:10.17632/nr7cs764rc.158."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32415162", "asset:table:pmid:32415162:1", "asset:table:pmid:32415162:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:02:21Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 40379, "completion_tokens": 2056, "cached_tokens": 792}}, "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:32415162", "type": "paper", "label": "pmid:32415162"}, {"id": "source:pmid:32415162", "type": "manuscript", "label": "PMID 32415162 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32415162", "type": "paper", "label": "pmid:32415162"}, {"id": "source:pmid:32415162", "type": "manuscript", "label": "PMID 32415162 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32415162", "type": "extraction", "used": ["source:pmid:32415162"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:32415162", "parent_hash": "sha256:c3c800ba8681fe9f4efc18ab59e54efd20aeaeea22ebccd1f275bff59379a2c8", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]},"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":"2026-11-04T01:25:00+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}}}