{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28540588", "kind": "science-record", "revision": 6, "content_hash": "sha256:2eff992832cdc01814e24b3702fc03d5860fab91576037d07dde271bb6e40843", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga Guillardia theta cultured under different light intensities.", "doi": "10.1007/s11120-017-0400-0", "pmid": "28540588", "authors": ["Thomas Kieselbach", "Otilia Cheregi", "Beverley R Green", "Christiane Funk"], "journal": "Photosynthesis research", "year": 2018, "abstract": "Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active α1β·α2β-tetramer. In all cryptophyte algae investigated so far, the α-subunits have duplicated and diversified into a large gene family. Although there is transcriptional evidence for expression of all these genes, the X-ray structures determined to date suggest that only two of the α-subunit genes might be significantly expressed at the protein level. Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light. The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied. GtcpeA10 seems to be a special member of the α-subunit family, because it consists of two similar N- and C-terminal domains, which likely are the result of a partial tandem gene duplication. The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.", "claims": [{"id": "claim-method", "statement": "In this study, we used a semiquantitative evaluation by peptide counting to test if individual α-subunits are regulated by the different intensities of the white growth light, under which the algae were grown.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28540588", "locator": "sections[14] \"Proteomics analysis\" paragraph 9", "quote": "In this study, we used a semiquantitative evaluation by peptide counting to test if individual α-subunits are regulated by the different intensities of the white growth light, under which the algae were grown."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using semiquantitative peptide counting, the study found that all 20 PE545 α-subunits of Guillardia theta were expressed under white light; their relative abundances did not significantly change across low, standard, and high light, indicating regulation of the antenna pool size rather than individual α-subunits. The proteomics source data were deposited with ProteomeXchange/PRIDE under PXD006301 and 10.6019/PXD006301.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light."}, {"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied."}, {"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301."}, {"asset": "source:pmid:28540588", "locator": "sections[9] \"Mass spectrometry analysis and bioinformatics\" paragraph 5", "quote": "A semiquantitative analysis of the relative expression of the α- and β-subunits was performed according to Dowle et al. (2016)."}, {"asset": "source:pmid:28540588", "locator": "sections[14] \"Proteomics analysis\" paragraph 10", "quote": "The result of this evaluation is that the relative ratios of each α- and β-subunit do not change significantly under LL, SL or HL conditions within the limits of the standard deviations of our quantization."}, {"asset": "source:pmid:28540588", "locator": "sections[14] \"Proteomics analysis\" paragraph 10", "quote": "It therefore appears that the PE545 antennas function as a pool that is regulated by light intensity."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using semiquantitative peptide counting, the study found that all 20 PE545 α-subunits of Guillardia theta were expressed under white light; their relative abundances did not significantly change across low, standard, and high light, indicating regulation of the antenna pool size rather than individual α-subunits. The proteomics source data were deposited with ProteomeXchange/PRIDE under PXD006301 and 10.6019/PXD006301.", "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:28540588"], "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:28540588", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s11120-017-0400-0", "sha256": 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"read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab2", "version": null, "note": "Phycoerythrins of G. theta expressed under different light growth conditions", "structure": {"pmcid": "PMC5784005", "section_index": 14, "section_title": "Proteomics analysis", "row_count": 24, "column_count": 16}, "table": {"label": "Table 2", "caption": "Phycoerythrins of G. theta expressed under different light growth conditions", "rows": [["Gene model", "Low-light growth conditions", "Standard-light growth conditions", "High-light growth conditions"], ["1", "2", "3", "4", "5", "1", "2", "3", "4", "5", "1", "2", "3", "4", "5"], ["GtcpeA1", "988", "1298", "478", "700", "697", "1421", "667", "730", "1390", "860", "971", "733", "495", "802", "855"], ["GtcpeA2", "102", "130", "106", "47", "42", "204", "181", "68", "280", "276", "", "", "26", "", ""], ["GtcpeA3", "511", "453", "254", "274", "369", "983", "423", "423", "669", "394", "86", "453", "172", "313", "183"], ["GtcpeA4", "208", "256", "83", "67", "116", "387", "226", "172", "205", "89", "", "", "", "", ""], ["GtcpeA5", "138", "223", "169", "138", "184", "466", "223", "297", "378", "285", "", "64", "62", "176", "48"], ["GtcpeA6", "342", "673", "299", "563", "379", "653", "256", "439", "753", "810", "332", "423", "216", "581", "377"], ["GtcpeA8", "158", "270", "136", "18", "200", "327", "262", "239", "368", "365", "", "42", "", "", ""], ["GtcpeA9", "", "909", "", "", "381", "", "", "", "", "", "", "", "", "", ""], ["GtcpeA10", "858", "1037", "384", "537", "539", "1421", "621", "554", "1553", "876", "81", "509", "194", "220", "178"], ["GtcpeA11", "365", "411", "134", "236", "191", "612", "324", "223", "716", "535", "240", "323", "202", "302", "244"], ["GtcpeA12", "576", "825", "325", "500", "301", "613", "298", "425", "728", "426", "133", "412", "237", "560", "583"], ["GtcpeA13", "31", "89", "", "", "25", "172", "102", "93", "92", "93", "", "50", "35", "42", "18"], ["GtcpeA14", "381", "440", "213", "332", "290", "750", "283", "292", "812", "646", "162", "189", "224", "367", "152"], ["GtcpeA15", "355", "477", "205", "333", "281", "484", "210", "332", "581", "441", "231", "194", "130", "278", "318"], ["GtcpeA16", "774", "1679", "810", "700", "1019", "1913", "779", "793", "1461", "996", "1026", "925", "889", "1592", "909"], ["GtcpeA17", "78", "359", "165", "98", "159", "567", "479", "217", "253", "147", "", "", "", "", ""], ["GtcpeA18", "516", "968", "381", "589", "610", "1448", "953", "440", "529", "507", "263", "301", "460", "811", "438"], ["GtcpeA19", "", "975", "269", "", "404", "", "", "370", "1136", "852", "404", "375", "278", "", ""], ["GtcpeA9 or GtcpeA19", "", "", "", "323*", "", "754*", "", "", "", "", "", "", "", "477*", ""], ["GtcpeA20", "543", "1031", "375", "675", "615", "1282", "573", "605", "1514", "900", "638", "447", "405", "558", "608"], ["GtcpeA21", "973", "1241", "469", "681", "677", "1283", "660", "702", "1320", "816", "883", "730", "463", "767", "848"], ["Gt-Beta", "2308", "3619", "2077", "2400", "1500", "2869", "1151", "1437", "4407", "4133", "1443", "1304", "1139", "1768", "1581"]], "row_count": 24, "column_count": 16, "numeric_cells": 305, "header_rows": 2, "locator": "section[14]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:28540588:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d9f8853dfb57f1e9852e97c4fd7b15475a36842553cca1b438f9a05876166079", "bytes": 6278, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab3", "version": null, "note": "Experimentally detected unique peptides of the phycobiliproteins of G. theta", "structure": {"pmcid": "PMC5784005", "section_index": 14, "section_title": "Proteomics analysis", "row_count": 86, "column_count": 7}, "table": {"label": "Table 3", "caption": "Experimentally detected unique peptides of the phycobiliproteins of G. theta", "rows": [["Protein", "Start and end in precursor", "Start and end in predicted mature protein", "Unique tryptic peptide", "Highest peptide score", "Lowest peptide expectation value", "Spectra with expectation values <0.05"], ["Beta", "", "1–7", "MLDAFSR (N-terminus)", "47.64", "1.70E−05", "14"], ["", "", "16–28", "AAYVGGADLQALK", "117.63", "1.70E−12", "90"], ["", "16–29", "AAYVGGADLQALKK", "90.98", "8.10E−10", "147"], ["", "85–91", "DGEIILR", "39.35", "0.00012", "6"], ["", "92–108", "YVSYALLSGDSSVLEDR", "155.02", "3.20E−16", "289"], ["", "115–129", "ETYSSLGVPANSNAR", "120", "1.00E−12", "230"], ["", "130–149", "AVSIMKACAVAFINNTASQR", "145.61", "2.80E−15", "30"], ["", "136–149", "ACAVAFINNTASQR", "155.02", "3.20E−16", "160"], ["", "150–171", "KLSTPQGDCSGLASECASYFDK", "114.82", "3.30E−12", "31"], ["", "151–171", "LSTPQGDCSGLASECASYFDK", "155.02", "3.20E−16", "26"], ["GtcpeA1", "42–51", "9–18", "APVITVFDHR", "73.05", "5.00E−08", "181"], ["GtcpeA2", "59–68", "1–10", "IPLGTQIAGK (N-terminus)", "25.67", "0.0027", "30"], ["75–88", "17–30", "ANFYAPEVTIFDHR", "76.29", "2.40E−08", "6"], ["102–112", "44–54", "TGDQDDEMLVR", "89.35", "1.20E−09", "10"], ["118–127", "60–69", "VFCPEAEAAK", "13.82", "0.041", "1"], ["128–137", "70–79", "VLASTLSVLK", "77.34", "1.80E−08", "39"], ["GtcpeA3", "45–54", "9–19", "APVVTVFDHR", "91.3", "7.40E−10", "35"], ["62–80", "26–44", "NTEYQGLPANSQDDEMLVK", "155.02", "3.20E−16", "90"], ["61–80", "25–44", "RNTEYQGLPANSQDDEMLVK", "18.77", "0.013", "1"], ["86–105", "50–69", "VAINEAAATDLVQQLLGTLK", "120.64", "8.60E−13", "16"], ["86–106", "50–70", "VAINEAAATDLVQQLLGTLKK (C-terminus)", "106.65", "2.20E−11", "13"], ["GtcpeA4", "43–55", "6–18", "SNTAPIVQIFDHR", "92.01", "6.30E−10", "35"], ["84–104", "47–67", "VIPAPEALAASVLQVTVGNLK", "93.35", "4.60E−10", "12"], ["GtcpeA5", "63–74", "6–17", "AIAPVITIFDHR", "112.95", "5.10E−12", "20"], ["88–98", "31–41", "ANTYDDYMLVK", "58.6", "1.40E−06", "16"], ["87–98", "30–41", "KANTYDDYMLVK", "58.06", "1.60E−06", "8"], ["101–124", "44–52", "GEVITVSTSTAASVLAETFGLLDR", "37.6", "0.00017", "1"], ["99–124", "42–67", "VKGEVITVSTSTAASVLAETFGLLDR", "141.73", "6.70E−15", "32"], ["GtcpeA6", "78–89", "9–20", "GFLAPQSYQSYR", "91.23", "7.50E−10", "120"], ["90–106", "21–37", "KGQLLNIAPVIQVHDER", "55.2", "3.00E−06", "16"], ["91–106", "22–37", "GQLLNIAPVIQVHDER", "97.83", "1.60E−10", "16"], ["120–132", "51–63", "VGTEDDAMCVSVK", "132.58", "5.50E−14", "174"], ["135–161", "66–92", "AIPANTNLAASILSDFQIYCQDGSCPK (C-terminus)", "126.81", "2.10E−13", "129"], ["GtcpeA8", "77–90", "25–38", "EYVGPASGDEDDNR", "76.52", "2.20E−08", "6"], ["99–117", "47–65", "ITVSETEAAAALQEFISYR", "154.66", "3.40E−16", "41"], ["GtcpeA9", "98–107", "48–57", "IAVSEGDAAK", "26.6", "0.0022", "3"], ["GtcpeA10", "34–46", "2–14", "AAGYSTASPYSSK (N-terminus)", "28.85", "0.0013", "3"], ["47–64", "15–32", "NSNMGPAFAPVITIFDNR", "155.02", "3.20E−16", "71"], ["79–89", "47–57", "AGDENDEMLVK", "28.24", "0.0015", "10"], ["95–107", "63–75", "IPFPTDDVVNEFR", 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"2.60E−16", "186"], ["111–122", "49–60", "LEPDTGFAEQIK", "57.2", "1.90E−06", "7"], ["110–122", "48–60", "KLEPDTGFAEQIK", "88.18", "1.50E−09", "31"], ["111–131", "49–69", "LEPDTGFAEQIKAETLGLMSK", "19.97", "0.01", "1"], ["GtcpeA17", "44–55", "8–19", "GVAPIITVFDHR", "44.81", "3.30E−05", "3"], ["60–81", "24–45", "GKADSEYQGALANGPEDEMLVK", "28.48", "0.0014", "3"], ["62–81", "26–45", "ADSEYQGALANGPEDEMLVK", "154.68", "3.40E−16", "31"], ["87–96", "51–60", "VPLSAGFADK", "35.26", "0.0003", "3"], ["97–113", "61–77", "VLQQTLGTFGQAPAGAK", "155.02", "3.20E−16", "21"], ["GtcpeA18", "59–75", "4–20", "TMPADGYAPVITVFDHR", "113.61", "4.40E−12", "81"], ["89–99", "34–44", "SNDMEDGMLVK", "54.99", "3.20E−06", "54"], ["107–126", "52–71", "VTESYAASLLQEQLGYINDK", "153.61", "4.40E−16", "60"], ["107–127", "52–72", "VTESYAASLLQEQLGYINDKA (C-terminus)", "154.66", "3.40E−16", "64"], ["GtcpeA19", "98–107", "48–57", "IAVSEGDAAR", "51.02", "7.90E−06", "15"], ["GtcpeA20", "77–93", "25–41", "EYTGGLSNTQDDQMCVK", "155.02", "3.20E−16", "84"], ["109–120", "57–68", "LLQENLSSMFGK (C-terminus)", "153.03", "5.00E−16", "56"], ["GtcpeA21", "42–51", "9–18", "APVVTIFDHR", "66.35", "2.30E−07", "176"]], "row_count": 86, "column_count": 7, "numeric_cells": 428, "header_rows": 1, "locator": "section[14]/table-wrap[2]#Tab3"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "semiquantitative evaluation by peptide counting", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this study, we used a semiquantitative evaluation by peptide counting to test if individual α-subunits are regulated by the different intensities of the white growth light, under which the algae were grown."}}], "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": "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 (semiquantitative evaluation by peptide counting), 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD006301 and 10.6019/PXD006301"], "resolved_accessions": [], "statements": ["The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301."], "basis": "The paper names PXD006301 and 10.6019/PXD006301, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28540588", "asset:table:pmid:28540588:1", "asset:table:pmid:28540588:2", "asset:table:pmid:28540588:3"], "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": "2026-10-31T18:31:20Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 116559, "completion_tokens": 3402, "cached_tokens": 2080}}, "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:28540588", "type": "paper", "label": "pmid:28540588"}, {"id": "source:pmid:28540588", "type": "manuscript", "label": "PMID 28540588 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28540588", "type": "paper", "label": "pmid:28540588"}, {"id": "source:pmid:28540588", "type": "manuscript", "label": "PMID 28540588 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28540588", "type": "extraction", "used": ["source:pmid:28540588"], "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:28540588", "parent_hash": "sha256:1b38456316953fdbccbc6e73fe1129f2aab8d2389f40649e3c5158bc0d5dedf7", "fork_of": null, "generation": 5}, "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":"2026-11-04T01:20:56+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}}}