{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35419359", "kind": "science-record", "revision": 4, "content_hash": "sha256:f6c5b34b23f7cec4c790387f85e47d08f0e3cceb460c99afd64c27e2c37f3fc0", "created_at": "2026-11-01T18:14:14Z", "updated_at": "2026-11-01T22:06:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SLC1A5 Prefers to Play as an Accomplice Rather Than an Opponent in Pancreatic Adenocarcinoma.", "doi": "10.3389/fcell.2022.800925", "pmid": "35419359", "authors": ["Fangshi Xu", "Hai Wang", "Honghong Pei", "Zhengliang Zhang", "Liangliang Liu", "Long Tang", "Shuang Wang", "Bin-Cheng Ren"], "journal": "Frontiers in cell and developmental biology", "year": 2022, "abstract": "Background: SLC1A5, a ferroptosis regulator gene, plays a dual role in cancer regulation. However, the roles of SLC1A5 in pancreatic adenocarcinoma (PAAD) remain elusive. Methods: SLC1A5's expression and somatic mutation information were determined by TCGA, GEO, Oncomine, and cBioPortal databases. Its prognostic value was assessed in TCGA cohort and was validated in three independent cohorts. The effects of SLC1A5 on the tumor immune microenvironment were analyzed by the CIBERSORT algorithm, ssGSEA method, and TISIDB and TIMER databases. The \"oncoPredict\" R package, TIDE algorithm, ImmuCellAI online tool, and GSE35141 and GSE59357 datasets were used to ascertain its therapeutic correlations. GSEA and Western blot were applied to reveal the effects of SLC1A5 on the mTORC1 signaling pathway and ferroptosis process. The biofunctions of SLC1A5 were assessed by MTT, wound-healing, Transwell, and xenograft assays. Results: SLC1A5 was significantly upregulated in the PAAD samples but was not commonly accompanied with somatic mutation (2.3%). Overexpression of SLC1A5 led to a poor prognosis and was identified as an independent prognostic factor. Moreover, high SLC1A5 expression suppressed the antitumor immune process by changing the infiltrating levels of immune cells. As for therapeutic correlations, SLC1A5 was related to the efficacy of dasatinib, sunitinib, sorafenib, and imatinib but may not predict that of radiotherapy, chemotherapeutic drugs, and immune checkpoints inhibitors (ICIs). Notably, the overexpression of SLC1A5 could activate the mTORC1 signaling pathway and may increase the cellular sensitivity to ferroptosis. Finally, the overexpression of SLC1A5 markedly promoted proliferation, migration, and invasion of pancreatic cancer cells. At the in vivo level, SLC1A5 deletion inhibited tumor growth in a mice xenograft model. Conclusions: SLC1A5 prefers to play as an accomplice rather than an opponent in PAAD. Our findings provide novel insights into PAAD treatment.", "claims": [{"id": "claim-method", "statement": "Through univariate and multivariate cox analyses, SLC1A5 (HR = 2.109, p = 0.015) and N stage (HR = 1.957, p = 0.02) were identified as the independent prognostic factors of PAAD (Figures 3F,G).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35419359", "locator": "sections[20] \"3.3 SLC1A5 Is a Critical Complement to the PAAD Prognostic Assessment\" paragraph 2", "quote": "Through univariate and multivariate cox analyses, SLC1A5 (HR = 2.109, p = 0.015) and N stage (HR = 1.957, p = 0.02) were identified as the independent prognostic factors of PAAD (Figures 3F,G)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35419359", "locator": "sections[30] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SLC1A5 overexpression was associated with poor prognosis in pancreatic adenocarcinoma and was identified as an independent prognostic factor.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35419359", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Overexpression of SLC1A5 led to a poor prognosis and was identified as an independent prognostic factor."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SLC1A5 overexpression was associated with poor prognosis in pancreatic adenocarcinoma and was identified as an independent prognostic factor.", "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:35419359"], "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:GSE16515"], "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:GSE16515"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35419359", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2022.800925", "sha256": "sha256:ae004716a350dfb46f2e5d701251034ad20fe6dec62bef433e101fada07f0440", "bytes": 62429, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2022.800925", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8995533", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16515", "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=GSE16515", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16515", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM414924", "GSM414925", "GSM414926", "GSM414927", "GSM414928", "GSM414929", "GSM414930", "GSM414931", "GSM414932", "GSM414933", "GSM414934", "GSM414935", "GSM414936", "GSM414937", "GSM414938", "GSM414939", "GSM414940", "GSM414941", "GSM414942", "GSM414943", "GSM414944", "GSM414945", "GSM414946", "GSM414947", "GSM414948", "GSM414949", "GSM414950", "GSM414951", "GSM414952", "GSM414953", "GSM414954", "GSM414955", "GSM414956", "GSM414957", "GSM414958", "GSM414959", "GSM414960", "GSM414961", "GSM414962", "GSM414963", "GSM414964", "GSM414965", "GSM414966", "GSM414967", "GSM414968", "GSM414969", "GSM414970", "GSM414971", "GSM414972", "GSM414973", "GSM414974", "GSM414975"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from Mayo Clinic Pancreatic Tumor and Normal samples", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE21501", "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=GSE21501", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21501", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM535948", "GSM535949", "GSM535950", "GSM535951", "GSM536032", "GSM536033", "GSM536034", "GSM536035", "GSM536036", "GSM536037", "GSM536038", "GSM536039", "GSM536040", "GSM536041", "GSM536042", "GSM536043", "GSM536044", "GSM536045", "GSM536046", "GSM536443", "GSM536444", "GSM536445", "GSM536446", "GSM536447", "GSM536448", "GSM536449", "GSM536450", "GSM536451", "GSM536452", "GSM536453", "GSM536454", "GSM536455", "GSM536456", "GSM536457", "GSM536458", "GSM536459", "GSM536460", "GSM536461", "GSM536462", "GSM536463", "GSM536464", "GSM536465", "GSM536466", "GSM536467", "GSM536468", "GSM536469", "GSM536470", "GSM536471", "GSM536472", "GSM536473", "GSM536474", "GSM536475", "GSM536476", "GSM536477", "GSM536478", "GSM536479", "GSM536480", "GSM536481", "GSM536482", "GSM536483", "GSM536484", "GSM536485", "GSM536486", "GSM536487", "GSM536488", "GSM536489", "GSM536490", "GSM536491", "GSM536492", "GSM536882", "GSM536883", "GSM536884", "GSM536885", "GSM536886", "GSM536887", "GSM536888", "GSM536889", "GSM536890", "GSM536891", "GSM536892", "GSM536893", "GSM536894", "GSM536895", "GSM536896", "GSM536897", "GSM536898", "GSM536899", "GSM536900", "GSM536901", "GSM536902", "GSM536903", "GSM536904", "GSM536905", "GSM536906", "GSM536907", "GSM536908", "GSM536909", "GSM536910", "GSM536911", "GSM536917", "GSM536918", "GSM536919", "GSM536920", "GSM536921", "GSM536922", "GSM536923", "GSM536924", "GSM536925", "GSM536926", "GSM536927", "GSM536928", "GSM536929", "GSM536930", "GSM536931", "GSM536932", "GSM536933", "GSM536934", "GSM536935", "GSM536936", "GSM536937", "GSM536938", "GSM536939", "GSM536940", "GSM536941", "GSM536942", "GSM536943", "GSM536944", "GSM536945", "GSM536946", "GSM536947", "GSM536948", "GSM536949"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE35141", "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=GSE35141", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35141", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM862564", "GSM862565", "GSM862566", "GSM862567", "GSM862568", "GSM862569", "GSM862570", "GSM862571", "GSM862572", "GSM862573", "GSM862574", "GSM862575"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "DCK is frequently inactivated in acquired gemcitabine-resistant human cancer cells.", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE43795", "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=GSE43795", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43795", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1071356", "GSM1071357", "GSM1071358", "GSM1071359", "GSM1071360", "GSM1071361", "GSM1071362", "GSM1071363", "GSM1071364", "GSM1071365", "GSM1071366", "GSM1071367", "GSM1071368", "GSM1071369", "GSM1071370", "GSM1071371", "GSM1071372", "GSM1071373", "GSM1071374", "GSM1071375", "GSM1071376", "GSM1071377", "GSM1071378", "GSM1071379", "GSM1071380", "GSM1071381", "GSM1071382", "GSM1071383", "GSM1071384", "GSM1071385", "GSM1071386"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression of pancreatic tumors", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE59357", "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=GSE59357", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59357", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1435684", "GSM1435685", "GSM1435686", "GSM1435687", "GSM1435688", "GSM1435689", "GSM1435690", "GSM1435691", "GSM1435692", "GSM1435693", "GSM1435694", "GSM1435695", "GSM1435696", "GSM1435697", "GSM1435698", "GSM1435699", "GSM1435700", "GSM1435701"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression profiles of dasatinib-resistant and dasatinib-sensitive pancreatic cancer cell lines", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE62165", "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=GSE62165", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62165", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1520738", "GSM1520739", "GSM1520740", "GSM1520741", "GSM1520742", "GSM1520743", "GSM1520744", "GSM1520745", "GSM1520746", "GSM1520747", "GSM1520748", "GSM1520749", "GSM1520750", "GSM1520751", "GSM1520752", "GSM1520753", "GSM1520754", "GSM1520755", "GSM1520756", "GSM1520757", "GSM1520758", "GSM1520759", "GSM1520760", "GSM1520761", "GSM1520762", "GSM1520763", "GSM1520764", "GSM1520765", "GSM1520766", "GSM1520767", "GSM1520768", "GSM1520769", "GSM1520770", "GSM1520771", "GSM1520772", "GSM1520773", "GSM1520774", "GSM1520775", "GSM1520776", "GSM1520777", "GSM1520778", "GSM1520779", "GSM1520780", "GSM1520781", "GSM1520782", "GSM1520783", "GSM1520784", "GSM1520785", "GSM1520786", "GSM1520787", "GSM1520788", "GSM1520789", "GSM1520790", "GSM1520791", "GSM1520792", "GSM1520793", "GSM1520794", "GSM1520795", "GSM1520796", "GSM1520797", "GSM1520798", "GSM1520799", "GSM1520800", "GSM1520801", "GSM1520802", "GSM1520803", "GSM1520804", "GSM1520805", "GSM1520806", "GSM1520807", "GSM1520808", "GSM1520809", "GSM1520810", "GSM1520811", "GSM1520812", "GSM1520813", "GSM1520814", "GSM1520815", "GSM1520816", "GSM1520817", "GSM1520818", "GSM1520819", "GSM1520820", "GSM1520821", "GSM1520822", "GSM1520823", "GSM1520824", "GSM1520825", "GSM1520826", "GSM1520827", "GSM1520828", "GSM1520829", "GSM1520830", "GSM1520831", "GSM1520832", "GSM1520833", "GSM1520834", "GSM1520835", "GSM1520836", "GSM1520837", "GSM1520838", "GSM1520839", "GSM1520840", "GSM1520841", "GSM1520842", "GSM1520843", "GSM1520844", "GSM1520845", "GSM1520846", "GSM1520847", "GSM1520848", "GSM1520849", "GSM1520850", "GSM1520851", "GSM1520852", "GSM1520853", "GSM1520854", "GSM1520855", "GSM1520856", "GSM1520857", "GSM1520858", "GSM1520859", "GSM1520860", "GSM1520861", "GSM1520862", "GSM1520863", "GSM1520864", "GSM1520865", "GSM1520866", "GSM1520867", "GSM1520868"], "sample_count": 131, "group_sizes": null, "group_sizes_basis": null, "platform": "13667", "taxon": "Homo sapiens", "title": "Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE62452", "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=GSE62452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62452", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1527105", "GSM1527106", "GSM1527107", "GSM1527108", "GSM1527109", "GSM1527110", "GSM1527111", "GSM1527112", "GSM1527113", "GSM1527114", "GSM1527115", "GSM1527116", "GSM1527117", "GSM1527118", "GSM1527119", "GSM1527120", "GSM1527121", "GSM1527122", "GSM1527123", "GSM1527124", "GSM1527125", "GSM1527126", "GSM1527127", "GSM1527128", "GSM1527129", "GSM1527130", "GSM1527131", "GSM1527132", "GSM1527133", "GSM1527134", "GSM1527135", "GSM1527136", "GSM1527137", "GSM1527138", "GSM1527139", "GSM1527140", "GSM1527141", "GSM1527142", "GSM1527143", "GSM1527144", "GSM1527145", "GSM1527146", "GSM1527147", "GSM1527148", "GSM1527149", "GSM1527150", "GSM1527151", "GSM1527152", "GSM1527153", "GSM1527154", "GSM1527155", "GSM1527156", "GSM1527157", "GSM1527158", "GSM1527159", "GSM1527160", "GSM1527161", "GSM1527162", "GSM1527163", "GSM1527164", "GSM1527165", "GSM1527166", "GSM1527167", "GSM1527168", "GSM1527169", "GSM1527170", "GSM1527171", "GSM1527172", "GSM1527173", "GSM1527174", "GSM1527175", "GSM1527176", "GSM1527177", "GSM1527178", "GSM1527179", "GSM1527180", "GSM1527181", "GSM1527182", "GSM1527183", "GSM1527184", "GSM1527185", "GSM1527186", "GSM1527187", "GSM1527188", "GSM1527189", "GSM1527190", "GSM1527191", "GSM1527192", "GSM1527193", "GSM1527194", "GSM1527195", "GSM1527196", "GSM1527197", "GSM1527198", "GSM1527199", "GSM1527200", "GSM1527201", "GSM1527202", "GSM1527203", "GSM1527204", "GSM1527205", "GSM1527206", "GSM1527207", "GSM1527208", "GSM1527209", "GSM1527210", "GSM1527211", "GSM1527212", "GSM1527213", "GSM1527214", "GSM1527215", "GSM1527216", "GSM1527217", "GSM1527218", "GSM1527219", "GSM1527220", "GSM1527221", "GSM1527222", "GSM1527223", "GSM1527224", "GSM1527225", "GSM1527226", "GSM1527227", "GSM1527228", "GSM1527229", "GSM1527230", "GSM1527231", "GSM1527232", "GSM1527233", "GSM1527234"], "sample_count": 130, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 69 pancreatic tumors and 61 adjacent non-tumor tissue from patients with pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE71729", "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=GSE71729", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71729", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1843893", "GSM1843894", "GSM1843895", "GSM1843896", "GSM1843897", "GSM1843898", "GSM1843899", "GSM1843900", "GSM1843901", "GSM1843902", "GSM1843903", "GSM1843904", "GSM1843905", "GSM1843906", "GSM1843907", "GSM1843908", "GSM1843909", "GSM1843910", "GSM1843911", "GSM1843912", "GSM1843913", "GSM1843914", "GSM1843915", "GSM1843916", "GSM1843917", "GSM1843918", "GSM1843919", "GSM1843920", "GSM1843921", "GSM1843922", "GSM1843923", "GSM1843924", "GSM1843925", "GSM1843926", "GSM1843927", "GSM1843928", "GSM1843929", "GSM1843930", "GSM1843931", "GSM1843932", "GSM1843933", "GSM1843934", "GSM1843935", "GSM1843936", "GSM1843937", "GSM1843938", "GSM1843939", "GSM1843940", "GSM1843941", "GSM1843942", "GSM1843943", "GSM1843944", "GSM1843945", "GSM1843946", "GSM1843947", "GSM1843948", "GSM1843949", "GSM1843950", "GSM1843951", "GSM1843952", "GSM1843953", "GSM1843954", "GSM1843955", "GSM1843956", "GSM1843957", "GSM1843958", "GSM1843959", "GSM1843960", "GSM1843961", "GSM1843962", "GSM1843963", "GSM1843964", "GSM1843965", "GSM1843966", "GSM1843967", "GSM1843968", "GSM1843969", "GSM1843970", "GSM1843971", "GSM1843972", "GSM1843973", "GSM1843974", "GSM1843975", "GSM1843976", "GSM1843977", "GSM1843978", "GSM1843979", "GSM1843980", "GSM1843981", "GSM1843982", "GSM1843983", "GSM1843984", "GSM1843985", "GSM1843986", "GSM1843987", "GSM1843988", "GSM1843989", "GSM1843990", "GSM1843991", "GSM1843992", "GSM1843993", "GSM1843994", "GSM1843995", "GSM1843996", "GSM1843997", "GSM1843998", "GSM1843999", "GSM1844000", "GSM1844001", "GSM1844002", "GSM1844003", "GSM1844004", "GSM1844005", "GSM1844006", "GSM1844007", "GSM1844008", "GSM1844009", "GSM1844010", "GSM1844011", "GSM1844012", "GSM1844013", "GSM1844014", "GSM1844015", "GSM1844016", "GSM1844017", "GSM1844018", "GSM1844019", "GSM1844020", "GSM1844021", "GSM1844022", "GSM1844023", "GSM1844024", "GSM1844025", "GSM1844026", "GSM1844027", "GSM1844028", "GSM1844029", "GSM1844030", "GSM1844031", "GSM1844032", "GSM1844033", "GSM1844034", "GSM1844035", "GSM1844036", "GSM1844037", "GSM1844038", "GSM1844039", "GSM1844040", "GSM1844041", "GSM1844042", "GSM1844043", "GSM1844044", "GSM1844045", "GSM1844046", "GSM1844047", "GSM1844049", "GSM1844050", "GSM1844051", "GSM1844052", "GSM1844053", "GSM1844054", "GSM1844055", "GSM1844056", "GSM1844057", "GSM1844058", "GSM1844059", "GSM1844060", "GSM1844061", "GSM1844062", "GSM1844063", "GSM1844064", "GSM1844065", "GSM1844066", "GSM1844067", "GSM1844068", "GSM1844069", "GSM1844070", "GSM1844071", "GSM1844072", "GSM1844073", "GSM1844074", "GSM1844075", "GSM1844076", "GSM1844077", "GSM1844078", "GSM1844079", "GSM1844080", "GSM1844081", "GSM1844082", "GSM1844083", "GSM1844084", "GSM1844085", "GSM1844086", "GSM1844088", "GSM1844089", "GSM1844090", "GSM1844091", "GSM1844092", "GSM1844093", "GSM1844094", "GSM1844095", "GSM1844096", "GSM1844097", "GSM1844098", "GSM1844099", "GSM1844100", "GSM1844101", "GSM1844102", "GSM1844103", "GSM1844104", "GSM1844105", "GSM1844106", "GSM1844107", "GSM1844108", "GSM1844109", "GSM1844110", "GSM1844111", "GSM1844112", "GSM1844113", "GSM1844114", "GSM1844115", "GSM1844116", "GSM1844117", "GSM1844118", "GSM1844119", "GSM1844120", "GSM1844121", "GSM1844122", "GSM1844123", "GSM1844124", "GSM1844125", "GSM1844126", "GSM1844127", "GSM1844128", "GSM1844129", "GSM1844130", "GSM1844131", "GSM1844132", "GSM1844133", "GSM1844134", "GSM1844135", "GSM1844136", "GSM1844137", "GSM1844138", "GSM1844139", "GSM1844140", "GSM1844141", "GSM1844142", "GSM1844143", "GSM1844144", "GSM1844145", "GSM1844146", "GSM1844147", "GSM1844148", "GSM1844149", "GSM1844150", "GSM1844151", "GSM1844152", "GSM1844153", "GSM1844154", "GSM1844155", "GSM1844156", "GSM1844157", "GSM1844158", "GSM1844159", "GSM1844160", "GSM1844161", "GSM1844162", "GSM1844163", "GSM1844164", "GSM1844165", "GSM1844166", "GSM1844167", "GSM1844168", "GSM1844169", "GSM1844170", "GSM1844171", "GSM1844172", "GSM1844173", "GSM1844174", "GSM1844175", "GSM1844176", "GSM1844177", "GSM1844178", "GSM1844179", "GSM1844180", "GSM1844181", "GSM1844182", "GSM1844183", "GSM1844184", "GSM1844185", "GSM1844186", "GSM1844187", "GSM1844188", "GSM1844189", "GSM1844190", "GSM1844191", "GSM1844192", "GSM1844193", "GSM1844194", "GSM1844195", "GSM1844196", "GSM1844197", "GSM1844198", "GSM1844199", "GSM1844200", "GSM1844201", "GSM1844202", "GSM1844203", "GSM1844204", "GSM1844205", "GSM1844206", "GSM1844207", "GSM1844208", "GSM1844209", "GSM1844210", "GSM1844211", "GSM1844212", "GSM1844213", "GSM1844214", "GSM1844215", "GSM1844216", "GSM1844217", "GSM1844218", "GSM1844219", "GSM1844220", "GSM1844221", "GSM1844222", "GSM1844223", "GSM1844224", "GSM1844225", "GSM1844226", "GSM1844227", "GSM1844228", "GSM1844229", "GSM1844230", "GSM1844231", "GSM1844232", "GSM1844233", "GSM1844234", "GSM1844235", "GSM1844236", "GSM1844237", "GSM1844238", "GSM1844239", "GSM1844240", "GSM1844241", "GSM1844242", "GSM1844243", "GSM1844244", "GSM1844245", "GSM1844246", "GSM1844247", "GSM1844248", "GSM1844249", "GSM1844250", "GSM1844251"], "sample_count": 357, "group_sizes": null, "group_sizes_basis": null, "platform": "20769", "taxon": "Homo sapiens", "title": "Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE16515 not downloaded", "asset:data:geo:GSE16515 licence not read", "asset:data:geo:GSE21501 not downloaded", "asset:data:geo:GSE21501 licence not read", "asset:data:geo:GSE35141 not downloaded", "asset:data:geo:GSE35141 licence not read", "asset:data:geo:GSE43795 not downloaded", "asset:data:geo:GSE43795 licence not read", "asset:data:geo:GSE59357 not downloaded", "asset:data:geo:GSE59357 licence not read", "asset:data:geo:GSE62165 not downloaded", "asset:data:geo:GSE62165 licence not read", "asset:data:geo:GSE62452 not downloaded", "asset:data:geo:GSE62452 licence not read", "asset:data:geo:GSE71729 not downloaded", "asset:data:geo:GSE71729 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Through univariate and multivariate cox analyses, SLC1A5 (HR = 2.109, p = 0.015) and N stage (HR = 1.957, p = 0.02) were identified as the independent prognostic factors of PAAD (Figures 3F,G)."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.8, "band": "high", "quote": "decision curve analysis"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE71729", "GSE62165", "GSE16515", "GSE43795", "GSE62452", "GSE21501", "GSE35141", "GSE59357"], "resolved_accessions": ["GSE71729", "GSE62165", "GSE16515", "GSE43795", "GSE62452", "GSE21501", "GSE35141", "GSE59357"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE71729, GSE62165, GSE16515, GSE43795, GSE62452, GSE21501, GSE35141, GSE59357 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:35419359", "data:geo:GSE16515"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16515"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:41:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17517, "completion_tokens": 2402, "cached_tokens": 256}}, "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:35419359", "type": "paper", "label": "pmid:35419359"}, {"id": "source:pmid:35419359", "type": "manuscript", "label": "PMID 35419359 full text"}, {"id": "data:geo:GSE16515", "type": "dataset", "label": "GEO GSE16515"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35419359", "type": "paper", "label": "pmid:35419359"}, {"id": "source:pmid:35419359", "type": "manuscript", "label": "PMID 35419359 full text"}, {"id": "data:geo:GSE16515", "type": "dataset", "label": "GEO GSE16515"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35419359", "type": "extraction", "used": ["source:pmid:35419359"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16515", "type": "accession_resolution", "used": ["data:geo:GSE16515"], "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:35419359", "parent_hash": "sha256:21f3e891a2465dd15685bd6f84c072a524663052ffa4018d27fa76645287b134", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE16515 licence not read", "asset:data:geo:GSE16515 not downloaded", "asset:data:geo:GSE21501 licence not read", "asset:data:geo:GSE21501 not downloaded", "asset:data:geo:GSE35141 licence not read", "asset:data:geo:GSE35141 not downloaded", "asset:data:geo:GSE43795 licence not read", "asset:data:geo:GSE43795 not downloaded", "asset:data:geo:GSE59357 licence not read", "asset:data:geo:GSE59357 not downloaded", "asset:data:geo:GSE62165 licence not read", "asset:data:geo:GSE62165 not downloaded", "asset:data:geo:GSE62452 licence not read", "asset:data:geo:GSE62452 not downloaded", "asset:data:geo:GSE71729 licence not read", "asset:data:geo:GSE71729 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["rtain its therapeutic correlations. GSEA and Western blot were applied to reveal the effects of SLC1A5"], "order_basis": "paper_text_order:759", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["The biofunctions of SLC1A5 were assessed by MTT, wound-healing, Transwell, and xenograft ass"], "order_basis": "paper_text_order:919", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["invasion of pancreatic cancer cells. At the in vivo level, SLC1A5 deletion inhibited tumor growt"], "order_basis": "paper_text_order:1827", "id": "assay:3"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["2 Materials and Methods 2.8 Cell Culture and Transfection Two human pancreatic cancer cell lines (PANC", "ciency was tested by RT-qPCR after 72 h post-transfection. Supplementary Material The Supplementary Ma", "tions were 37°C with 5% CO2. SLC1A5-specific shRNA and amplification plasmids were designed by"], "order_basis": "paper_text_order:2095", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Technology (Wuhan, China). PANC-1 cells were cultured in DMEM (Dulbecco’s Modified Eagle Medium) cont", ") (Procell, Wuhan, China). SW1990 cells were cultured in Leibovitz’s L-15 medium containing 10% FBS a", "(Procell, Wuhan, China). HPDE6-C7 cells were cultured in DMEM (Dulbecco’s Modified Eagle Medium) cont"], "order_basis": "paper_text_order:2313", "id": "assay:5"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s. The interference efficiency was tested by RT-qPCR after 72 h post-transfection. Supplementary", "The interference efficiency was tested by RT-qPCR after 72 h post-transfection. Supplementary"], "order_basis": "paper_text_order:3013", "id": "assay:6"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Through univariate and multivariate cox analyses, SLC1A5 (HR = 2.109, p = 0.015) and N stage (HR = 1.957, p = 0.02) were identified as the independent prognostic factors of PAAD (Figures 3F,G)."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]},"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":"2026-11-04T02:45:39+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}}}