{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40748556", "kind": "science-record", "revision": 2, "content_hash": "sha256:ea92c6aa36edb490bdcce3852d09ac4b9067992c45e84639a36d4a8893712cf4", "created_at": "2026-11-01T20:30:50Z", "updated_at": "2026-11-01T21:35:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Meta-Analysis of Gene Expression Reveals the Core Transcriptomic Profile of Lesional Scalp in Alopecia Areata.", "doi": "10.1007/s13555-025-01471-6", "pmid": "40748556", "authors": ["Irene Rivera-Ruiz", "Jesús Gay-Mimbrera", "Pedro J Gómez-Arias", "Macarena Aguilar-Luque", "Miguel Juan-Cencerrado", "Carmen Mochón-Jiménez", "Esmeralda Parra-Peralbo", "Beatriz Isla-Tejera", "Francisco Gómez-García", "Juan Ruano"], "journal": "Dermatology and therapy", "year": 2025, "abstract": "INTRODUCTION: Alopecia areata (AA) is an immune-mediated inflammatory skin disease that targets hair follicles. Current research yields varied lists of differentially expressed genes (DEGs). A meta-analytic approach is essential to consolidate these findings into a consistent tissue signature. This study aimed to perform a meta-analysis of gene expression datasets to establish a comprehensive molecular signature of AA lesional scalp.\nMETHODS: We conducted a meta-analysis of transcriptomic data from human studies on lesional skin gene expression in AA. Reanalyzing 132 samples (82 patients with AA and 50 controls) from five Gene Expression Omnibus (GEO) datasets (GSE68801, GSE45512, GSE80342, GSE58573, GSE74761), we employed an effect size approach within a random-effects model to identify unique and shared DEGs and enriched biological pathways. The protocol is registered in PROSPERO (CRD42024559847).\nRESULTS: The meta-analysis identified 5109 DEGs, with 2710 upregulated and 2399 downregulated genes, significantly more than the 120 DEGs shared across the five studies. Consistently expressed genes included CXCL9, CCL18, CXCL10, CD8A, and GZMB (FDR < 0.05). The analysis highlighted chemokines/receptors (CCL13, CCR1, XCL1) and markers of cytotoxic T lymphocytes (GZMA, GZMH, GZMK) and NK cells (NKG2A, NKG2D). Downregulated genes involved type I (KRT31-35, KRT38) and type II (KRT81-86) keratins and proteins crucial for hair follicle structure and function (PADI3, GPRC5D, DSG4, FGF18). Functional analysis showed enrichment in Th1, Th2, and Th17 pathways, particularly through JAK-STAT signaling (p < 0.01).\nCONCLUSION: This core transcriptome of AA lesions provides new insights into the disease's pathogenesis and identifies potential targets for treatment.", "claims": [{"id": "claim-method", "statement": "After categorizing genes from the GEO datasets into AA or control groups, a random-effects model incorporating an effect-size approach was used to manage batch effects and harmonize data across studies. Z-scores derived from p values were crucial for evaluating the consistency and scale of gene expression variations. The false discovery rate (FDR) was controlled via the Benjamini/Hochberg method, setting a significance threshold at FDR < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40748556", "locator": "sections[6] \"Meta-Analysis\" paragraph 2", "quote": "After categorizing genes from the GEO datasets into AA or control groups, a random-effects model incorporating an effect-size approach was used to manage batch effects and harmonize data across studies. Z-scores derived from p values were crucial for evaluating the consistency and scale of gene expression variations. The false discovery rate (FDR) was controlled via the Benjamini/Hochberg method, setting a significance threshold at FDR < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40748556", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The meta-analysis identified 5109 DEGs, with 2710 upregulated and 2399 downregulated genes, significantly more than the 120 DEGs shared across the five studies.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40748556", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The meta-analysis identified 5109 DEGs, with 2710 upregulated and 2399 downregulated genes, significantly more than the 120 DEGs shared across the five studies."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The meta-analysis identified 5109 DEGs, with 2710 upregulated and 2399 downregulated genes, significantly more than the 120 DEGs shared across the five studies.", "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:40748556"], "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:GSE45512"], "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:GSE45512"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40748556", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s13555-025-01471-6", "sha256": "sha256:1d5492b14f4fc82d033d43b41eff78aa624942282813eb60f3a068866c3dd69a", "bytes": 39346, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s13555-025-01471-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12454715", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE45512", "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=GSE45512", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45512", "version": null, "note": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1105869", "GSM1105870", "GSM1105871", "GSM1105872", "GSM1105873", "GSM1105874", "GSM1105875", "GSM1105876", "GSM1105877", "GSM1105878"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Human Alopecia Areata Skin Profiling", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE58573", "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=GSE58573", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58573", "version": null, "note": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1414312", "GSM1414313", "GSM1414314", "GSM1414315", "GSM1414316", "GSM1414317", "GSM1414318"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "First ruxolitinib treatment of human alopecia areata patients", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE68801", "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=GSE68801", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68801", "version": null, "note": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681981", "GSM1681982", "GSM1681983", "GSM1681984", "GSM1681985", "GSM1681986", "GSM1681987", "GSM1681988", "GSM1681989", "GSM1681990", "GSM1681991", "GSM1681992", "GSM1681993", "GSM1681994", "GSM1681995", "GSM1681996", "GSM1681997", "GSM1681998", "GSM1681999", "GSM1682000", "GSM1682001", "GSM1682002", "GSM1682003", "GSM1682004", "GSM1682005", "GSM1682006", "GSM1682007", "GSM1682008", "GSM1682009", "GSM1682010", "GSM1682011", "GSM1682012", "GSM1682013", "GSM1682014", "GSM1682015", "GSM1682016", "GSM1682017", "GSM1682018", "GSM1682019", "GSM1682020", "GSM1682021", "GSM1682022", "GSM1682023", "GSM1682024", "GSM1682025", "GSM1682026", "GSM1682027", "GSM1682028", "GSM1682029", "GSM1682030", "GSM1682031", "GSM1682032", "GSM1682033", "GSM1682034", "GSM1682035", "GSM1682036", "GSM1682037", "GSM1682038", "GSM1682039", "GSM1682040", "GSM1682041", "GSM1682042", "GSM1682043", "GSM1682044", "GSM1682045", "GSM1682046", "GSM1682047", "GSM1682048", "GSM1682049", "GSM1682050", "GSM1682051", "GSM1682052", "GSM1682053", "GSM1682054", "GSM1682055", "GSM1682056", "GSM1682057", "GSM1682058", "GSM1682059", "GSM1682060", "GSM1682061", "GSM1682062", "GSM1682063", "GSM1682064", "GSM1682065", "GSM1682066", "GSM1682067", "GSM1682068", "GSM1682069", "GSM1682070", "GSM1682071", "GSM1682072", "GSM1682073", "GSM1682074", "GSM1682075", "GSM1682076", "GSM1682077", "GSM1682078", "GSM1682079", "GSM1682080", "GSM1682081", "GSM1682082", "GSM1682083", "GSM1682084", "GSM1682085", "GSM1682086", "GSM1682087", "GSM1682088", "GSM1682089", "GSM1682090", "GSM1682091", "GSM1682092", "GSM1682093", "GSM1682094", "GSM1682095", "GSM1682096", "GSM1682097", "GSM1682098", "GSM1682099", "GSM1682100", "GSM1682101", "GSM1682102"], "sample_count": 122, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Human Alopecia Areata Skin Biopsy Samples", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE74761", "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=GSE74761", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE74761", "version": null, "note": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1931832", "GSM1931833", "GSM1931834", "GSM1931835", "GSM1931836", "GSM1931837", "GSM1931838", "GSM1931839", "GSM1931840", "GSM1931841", "GSM1931842"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Extensive alopecia areata is reversed by IL-23 cytokine antagonism", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE80342", "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=GSE80342", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE80342", "version": null, "note": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2124815", "GSM2124816", "GSM2124817", "GSM2124818", "GSM2124819", "GSM2124820", "GSM2124821", "GSM2124822", "GSM2124823", "GSM2124824", "GSM2124825", "GSM2124826", "GSM2124827", "GSM2124828", "GSM2124829", "GSM2124830", "GSM2124831", "GSM2124832", "GSM2124833", "GSM2124834", "GSM2124835", "GSM2124836", "GSM2124837", "GSM2124838", "GSM2124839", "GSM2124840", "GSM2124841", "GSM2124842", "GSM2124843", "GSM2124844", "GSM2124845"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Pilot open label clinical trial of oral ruxolitinib in patients with alopecia areata", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE45512 not downloaded", "asset:data:geo:GSE45512 licence not read", "asset:data:geo:GSE58573 not downloaded", "asset:data:geo:GSE58573 licence not read", "asset:data:geo:GSE68801 not downloaded", "asset:data:geo:GSE68801 licence not read", "asset:data:geo:GSE74761 not downloaded", "asset:data:geo:GSE74761 licence not read", "asset:data:geo:GSE80342 not downloaded", "asset:data:geo:GSE80342 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "meta_analysis", "specific": "random_effects", "label": "Meta-analysis / evidence synthesis", "dsl_operations": ["random_effects_pool"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["study_level_effect_estimates"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After categorizing genes from the GEO datasets into AA or control groups, a random-effects model incorporating an effect-size approach was used to manage batch effects and harmonize data across studies. Z-scores derived from p values were crucial for evaluating the consistency and scale of gene expression variations. The false discovery rate (FDR) was controlled via the Benjamini/Hochberg method, setting a significance threshold at FDR < 0.05."}}], "targets": [], "gaps": []}, "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": ["random_effects_pool"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_effects."}, "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": ["GSE68801", "GSE45512", "GSE80342", "GSE58573", "GSE74761"], "resolved_accessions": ["GSE68801", "GSE45512", "GSE80342", "GSE58573", "GSE74761"], "statements": ["The datasets analyzed during the current study are available in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository, and can be accessed through the following accession numbers: GSE68801, GSE45512, GSE80342, GSE58573, GSE74761, GSE111061. These public datasets were used under open access terms and can be freely accessed for further research. Additional data that support the findings of this study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE68801, GSE45512, GSE80342, GSE58573, GSE74761 in National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["random_effects_pool"], "assets": ["source:pmid:40748556", "data:geo:GSE45512"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE45512"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:58:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9897, "completion_tokens": 1844, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40748556", "type": "paper", "label": "pmid:40748556"}, {"id": "source:pmid:40748556", "type": "manuscript", "label": "PMID 40748556 full text"}, {"id": "data:geo:GSE45512", "type": "dataset", "label": "GEO GSE45512"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40748556", "type": "paper", "label": "pmid:40748556"}, {"id": "source:pmid:40748556", "type": "manuscript", "label": "PMID 40748556 full text"}, {"id": "data:geo:GSE45512", "type": "dataset", "label": "GEO GSE45512"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40748556", "type": "extraction", "used": ["source:pmid:40748556"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE45512", "type": "accession_resolution", "used": ["data:geo:GSE45512"], "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:40748556", "parent_hash": "sha256:2fed921adc6c2fdeaa0b49ca89bc033ff54cb343944aac610421a249e26a4f36", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE45512 licence not read", "asset:data:geo:GSE45512 not downloaded", "asset:data:geo:GSE58573 licence not read", "asset:data:geo:GSE58573 not downloaded", "asset:data:geo:GSE68801 licence not read", "asset:data:geo:GSE68801 not downloaded", "asset:data:geo:GSE74761 licence not read", "asset:data:geo:GSE74761 not downloaded", "asset:data:geo:GSE80342 licence not read", "asset:data:geo:GSE80342 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "meta_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["random_effects_pool"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["After categorizing genes from the GEO datasets into AA or control groups, a random-effects model incorporating an effect-size approach was used to manage batch effects and harmonize data across studies. Z-scores derived from p values were crucial for evaluating the consistency and scale of gene expression variations. The false discovery rate (FDR) was controlled via the Benjamini/Hochberg method, setting a significance threshold at FDR < 0.05."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T01:25:28+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}}}