{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35178872", "kind": "science-record", "revision": 4, "content_hash": "sha256:86b684e37125c9ab36e36315cef851890c17a8d117dacf219b63acdd283e811d", "created_at": "2026-11-01T17:36:56Z", "updated_at": "2026-11-01T21:27:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.", "doi": "10.1111/1755-0998.13597", "pmid": "35178872", "authors": ["Fleur Gawehns", "Maarten Postuma", "Morgane van Antro", "Adam Nunn", "Bernice Sepers", "Samar Fatma", "Thomas P van Gurp", "Niels C A M Wagemaker", "A Christa Mateman", "Slavica Milanovic-Ivanovic", "Ivo Groβe", "Kees van Oers", "Philippine Vergeer", "Koen J F Verhoeven"], "journal": "Molecular ecology resources", "year": 2022, "abstract": "Several reduced-representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without a reference genome. epiGBS2 is cost- and time-efficient and the computational workflow is designed in a user-friendly and reproducible manner. The library protocol allows a flexible choice of restriction enzymes and a double digest. The bioinformatics pipeline was integrated in the Snakemake workflow management system, which makes the pipeline easy to execute and modular, and parameter settings for important computational steps flexible. We implemented bismark for alignment and methylation analysis and we preprocessed alignment files by double masking to enable single nucleotide polymorphism calling with Freebayes (epiFreebayes). The performance of several critical steps in epiGBS2 was evaluated against baseline data sets from Arabidopsis thaliana and great tit (Parus major), which confirmed its overall good performance. We provide a detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo-knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.4764652).", "claims": [{"id": "claim-method", "statement": "The performance of the epiGBS2 data was evaluated with correlation plots that were created in R (version 4.0.1) (R Core Team, 2021), using ggplot2 version 3.3.3 (Wickham, 2016). The coefficient of determination (R 2) was calculated using the ggpmisc package version 0.3.9 (Aphalo, 2021).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35178872", "locator": "sections[20] \"Parus major samples and description of benchmarking data\" paragraph 4", "quote": "The performance of the epiGBS2 data was evaluated with correlation plots that were created in R (version 4.0.1) (R Core Team, 2021), using ggplot2 version 3.3.3 (Wickham, 2016). The coefficient of determination (R 2) was calculated using the ggpmisc package version 0.3.9 (Aphalo, 2021)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35178872", "locator": "sections[41] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking."}], "state": "complete"}, {"id": "claim-target-result", "statement": "For all individuals, the epiGBS2 methylation calls correlated with the RRBS‐derived methylation calls (R 2 ≥ .76) (Figure 9).", "kind": "quantitative", "target": {"value": 2.0, "unit": "correlation coefficient", "tolerance": null, "source": "For all individuals, the epiGBS2 methylation calls correlated with the RRBS‐derived methylation calls (R 2 ≥ .76) (Figure 9)."}, "evidence": [{"asset": "source:pmid:35178872", "locator": "sections[30] \"Performance epiGBS vs. RRBS\" paragraph 2", "quote": "For all individuals, the epiGBS2 methylation calls correlated with the RRBS‐derived methylation calls (R 2 ≥ .76) (Figure 9)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "For all individuals, the epiGBS2 methylation calls correlated with the RRBS‐derived methylation calls (R 2 ≥ .76) (Figure 9).", "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:35178872"], "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_unresolved", "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:PRJNA208335"], "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:PRJNA208335"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35178872", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/1755-0998.13597", "sha256": "sha256:e9e5b036aef269b95336450a025fb19fd4bf87668ee9e7b675e719131c23cdd1", "bytes": 62984, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/1755-0998.13597", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9311447", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJNA208335", "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=PRJNA208335", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA208335", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:52Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA764918", "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=PRJNA764918", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA764918", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:52Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10989860", "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=SRX10989860", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10989860", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10989861", "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=SRX10989861", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10989861", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10989862", "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=SRX10989862", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10989862", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10989863", "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=SRX10989863", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10989863", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10994457", "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=SRX10994457", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10994457", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10994458", "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=SRX10994458", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10994458", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10994459", "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=SRX10994459", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10994459", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX10994460", "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=SRX10994460", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX10994460", "version": null, "note": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:45Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PRJNA208335 not downloaded", "asset:data:geo:PRJNA208335 licence not read", "asset:data:geo:PRJNA764918 not downloaded", "asset:data:geo:PRJNA764918 licence not read", "asset:data:geo:SRX10989860 not downloaded", "asset:data:geo:SRX10989860 licence not read", "asset:data:geo:SRX10989861 not downloaded", "asset:data:geo:SRX10989861 licence not read", "asset:data:geo:SRX10989862 not downloaded", "asset:data:geo:SRX10989862 licence not read", "asset:data:geo:SRX10989863 not downloaded", "asset:data:geo:SRX10989863 licence not read", "asset:data:geo:SRX10994457 not downloaded", "asset:data:geo:SRX10994457 licence not read", "asset:data:geo:SRX10994458 not downloaded", "asset:data:geo:SRX10994458 licence not read", "asset:data:geo:SRX10994459 not downloaded", "asset:data:geo:SRX10994459 licence not read", "asset:data:geo:SRX10994460 not downloaded", "asset:data:geo:SRX10994460 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Correlation analysis using the coefficient of determination (R 2)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The performance of the epiGBS2 data was evaluated with correlation plots that were created in R (version 4.0.1) (R Core Team, 2021), using ggplot2 version 3.3.3 (Wickham, 2016). The coefficient of determination (R 2) was calculated using the ggpmisc package version 0.3.9 (Aphalo, 2021)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 2.0, "unit": "correlation coefficient", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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 (Correlation analysis using the coefficient of determination (R 2)), 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": ["PRJNA764918", "PRJNA208335", "SRX10989860", "SRX10989861", "SRX10989862", "SRX10989863", "SRX10994457", "SRX10994458", "SRX10994459", "SRX10994460"], "resolved_accessions": [], "statements": ["The demultiplexed A. thaliana epiGBS data were deposited on NCBI with BioProject ID PRJNA764918 and raw data files are accessible on Zenodo (https://doi.org/10.5281/zenodo.5519370). Great tit data can be accessed on NCBI with BioProject ID PRJNA208335. The RRBS reads are available under the SRA accessions SRX10989860, SRX10989861, SRX10989862 and SRX10989863, and the epiGBS2 reads are available under the SRA accessions SRX10994457, SRX10994458, SRX10994459 and SRX10994460. The epiGBS2 laboratory protocol can be found in the Supporting Information. The bioinformatics pipeline and documentation can be accessed on github (https://github.com/nioo‐knaw/epiGBS2) and was deposited on Zenodo (https://doi.org/10.5281/zenodo.4764652). An example data set can also be accessed on Zenodo (https://zenodo.org/record/5878925). All scripts used for benchmarking are available at https://github.com/MaartenPostuma/epiGBS‐Benchmarking."], "basis": "The paper names PRJNA764918, PRJNA208335, SRX10989860, SRX10989861, SRX10989862, SRX10989863, SRX10994457, SRX10994458, SRX10994459, SRX10994460, but the accession does not resolve in the repository (not_in_ncbi_bioproject, not_in_ncbi_bioproject, not_in_ncbi_sra, not_in_ncbi_sra, not_in_ncbi_sra, not_in_ncbi_sra, not_in_ncbi_sra, not_in_ncbi_sra, not_in_ncbi_sra, not_in_ncbi_sra), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35178872", "data:geo:PRJNA208335"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PRJNA208335"]}, "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": "2026-11-01T17:34:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16710, "completion_tokens": 3879, "cached_tokens": 128}}, "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:35178872", "type": "paper", "label": "pmid:35178872"}, {"id": "source:pmid:35178872", "type": "manuscript", "label": "PMID 35178872 full text"}, {"id": "data:geo:PRJNA208335", "type": "dataset", "label": "GEO PRJNA208335"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35178872", "type": "paper", "label": "pmid:35178872"}, {"id": "source:pmid:35178872", "type": "manuscript", "label": "PMID 35178872 full text"}, {"id": "data:geo:PRJNA208335", "type": "dataset", "label": "GEO PRJNA208335"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35178872", "type": "extraction", "used": ["source:pmid:35178872"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PRJNA208335", "type": "accession_resolution", "used": ["data:geo:PRJNA208335"], "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:35178872", "parent_hash": "sha256:b98f59caac095ea61348d6b855231d77f26966a9e84fbdb1ac7e8264dfacefe7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PRJNA208335 licence not read", "asset:data:geo:PRJNA208335 not downloaded", "asset:data:geo:PRJNA764918 licence not read", "asset:data:geo:PRJNA764918 not downloaded", "asset:data:geo:SRX10989860 licence not read", "asset:data:geo:SRX10989860 not downloaded", "asset:data:geo:SRX10989861 licence not read", "asset:data:geo:SRX10989861 not downloaded", "asset:data:geo:SRX10989862 licence not read", "asset:data:geo:SRX10989862 not downloaded", "asset:data:geo:SRX10989863 licence not read", "asset:data:geo:SRX10989863 not downloaded", "asset:data:geo:SRX10994457 licence not read", "asset:data:geo:SRX10994457 not downloaded", "asset:data:geo:SRX10994458 licence not read", "asset:data:geo:SRX10994458 not downloaded", "asset:data:geo:SRX10994459 licence not read", "asset:data:geo:SRX10994459 not downloaded", "asset:data:geo:SRX10994460 licence not read", "asset:data:geo:SRX10994460 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "assays": [{"role": "data_generation", "definition_id": "methylation_array", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["iplexed, epiGBS-based reduced representation bisulfite sequencing.", "Several reduced-representation bisulfite sequencing methods have been developed in re", "rary were compared to reduced representation bisulfite sequencing (RRBS) data (Meissner et al., 200", "version 0.11.1 (Wingett & Andrews, 2018) in bisulfite mode was used to detect possible contaminati"], "order_basis": "paper_text_order:51", "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":"2026-11-04T01:45:49+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}}}