{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31911466", "kind": "science-record", "revision": 4, "content_hash": "sha256:4c3477611d73a2aeffb0537332fcbf2374734c415ab51a82f94dab84209ad962", "created_at": "2026-11-01T15:40:54Z", "updated_at": "2026-11-01T21:22:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment.", "doi": "10.1128/mSystems.00795-19", "pmid": "31911466", "authors": ["Zhichao Zhou", "Yang Liu", "Wei Xu", "Jie Pan", "Zhu-Hua Luo", "Meng Li"], "journal": "mSystems", "year": 2020, "abstract": "Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.", "claims": [{"id": "claim-method", "statement": "The P value and odds ratios were calculated by Fisher’s exact test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31911466", "locator": "sections[10] \"Clade-distinctive LGT.\" paragraph 4", "quote": "The P value and odds ratios were calculated by Fisher’s exact test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31911466", "locator": "sections[21] \"Data availability.\" paragraphs 1-3", "quote": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31911466"], "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:PRJNA385762"], "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:PRJNA385762"], "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:31911466", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1128/mSystems.00795-19", "sha256": "sha256:3e178ceb5cca6c7aa6106c15cb8a9031e10dc8e3d482a9dccb66b74efc5118e1", "bytes": 75340, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1128/mSystems.00795-19", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6946796", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJNA385762", "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=PRJNA385762", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA385762", "version": null, "note": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.", "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": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA480137", "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=PRJNA480137", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA480137", "version": null, "note": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.", "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": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRR7786998", "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=SRR7786998", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRR7786998", "version": null, "note": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.", "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": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31911466:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fcbeab0f28ba19cfef40467aff285c2d7d304abb326ff071e1b7079da2660455", "bytes": 1510, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tab1", "version": null, "note": "Overview of genomic statistics for archaeal MAGs constructed in the current study and reference and NCBI SRA depositsa", "structure": {"pmcid": "PMC6946796", "section_index": 3, "section_title": "Hydrothermarchaeota is a novel archaeal phylum.", "row_count": 19, "column_count": 8}, "table": {"label": "TABLE 1", "caption": "Overview of genomic statistics for archaeal MAGs constructed in the current study and reference and NCBI SRA depositsa", "rows": [["Characteristic", "Value for the following Hydrothermarchaeota MAG:"], ["SZUA-158 (TVG10)", "SZUA-236 (TVG13)", "SZUA-237 (TVG13)", "JdFR-16", "JdFR-17", "JdFR-18", "HyVt-292"], ["No. of copies of individual markers", "", "", "", "", "", "", ""], ["0", "9", "21", "49", "99", "87", "2", "30"], ["1", "139", "128", "136", "25", "59", "145", "141"], ["2", "1", "0", "3", "25", "29", "2", "17"], ["3", "0", "0", "0", "0", "12", "0", "0"], ["4", "0", "0", "0", "0", "1", "0", "0"], ["5+", "0", "0", "0", "0", "0", "0", "0"], ["Completeness (%)", "92.53", "84.97", "65.82", "31.93", "53.87", "98.13", "80.43"], ["Contamination (%)", "0.93", "0.00", "1.76", "13.55", "25.15", "1.87", "9.06"], ["Strain heterogeneity (%)", "0.00", "0.00", "33.33", "84.00", "71.83", "0.00", "35.29"], ["Bin size (bp)", "1,749,358", "1,270,198", "1,228,833", "1,353,114", "2,178,134", "2,062,134", "1,426,722"], ["N50 (bp)", "9,590", "6,219", "3,825", "6,267", "7,687", "149,032", "5,600"], ["Mean scaffold length (bp)", "7,706.42", "5,747.50", "3,510.95", "5,614.58", "6,331.78", "93,733.36", "4,988.54"], ["No. of scaffolds", "227", "221", "350", "241", "344", "22", "286"], ["GC (%)", "38.99", "47.58", "45.76", "49.68", "49.64", "39.14", "40.02"], ["GC SD (%)", "1.91", "1.99", "2.89", "3.92", "4.50", "1.54", "1.98"], ["Coding density (%)", "84.96", "91.48", "84.96", "91.98", "91.94", "92.12", "89.88"]], "row_count": 19, "column_count": 8, "numeric_cells": 126, "header_rows": 2, "locator": "section[3]/table-wrap[1]#tab1"}}], "gaps": ["asset:data:geo:PRJNA385762 not downloaded", "asset:data:geo:PRJNA385762 licence not read", "asset:data:geo:PRJNA480137 not downloaded", "asset:data:geo:PRJNA480137 licence not read", "asset:data:geo:SRR7786998 not downloaded", "asset:data:geo:SRR7786998 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Fisher’s exact test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The P value and odds ratios were calculated by Fisher’s exact test."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Fisher’s exact test), 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": ["PRJNA385762", "PRJNA480137", "SRR7786998"], "resolved_accessions": [], "statements": ["Accession numbers for the initial assemblies were as follows: IMG accession number 3300003886 for TVG10 and IMG accession number 3300003885 for TVG13. Accession numbers for the second-round assemblies were as follows: IMG accession number 3300020233 for TVG10 and IMG accession number 3300020236 for TVG13. The MAGs that were resolved in the current study are deposited in NCBI under BioProject accession numbers PRJNA385762 and PRJNA480137. Detailed genomic parameters of the assembled genomes are summarized in Text S1. The NCBI and IMG genome accession numbers for the MAGs that were used in this study are NCBI accession number GCA_003230355.1 for SZUA-236, NCBI accession number GCA_003229275.1 for SZUA-237, NCBI accession number GCA_003229935.1 for SZUA-158, NCBI accession number SRR7786998 for HyVt-292, IMG accession number 2728369317 for JdFR-16, IMG accession number 2728369322 for JdFR-17, and IMG accession number 2728369320 for JdFR-18.\nDATA SET S1Metabolic profile of seven Hydrothermarchaeota MAGs. Download Data Set S1, XLSX file, 0.8 MB.Copyright © 2020 Zhou et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license."], "basis": "The paper names PRJNA385762, PRJNA480137, SRR7786998, but the accession does not resolve in the repository (not_in_ncbi_bioproject, not_in_ncbi_bioproject, 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:31911466", "data:geo:PRJNA385762", "asset:table:pmid:31911466:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PRJNA385762"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 58069, "completion_tokens": 4462, "cached_tokens": 19592}}, "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:31911466", "type": "paper", "label": "pmid:31911466"}, {"id": "source:pmid:31911466", "type": "manuscript", "label": "PMID 31911466 full text"}, {"id": "data:geo:PRJNA385762", "type": "dataset", "label": "GEO PRJNA385762"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31911466", "type": "paper", "label": "pmid:31911466"}, {"id": "source:pmid:31911466", "type": "manuscript", "label": "PMID 31911466 full text"}, {"id": "data:geo:PRJNA385762", "type": "dataset", "label": "GEO PRJNA385762"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31911466", "type": "extraction", "used": ["source:pmid:31911466"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PRJNA385762", "type": "accession_resolution", "used": ["data:geo:PRJNA385762"], "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:31911466", "parent_hash": "sha256:ced6000dcc70c8a6573fcd65cfaa06e719c42b5ecb813ae0b7546768f944b651", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PRJNA385762 licence not read", "asset:data:geo:PRJNA385762 not downloaded", "asset:data:geo:PRJNA480137 licence not read", "asset:data:geo:PRJNA480137 not downloaded", "asset:data:geo:SRR7786998 licence not read", "asset:data:geo:SRR7786998 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"]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:52:12+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}}}