Systems Biology Profiling of AMD on the Basis of Gene Expression.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24349763", "kind": "science-record", "revision": 5, "content_hash": "sha256:624676cf27212ed789a32fb3b7b53ee2f9db54431d4e3032123109d360247195", "created_at": "2026-11-01T15:40:04Z", "updated_at": "2026-11-01T21:19:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Systems Biology Profiling of AMD on the Basis of Gene Expression.", "doi": "10.1155/2013/453934", "pmid": "24349763", "authors": ["Mones S Abu-Asab", "Jose Salazar", "Jingsheng Tuo", "Chi-Chao Chan"], "journal": "Journal of ophthalmology", "year": 2013, "abstract": "Genetic pathways underlying the initiation and progression of age-related macular degeneration (AMD) have not been yet sufficiently revealed, and the correlations of AMD's genotypes, phenotypes, and disease spectrum are still awaiting resolution. We are tackling both problems with systems biology phylogenetic parsimony analysis. Gene expression data (GSE29801: NCBI, Geo) of macular and extramacular specimens of the retinas and retinal pigment epithelium (RPE) choroid complexes representing dry AMD without geographic atrophy (GA), choroidal neovascularization (CNV), GA, as well as pre-AMD and subclinical pre-AMD were polarized against their respective normal specimens and then processed through the parsimony program MIX to produce phylogenetic cladograms. Gene lists from cladograms' nodes were processed in Genomatix GePS to reveal the affected signaling pathway networks. Cladograms exposed a highly heterogeneous transcriptomic profiles within all the conventional phenotypes. Moreover, clades and nodal synapomorphies did not support the classical AMD phenotypes as valid transcriptomal genotypes. Gene lists defined by cladogram nodes showed that the AMD-related deregulations occurring in the neural retina were different from those in RPE-choroidal tissue. Our analysis suggests a more complex transcriptional profile of the phenotypes than expected. Evaluation of the disease in much earlier stages is needed to elucidate the initial events of AMD.", "claims": [{"id": "claim-data-access", "statement": "Dataset GSE29801 was downloaded from Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24349763", "locator": "sections[2] \"2. Materials and Methods\" paragraph 3", "quote": "Dataset GSE29801 was downloaded from Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used systems biology phylogenetic parsimony analysis with the MIX program to analyze gene-expression data obtained from GSE29801 at NCBI GEO, revealing heterogeneous transcriptomic profiles that did not support the classical AMD phenotypes as transcriptomal genotypes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24349763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Gene expression data (GSE29801: NCBI, Geo) of macular and extramacular specimens of the retinas and retinal pigment epithelium (RPE) choroid complexes representing dry AMD without geographic atrophy (GA), choroidal neovascularization (CNV), GA, as well as pre-AMD and subclinical pre-AMD were polarized against their respective normal specimens and then processed through the parsimony program MIX to produce phylogenetic cladograms."}, {"asset": "source:pmid:24349763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Cladograms exposed a highly heterogeneous transcriptomic profiles within all the conventional phenotypes."}, {"asset": "source:pmid:24349763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Moreover, clades and nodal synapomorphies did not support the classical AMD phenotypes as valid transcriptomal genotypes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used systems biology phylogenetic parsimony analysis with the MIX program to analyze gene-expression data obtained from GSE29801 at NCBI GEO, revealing heterogeneous transcriptomic profiles that did not support the classical AMD phenotypes as transcriptomal genotypes.", "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:24349763"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE29801"], "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:GSE29801"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24349763", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2013/453934", "sha256": "sha256:0ea42bb648d6c5724c6ba8033c65384a8efdd649d92d814321387afcbfd56590", "bytes": 23595, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2013/453934", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3851728", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29801", "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=GSE29801", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29801", "version": null, "note": "Dataset GSE29801 was downloaded from Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Dataset GSE29801 was downloaded from Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM738433", "GSM738434", "GSM738435", "GSM738436", "GSM738437", "GSM738438", "GSM738439", "GSM738440", "GSM738441", "GSM738442", "GSM738443", "GSM738444", "GSM738445", "GSM738446", "GSM738447", "GSM738448", "GSM738449", "GSM738450", "GSM738451", "GSM738452", "GSM738453", "GSM738454", "GSM738455", "GSM738456", "GSM738457", "GSM738458", "GSM738459", "GSM738460", "GSM738461", "GSM738462", "GSM738463", "GSM738464", "GSM738465", "GSM738466", "GSM738467", "GSM738468", "GSM738469", "GSM738470", "GSM738471", "GSM738472", "GSM738473", "GSM738474", "GSM738475", "GSM738476", "GSM738477", "GSM738478", "GSM738479", "GSM738480", "GSM738481", "GSM738482", "GSM738483", "GSM738484", "GSM738485", "GSM738486", "GSM738487", "GSM738488", "GSM738489", "GSM738490", "GSM738491", "GSM738492", "GSM738493", "GSM738494", "GSM738495", "GSM738496", "GSM738497", "GSM738498", "GSM738499", "GSM738500", "GSM738501", "GSM738502", "GSM738503", "GSM738504", "GSM738505", "GSM738506", "GSM738507", "GSM738508", "GSM738509", "GSM738510", "GSM738511", "GSM738512", "GSM738513", "GSM738514", "GSM738515", "GSM738516", "GSM738517", "GSM738518", "GSM738519", "GSM738520", "GSM738521", "GSM738522", "GSM738523", "GSM738524", "GSM738525", "GSM738526", "GSM738527", "GSM738528", "GSM738529", "GSM738530", "GSM738531", "GSM738532", "GSM738533", "GSM738534", "GSM738535", "GSM738536", "GSM738537", "GSM738538", "GSM738539", "GSM738540", "GSM738541", "GSM738542", "GSM738543", "GSM738544", "GSM738545", "GSM738546", "GSM738547", "GSM738548", "GSM738549", "GSM738550", "GSM738551", "GSM738552", "GSM738553", "GSM738554", "GSM738555", "GSM738556", "GSM738557", "GSM738558", "GSM738559", "GSM738560", "GSM738561", "GSM738562", "GSM738563", "GSM738564", "GSM738565", "GSM738566", "GSM738567", "GSM738568", "GSM738569", "GSM738570", "GSM738571", "GSM738572", "GSM738573", "GSM738574", "GSM738575", "GSM738576", "GSM738577", "GSM738578", "GSM738579", "GSM738580", "GSM738581", "GSM738582", "GSM738583", "GSM738584", "GSM738585", "GSM738586", "GSM738587", "GSM738588", "GSM738589", "GSM738590", "GSM738591", "GSM738592", "GSM738593", "GSM738594", "GSM738595", "GSM738596", "GSM738597", "GSM738598", "GSM738599", "GSM738600", "GSM738601", "GSM738602", "GSM738603", "GSM738604", "GSM738605", "GSM738606", "GSM738607", "GSM738608", "GSM738609", "GSM738610", "GSM738611", "GSM738612", "GSM738613", "GSM738614", "GSM738615", "GSM738616", "GSM738617", "GSM738618", "GSM738619", "GSM738620", "GSM738621", "GSM738622", "GSM738623", "GSM738624", "GSM738625", "GSM738626", "GSM738627", "GSM738628", "GSM738629", "GSM738630", "GSM738631", "GSM738632", "GSM738633", "GSM738634", "GSM738635", "GSM738636", "GSM738637", "GSM738638", "GSM738639", "GSM738640", "GSM738641", "GSM738642", "GSM738643", "GSM738644", "GSM738645", "GSM738646", "GSM738647", "GSM738648", "GSM738649", "GSM738650", "GSM738651", "GSM738652", "GSM738653", "GSM738654", "GSM738655", "GSM738656", "GSM738657", "GSM738658", "GSM738659", "GSM738660", "GSM738661", "GSM738662", "GSM738663", "GSM738664", "GSM738665", "GSM738666", "GSM738667", "GSM738668", "GSM738669", "GSM738670", "GSM738671", "GSM738672", "GSM738673", "GSM738674", "GSM738675", "GSM738676", "GSM738677", "GSM738678", "GSM738679", "GSM738680", "GSM738681", "GSM738682", "GSM738683", "GSM738684", "GSM738685", "GSM738686", "GSM738687", "GSM738688", "GSM738689", "GSM738690", "GSM738691", "GSM738692", "GSM738693", "GSM738694", "GSM738695", "GSM738696", "GSM738697", "GSM738698", "GSM738699", "GSM738700", "GSM738701", "GSM738702", "GSM738703", "GSM738704", "GSM738705", "GSM738706", "GSM738707", "GSM738708", "GSM738709", "GSM738710", "GSM738711", "GSM738712", "GSM738713", "GSM738714", "GSM738715", "GSM738716", "GSM738717", "GSM738718", "GSM738719", "GSM738720", "GSM738721", "GSM738722", "GSM738723", "GSM738724", "GSM738725"], "sample_count": 293, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Systems-level analysis of age-related macular degeneration reveals global and subtype-specific functional pathways", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:24349763:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:168dd896a308884d05d7220f78d25a5ddf2766cc7b4f84eab960f9f5c22f7073", "bytes": 1040, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#tab1", "version": null, "note": "Description of AMD phenotypic subtypes according to Newman et al. [1]. Abbreviated names in the first column are used in labeling the cladograms' legends in Figures 1 and 2.", "structure": {"pmcid": "PMC3851728", "section_index": 1, "section_title": "1. Introduction", "row_count": 12, "column_count": 3}, "table": {"label": "Table 1", "caption": "Description of AMD phenotypic subtypes according to Newman et al. [1]. Abbreviated names in the first column are used in labeling the cladograms' legends in Figures 1 and 2.", "rows": [["AMD phenotype", "Alternative name", "Description"], ["MD1", "Pre-AMD", "Hard macular drusen (<63 μm) only"], [""], ["MD2", "Subclinicalpre-AMD", "Soft, distinct macular drusen (>63 μm)Macular pigmentary irregularities without soft drusen"], [""], ["Dry AMD", "Dry AMD(non-GA)", "Soft, indistinct (>125 μm) or reticular macular drusenSoft distinct macular drusen (>63 μm) with pigmentary changes Soft indistinct macular drusen with pigmentary changes"], [""], ["GA", "Geographic atrophy", "Sharply demarcated area of apparent absence of the RPE (>175 μm) involving central macular region"], [""], ["CNV", "Wet AMD", "Subretinal choroidal neovascularization"], [""], ["GA/CNV", "", "Geographic atrophy with choroidal neovascularization"]], "row_count": 12, "column_count": 3, "numeric_cells": 4, "header_rows": 1, "locator": "section[1]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:24349763:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:314d460860ef4fc913449435495ebcf55a123fd0e79c61c6fbdf52f7c1e62e97", "bytes": 871, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#tab2", "version": null, "note": "The study collection's clinical phenotypes and the number of their specimens. Data source: GSE29801 at Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801).", "structure": {"pmcid": "PMC3851728", "section_index": 2, "section_title": "2. Materials and Methods", "row_count": 24, "column_count": 3}, "table": {"label": "Table 2", "caption": "The study collection's clinical phenotypes and the number of their specimens. Data source: GSE29801 at Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801).", "rows": [["Dx", "Retina"], ["Macular", "Extramacular"], ["Normal (n = 55)", "28", "27"], [""], ["Pre-AMD (n = 13)", "MD1 = 4", "MD1 = 4"], ["MD2 = 3", "MD2 = 2"], [""], ["AMD (n = 47)", "Dry = 15", "Dry = 16"], ["CNV = 5", "CNV = 4"], ["GA = 1", "GA = 1"], ["GA/CNV = 3", "GA/CNV = 2"], [""], ["", "RPE-choroid"], [""], ["Normal (n = 96)", "48", "48"], [""], ["Pre-AMD (n = 21)", "MD1 = 6", "MD1 = 5"], ["MD2 = 4", "MD2 = 4"], [""], ["AMD (n = 60)", "Dry = 15", "Dry = 15"], ["CNV = 5", "CNV = 5"], ["GA = 2", "GA = 2"], ["GA/CNV = 2", "GA/CNV = 2"], ["Undetermined = 6", "Undetermined = 6"]], "row_count": 24, "column_count": 3, "numeric_cells": 36, "header_rows": 2, "locator": "section[2]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:24349763:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a296da508869b83b313f59e13335f0cd40237fb57d73817aec330172ff51938e", "bytes": 1222, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tab3", "version": null, "note": "Affected retinal signaling pathways at different locations of cladogram in Figure 1. Sample identification follows http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801.", "structure": {"pmcid": "PMC3851728", "section_index": 3, "section_title": "3. Results", "row_count": 2, "column_count": 4}, "table": {"label": "Table 3", "caption": "Affected retinal signaling pathways at different locations of cladogram in Figure 1. Sample identification follows http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801.", "rows": [["First nodeShared by all retinal specimens", "RetMD1-106(Sample GSM738713)Lower part of the cladogram", "Specimen: RetDRY98(Sample GSM738705)Middle part of the cladogram", "Specimen: RetDRY70(Sample GSM738677)Upper part of the cladogram"], ["(1) Apoptosis(2) Cell cycle(3) Cytoskeleton(4) Differentiation(5) Growth(6) Insulin metabolism", "(1) Apoptosis(2) Cell cycle(3) Development(4) Growth(5) Neurotransmission(6) Transcription activation(7) Tumor suppression", "(1) Cytokine receptor degradation signaling(2) Cytosolic calcium ion concentration elevation (through IP3 receptor) (GPCR signaling (G alpha q))(3) EGFR1(4) ERK cascade GPCR signaling (G alpha s, PKA, and ERK)(5) Protein binding(6) Proteolysis", "(1) Amyloid metabolism(2) Apoptosis(3) Cell cycle(4) Cytoskeleton(5) Immunoregulation(6) Inflammation(7) Lipid metabolism(8) Retinoid metabolism(9) Ribosomal proteins(10) Telomere metabolism"]], "row_count": 2, "column_count": 4, "numeric_cells": 7, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:24349763:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:18dfff90f543722a1a1c808a0fe07e33aaafd932722d7961fc6c3704e50676d1", "bytes": 1704, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#tab4", "version": null, "note": "Affected RPE-choroidal signaling pathways at different locations of cladogram in Figure 2. Sample identification follows http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801. Updates on genes' functions can be obtained from http://www.ncbi.nlm.nih.gov/gene/.", "structure": {"pmcid": "PMC3851728", "section_index": 3, "section_title": "3. Results", "row_count": 2, "column_count": 3}, "table": {"label": "Table 4", "caption": "Affected RPE-choroidal signaling pathways at different locations of cladogram in Figure 2. Sample identification follows http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801. Updates on genes' functions can be obtained from http://www.ncbi.nlm.nih.gov/gene/.", "rows": [["Dry 135(Sample GSM738566)Lower part of the cladogram", "Dry 145(Sample GSM738575)Middle part of the cladogram", "Dry 136(Sample GSM738567)Upper part of the cladogram"], ["(1) CXCL12: activates lymphocytes(2) GDNF: promotes the survival and differentiation of dopaminergic neurons(3) MAPK1: proliferation, differentiation, transcription regulation, and development(4) PIK3CA: oncogenic(5) SFRP1: soluble modulator of Wnt signaling(6) SOD1 superoxide dismutase 1", "(1) ABL1 protooncogene implicated in cell differentiation, division, adhesion, and stress response(2) CAV1: cell cycle(3) CCL20: inflammation(4) CREB1: a transcription factor, cAMP pathway(5) CRY2: insulin metabolism(6) ERCC1: DNA repair(7) ESR1: hormone binding, DNA binding, and activation of transcription(8) IL8: inflammatory response(9) INS: insulin(10) MSN: cytoskeleton(11) MT1A: cytoskeleton, and so forth(12) PML: tumor suppressor(13) SERPINE1: inhibitor of fibrinolysis(14) TBP: assembly of transcription complex, and acts as a channel for regulatory signals(15) TMSB4X: cytoskeleton, proliferation, migration, and differentiation", "(1) CAV1: cell cycle(2) CCL5: inflammation(3) CXCL12: activates lymphocytes(4) EGF: growth, proliferation, and differentiation(5) PPARA peroxisome proliferator-activated receptor alpha"]], "row_count": 2, "column_count": 3, "numeric_cells": 6, "header_rows": 1, "locator": "section[3]/table-wrap[2]#tab4"}}], "gaps": ["asset:data:geo:GSE29801 not downloaded", "asset:data:geo:GSE29801 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Phylogenetic parsimony analysis using the MIX parsimony program", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“Dataset GSE29801 was downloaded from Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801).” “Pre-AMD and AMD gene expression values of retinal and RPE-choroidal specimens were polarized separately against their respective normal specimens (e.g., RPE-choroid data was polarized using normal RPE-choroid specimens data), and the new polarized data matrices were processed separately through MIX [12], a parsimony program of the PHYLIP package (http://evolution.genetics.washington.edu/phylip.html) to produce phylogenetic cladograms for both datasets (for details of this process see [7, 13]).”"}}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Phylogenetic parsimony analysis using the MIX parsimony program), 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": "R1", "reachable": true, "accessions": ["GSE29801"], "resolved_accessions": ["GSE29801"], "statements": ["Dataset GSE29801 was downloaded from Geo Datasets of NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801)."], "basis": "The paper names GSE29801 in Geo Datasets of NCBI and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:24349763", "data:geo:GSE29801", "asset:table:pmid:24349763:1", "asset:table:pmid:24349763:2", "asset:table:pmid:24349763:3", "asset:table:pmid:24349763:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29801"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:54Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 45944, "completion_tokens": 3052, "cached_tokens": 28168}}, "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:24349763", "type": "paper", "label": "pmid:24349763"}, {"id": "source:pmid:24349763", "type": "manuscript", "label": "PMID 24349763 full text"}, {"id": "data:geo:GSE29801", "type": "dataset", "label": "GEO GSE29801"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:24349763", "type": "paper", "label": "pmid:24349763"}, {"id": "source:pmid:24349763", "type": "manuscript", "label": "PMID 24349763 full text"}, {"id": "data:geo:GSE29801", "type": "dataset", "label": "GEO GSE29801"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-24349763", "type": "extraction", "used": ["source:pmid:24349763"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29801", "type": "accession_resolution", "used": ["data:geo:GSE29801"], "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:24349763", "parent_hash": "sha256:bf4381277950626d1ac4b4597209741258d611bcb707688091308336a4f3ff66", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE29801 licence not read", "asset:data:geo:GSE29801 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}