{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39949372", "kind": "science-record", "revision": 2, "content_hash": "sha256:fe539930c366f7b675fb74bd513e180e4478dd0c5cad0b66f55aa06557771f03", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T14:01:34Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Identification of Novel lncRNAs Related to Colorectal Cancer Through Bioinformatics Analysis.", "doi": "10.1155/bmri/5538575", "pmid": "39949372", "authors": null, "journal": "BioMed research international", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 6763.0, "unit": "degs", "tolerance": null, "source": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58"}, "evidence": [{"asset": "source:pmid:39949372", "locator": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "quote": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA)."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39949372"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:39949372", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39949372' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39949372", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/bmri/5538575", "sha256": "sha256:b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/bmri/5538575", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39949372:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:be24a4a45033001db971243d7f5485d8aa7324c6b425a92c30acea33e47fc695", "bytes": 3521, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#tab1", "version": null, "note": "Top upregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "structure": {"pmcid": "PMC11824705", "section_index": 4, "section_title": "2.2. Preprocessing and Analysis of Raw Dataset", "row_count": 23, "column_count": 8}, "table": {"label": "Table 1", "caption": "Top upregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "rows": [["Gene symbol", "lncRNA ID", "Ensemble gene ID", "Official name", "Log (FC)", "p value", "Adjusted p value", "Function in CRC"], ["lncRNA p3467", "ENST00000561864.1", "ENSG00000261650.1", "RP11-474D1.4 (LINC02418)", "4.480166", "2.85e − 06", "0.001741", "High expression of lncRNA p3467 promoted cancer progression in colon cancer cells [21, 22]"], ["lncRNA p15938", "ENST00000500112.1", "ENSG00000247844.1", "RP11-255B23.3", "4.028627", "5.46e − 07", "0.00082", "—"], ["lncRNA p30155", "XR_108886.3", "LOC100507056", "IDLOC100507056", "3.962785", "9.27e − 07", "0.001041", "—"], ["lncRNA p15421", "ENST00000419422.1", "ENSG00000232445.1", "RP11-132A1.4 (LNCPRESS1)", "3.776749", "4.71e − 06", "0.002226", "RP11-132A1.4 is upregulated in tissue from colon cancer [23]"], ["lncRNA p39026_v4", "ENST00000437781.1", "ENSG00000206195.6", "AP000525.9", "3.665108", "1.30e − 05", "0.003626", "High expression in CRC [24]"], ["lncRNA p15430", "ENST00000602761.1", "ENSG00000228742.5", "RP5-884M6.1", "3.471953", "1.41e − 05", "0.003794", "High expression in colon adenocarcinoma [24, 25]"], ["lncRNA p34144_v4", "ENST00000447298.1", "ENSG00000130600.10", "H19-014", "3.388798", "2.04e − 05", "0.004494", "—"], ["LOC340340", "Uncharacterized LOC340340", "—", "—", "3.239423", "8.20e − 05", "0.010084", "—"], ["lncRNA p29027", "ENST00000414790.1", "ENSG00000130600.10", "H19-001", "3.230258", "1.37e − 05", "0.003769", "—"], ["lncRNA p34360_v4", "ENST00000427798.1", "ENSG00000225210.5", "AL589743.1 (DUXAP9/LINC01296)", "3.207409", "4.19e − 05", "0.007123", "LINC01296 knockdown inhibited colon cancer cell proliferation, migration, and invasion in vivo [26]"], ["lncRNA p17009", "ENST00000456532.1", "ENSG00000231566.1", "RP5-1158E12.3", "3.193662", "7.45e − 07", "0.000929", "High expression of LINC02595 promoted tumor progression in CRC [24]"], ["lncRNA p30261", "uc004dgk.1", "AK098783", "", "3.089308", "1.29e − 06", "0.001291", "LncRNA-AK098783 expression level was frequently higher in CRC and RT-PCR [27]"], ["lncRNA p24045", "TCONS_00015168", "XLOC_007214", "linc-FAM84B-8", "3.084878", "1.22e − 06", "0.001291", "—"], ["lncRNA p23831", "TCONS_00014191", "XLOC_006200", "linc-PIK3CG-1", "3.08157", "0.000903", "0.029689", "—"], ["lncRNA p21811", "TCONS_00029614", "XLOC_014268", "linc-PPARA-1", "3.058199", "3.71e − 07", "0.00072", "—"], ["lncRNA p9376", "ENST00000424322.1", "ENSG00000227400.2", "AC012501.2", "3.050053", "0.001343", "0.035616", "—"], ["lncRNA p16370", "ENST00000521586.1", "ENSG00000253929.1", "RP11382A18.2", "2.990761", "2.45e − 05", "0.004912", "Colon cancer risk SNPs [28]"], ["lncRNA p21975", "TCONS_00006729", "XLOC_003364", "linc-BCL6-5", "2.926155", "0.000445", "0.0216", "—"], ["lncRNA p2786", "ENST00000544553.1", "ENSG00000256940.1", "RP11783K16.5 (PPP1R14B-AS1)", "2.904332", "2.08e − 05", "0.004494", "High expression in CRC [24]"], ["lncRNA p35380_v4", "ENST00000521989.2", "ENSG00000253414.2", "RP11150O12.6", "2.900774", "0.000235", "0.01617", "Upregulated in CRC cells [29, 30]"], ["lncRNA p956", "ENST00000432653.1", "ENSG00000234578.1", "RP4-784A16.1", "2.865494", "7.09e − 07", "0.000918", "—"], ["lncRNA p10603", "ENST00000445003.1", "ENSG00000224397.1", "RP11-290F20.3", "2.788621", "0.000184", "0.014888", "High expression of LINC01272, promoted EMT, and metastasis by regulating miR-876/ITGB2 [31]"]], "row_count": 23, "column_count": 8, "numeric_cells": 162, "header_rows": 1, "locator": "section[4]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:39949372:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0ff729c4aaf9457d5c63ef969402365a354b631c0549e11f098d2d3bcbd82ed6", "bytes": 3231, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#tab2", "version": null, "note": "Detail of top downregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "structure": {"pmcid": "PMC11824705", "section_index": 4, "section_title": "2.2. Preprocessing and Analysis of Raw Dataset", "row_count": 22, "column_count": 8}, "table": {"label": "Table 2", "caption": "Detail of top downregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "rows": [["Gene symbol", "lncRNA ID", "Ensemble gene ID", "Official name", "Log (FC)", "p value", "Adjusted p value", "Function in CRC"], ["lncRNA p33911", "uc.217+", "uc.217+", "uc.217+", "−4.93989", "7.23e − 06", "0.002648", "Decreased in CRC tissue [24]"], ["lncRNA p33840", "uc022axe.1", "FW340046", "auc022axe.1", "−3.893", "0.000264", "0.017247", "Decreased in CRC tissue [24]"], ["lncRNA p4715", "ENST00000497872.2", "ENSG00000253701.1", "AL928768.3", "−3.8548", "0.000469", "0.02198", "Decreased in CRC tissue [32]"], ["lncRNA p12653", "ENST00000506514.1", "ENSG00000249453.1", "RP13-497K6.1", "−3.58082", "5.85e − 05", "0.0087", "Decreased in CRC tissue [24]"], ["lncRNA p16717", "ENST00000422420.1", "ENSG00000240498.2", "CDKN2B-AS1", "−3.52951", "0.000343", "0.019", "Decreased in CRC. CDKN2B-AS induced cell apoptosis and suppressed EMT. CDKN2B-AS1 regulates cell growth and survival by targeting DUSP1 [33]"], ["lncRNA p28599", "ASO1844", "ASO1844", "Accession=AK097806", "−3.49506", "1.67e − 05", "0.004132", "—"], ["lncRNA p22463", "TCONS_00008010", "XLOC_003474", "linc-SOD3-2", "−3.45933", "9.77e − 05", "0.011", "—"], ["lncRNA p20354", "TCONS_00025506", "XLOC_012317", "linc-TNRC6C-3", "−3.37675", "0.000218", "0.015", "—"], ["lncRNA p20353", "TCONS_00025200", "XLOC_012317", "linc-TNRC6C-3", "−3.31869", "0.00018", "0.014", "—"], ["lncRNA p27381", "uc.70-", "uc.70-", "uc.70-", "−3.29996", "2.42e − 05", "0.0041", "—"], ["lncRNA p10205", "ENST00000416200.1", "ENSG00000225953.2", "SATB2-AS1", "−3.26443", "1.23e − 05", "0.003", "Decreased in CRC tissue, suppressed CRC aggressiveness by inhibiting SATB2-dependent snail transcription and EMT [34]"], ["lncRNA p25200", "NR_026542.1", "C21orf88", "C21 orf88(B3GALT5-AS1)", "−3.17449", "0.000467", "0.021", "Decreased in CRC tissue, the suppressive role of B3GALT5-AS1/miR-203/EMT regulation axis was in colon cancer liver metastasis [35, 36]"], ["lncRNA p16220", "ENST00000526382.1", "ENSG00000255130.1", "RP11-396J6.1-001", "−3.12744", "1.03e − 05", "0.003", "—"], ["lncRNA p20355", "TCONS_00025507", "XLOC_012317", "linc-TNRC6C-3", "−3.08187", "0.000289", "0.017", "—"], ["lncRNA p25346", "NR_024418.1", "LOC389332", "LOC389332", "−3.06741", "8.12e − 05", "0.01", "Decreased in CRC tissue. LOC389332 exhibited longer overall survival time than patients with low expression levels of these genes [37]"], ["lncRNA p11319", "ENST00000425296.1", "ENSG00000224822.1", "THRB-IT1", "−2.98159", "2.08e − 05", "0.0044", "—"], ["lncRNA p12499", "ENST00000508106.1", "ENSG00000234828.3", "RP11-526A4.1", "−2.81665", "0.000444", "0.02", "—"], ["lncRNA RNA143457|tRNA_374_71", "RNA143457|tRNA_374_71", "", "", "−2.8047", "7.57e − 05", "0.0097", "—"], ["lncRNA p21571", "TCONS_00028228", "XLOC_013571", "linc-PFDN4-2", "−2.65782", "0.000291", "0.0179", "—"], ["lncRNA p7182", "ENST00000577761.1", "ENSG00000266878.1", "RP11-1090M7.2", "−2.46434", "0.000319", "0.0183", "—"], ["lncRNA p42656_v4", "NR_104064.1", "None", "", "−2.43954", "0.00049", "0.0224", "—"]], "row_count": 22, "column_count": 8, "numeric_cells": 148, "header_rows": 1, "locator": "section[4]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:39949372:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:deb0d99142d657872a793bb285178b2eec1861ecb17862fddd755ece48311b74", "bytes": 1482, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#tab3", "version": null, "note": "Top DEmRNA in CRC based on analyses of the GSE134834 dataset. FC: fold change, DEmRNA: differentially expressed mRNA, CRC: colorectal cancer.", "structure": {"pmcid": "PMC11824705", "section_index": 9, "section_title": "3.1. Identification of DEG", "row_count": 11, "column_count": 6}, "table": {"label": "Table 3", "caption": "Top DEmRNA in CRC based on analyses of the GSE134834 dataset. FC: fold change, DEmRNA: differentially expressed mRNA, CRC: colorectal cancer.", "rows": [["Gene symbol", "Log FC", "p value", "Adjusted p value", "Expression and function in CRC in literature", "References"], ["MMP7", "6.941794", "7.06e − 10", "2.38e − 05", "Upregulated: Potential prognostic marker in CRC", "[41, 42]"], ["REG1A", "6.181124", "0.000264", "0.017247", "Upregulated: Potential prognostic marker in CRC", "[43, 44]"], ["THBS2", "6.164384", "3.78e − 09", "4.66e − 05", "Upregulated: Potential prognostic marker in CRC", "[45]"], ["CST2", "5.719364", "3.17e − 07", "0.000667", "Upregulated: Potential prognostic marker in CRC", "[46]"], ["CST1", "5.669326", "1.20e − 07", "0.000367", "Upregulated in CRC tissues", "[47–49]"], ["FOXQ1", "5.266674", "3.85e − 07", "0.00072", "Upregulated: Potential prognostic biomarker", "[50–52]"], ["CA1", "−6.90487", "0.000302", "0.018054", "Downregulated: Patients with lower CA1 expression levels had a worse prognosis", "[53]"], ["GCG", "−6.34476", "1.13e − 05", "0.003345", "Downregulated: Had a major role in suppressing the development of CRC", "[52, 54]"], ["SST", "−5.74713", "2.93e − 07", "0.000659", "Downregulated in CRC: Promising prognostic biomarkers", "[52, 55]"], ["CD177", "−5.57313", "0.00013", "0.012561", "Downregulated in CRC tissue", "[56, 57]"]], "row_count": 11, "column_count": 6, "numeric_cells": 41, "header_rows": 1, "locator": "section[9]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:39949372:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5baeedcda5a35573601e4099ac12c17d06332f1af8c0fa1ed5b6ae42b7932156", "bytes": 2282, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tab4", "version": null, "note": "Lightpink4 and pink modules enrichment results of analysis of GSE134834 microarray for CRC.", "structure": {"pmcid": "PMC11824705", "section_index": 11, "section_title": "3.3. Module Pathway Enrichment", "row_count": 29, "column_count": 4}, "table": {"label": "Table 4", "caption": "Lightpink4 and pink modules enrichment results of analysis of GSE134834 microarray for CRC.", "rows": [["Lightpink4 module gene ontology", "Pink module gene ontology"], ["Biological pathway", "p value", "Biological pathway", "p value"], ["Cell cycle, mitotic", "1.51e − 33", "β1 integrin cell surface interactions", "7.32e − 05"], ["DNA replication", "5.9e − 28", "Endothelin", "0.000101"], ["Mitotic M-M/G1 phases", "6.92e − 25", "Signaling events mediated by VEGFR1 and VEGFR2", "0.000148"], ["Cell cycle checkpoints", "1.01e − 18", "LKB1 signaling events", "0.000157"], ["S phase", "2.63e − 17", "Glypican 1 network", "0.000166"], ["Mitotic G1-G1/S phases", "6.9e − 17", "ErbB receptor signaling network", "0.000176"], ["Molecular function", "p value", "Molecular function", "p value"], ["Protein binding", "1.68e − 05", "Transmembrane receptor protein tyrosine kinase activity", "0.000171"], ["DNA binding", "7.16e − 05", "Ligase activity", "0.003422"], ["DNA-directed RNA polymerase activity", "8.2e − 05", "Catalytic activity", "0.010486"], ["Chaperone activity", "0.000109", "Transferase activity", "0.010898"], ["RNA binding", "0.000333", "Ligand-dependent nuclear receptor activity", "0.01265"], ["Complement activity", "0.001271", "Acyltransferase activity", "0.013939"], ["Cellular component", "p value", "Cellular component", "p value"], ["Nucleolus", "6.77e − 36", "Extracellular matrix", "5.92e − 06"], ["Centrosome", "4e − 22", "Membrane fraction", "0.001116"], ["Nucleoplasm", "3.55e − 19", "Nucleoplasm", "0.00122"], ["Nucleus", "2.99e − 16", "Cytosol", "0.001908"], ["Cytoplasm", "1.03e − 11", "Soluble fraction", "0.001939"], ["Kinetochore", "3.88e − 10", "Exosomes", "0.002625"], ["Biological process", "p value", "Biological process", "p value"], ["Regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolism", "6.24e − 05", "Energy pathways", "0.000194"], ["Regulation of cell cycle", "0.000108", "Metabolism", "0.000205"], ["Protein metabolism", "0.000325", "DNA repair", "0.003073"], ["Cell proliferation", "0.000533", "Electron transport", "0.006762"], ["DNA replication", "0.002767", "Meiosis", "0.015513"], ["Peptide metabolism", "0.0068", "Cell proliferation", "0.022418"]], "row_count": 29, "column_count": 4, "numeric_cells": 50, "header_rows": 1, "locator": "section[11]/table-wrap[1]#tab4"}}, {"id": "asset:table:pmid:39949372:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:baddf27d0409a27e1f81da38301002d0f64da36a268731c65714c3567feae35e", "bytes": 1176, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab5", "version": null, "note": "Top dysregulated lncRNA coexpression modules and module hub genes in the analysis of GSE134834 microarray related to CRC.", "structure": {"pmcid": "PMC11824705", "section_index": 12, "section_title": "3.4. PPI Network and Hub Genes", "row_count": 4, "column_count": 5}, "table": {"label": "Table 5", "caption": "Top dysregulated lncRNA coexpression modules and module hub genes in the analysis of GSE134834 microarray related to CRC.", "rows": [["Modules", "DElnc", "PPI networks", "Hub genes"], ["Upregulated lncRNAs", "Downregulated lncRNAs"], ["Lightpink4", "p3467, p15938, p30155, p15421, p39026_v4, p34144_v4, p29027, p34360_v4, p17009, p30261, p24045, p21811, p9376, p16370, p21975, p2786, p10603, p44527_v4, p28920, LOC100653147, p2227, p18281, p10499, p14903, p21076, p21710, and p30340", "17436, p42655_v4, p26713, p40499_v4, p42344_v4, p4428, p4443, p33911, RNA143457|tRNA_374_71, p42656_v4, p42366_v4, and p2983", "805 nodes and 4651 edges", "MRTO4, CDK1, CDC20, RPF2, NOP58, NIFK, GTPBP4, BUB1, BUB1B, and BOP1"], ["Pink", "p15430, p35380_v4, p956, p16534, p23831, and LOC340340", "p33840, p4715, p12653, p16717, p28599, p22463, p20354, p20353, p27381, p10205, p25200, p16220, p20355, p25346, p11319, p12499, p21571, p7182, p9438, p12621, and p12806", "713 nodes and 1656 edges", "BYSL, RPS23, RSL1D1, NAT10, NOP14, GNL2, MRPS12, NOL6, IMP4, and RRP12"]], "row_count": 4, "column_count": 5, "numeric_cells": 8, "header_rows": 2, "locator": "section[12]/table-wrap[1]#tab5"}}], "gaps": ["asset:source:pmid:39949372 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39949372", "asset:table:pmid:39949372:1", "asset:table:pmid:39949372:2", "asset:table:pmid:39949372:3", "asset:table:pmid:39949372:4", "asset:table:pmid:39949372:5"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39949372"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "f7cb0f9c793d0e45986a8dffff8be116d10abdb2ca5aa56cc00748fe7f287892", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response_sha256": "sha256:cb0e58d6b7f85d272dc74dcacffbc9f022a660290626cc334186c342b637f375", "raw_response_chars": 4016}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "60c0c6a1df828c7cd92d3c2641e79f6f7220323cc6d18f721159c216ee83967d", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response_sha256": "sha256:a0dac3cfc6dbe71959b66764df082aa56f0be1bd597eb508a1cc7aa85023ecb3", "raw_response_chars": 39684}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "f73ee1730f11704919577aae37c48bdd44eacdf5160ea5a84d43a4729e59e5df", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response": "{\"parent_value\":6763,\"unit\":\"DEGs\",\"evidence\":\"Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\",\"target_result\":\"The paper reports 6763 differentially expressed genes in colorectal cancer samples compared with normal samples.\",\"number_stated\":true}", "reading": {"parent_value": 6763, "unit": "DEGs", "evidence": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).", "target_result": "The paper reports 6763 differentially expressed genes in colorectal cancer samples compared with normal samples.", "number_stated": true, "source_locator": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58"}, "recorded_at": "2026-10-31T15:24:15.366041+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "d50ddacde4f8afde9f9c86ed98f4276cd37a7c455d731f60faa9795e49180a89", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response": "<think>We need answer JSON only. Need parse task carefully. Need identify \"single numerical result that a replication of the registered target has to reproduce. Report headline number only: the value the paper itself states for the registered target, not calculated... unit paper prints. Exact contiguous quotation containing number; attribution by wording etc. Registered target: headline numerical result paper states for main finding.\"\n\nWe need infer which number is headline main finding from source. Source abstract: Analysis revealed 6763 DEGs (p &lt;0.05 and |log FC| ≥0.5), two modules for lncRNAs obtained. Which is headline numerical result? Main finding likely \"6763 DEGs\". Registered target described generically, asks single numerical result replication has reproduce. We need output 6763, unit perhaps \"DEGs\" (paper prints number followed \"DEGs\"). Evidence exact contiguous quote entire clause: \"Analysis revealed 6763 DEGs (p &lt; 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\" Is headline number 6763 DEGs likely. Could be \"two modules for lncRNAs\" but headline numerical result main finding likely 6763 DEGs. Need unit string paper prints. \"DEGs\". parent_value number 6763. target_result likely \"6763 DEGs\" maybe concise. number_stated true.\n\nBut let's deeply inspect wording and potential traps. User says \"single numerical result that a replication of the registered target has to reproduce\" and target is \"the headline numerical result the paper itself states for its main finding\". The abstract's key quantitative result: 6763 DEGs. There are many thresholds and software versions. The central result likely count of DEGs. Quote exact contiguous. Unit could be \"DEGs\". Ensure no unit calculated. Evidence must exact quote. Exact source has \"Analysis revealed 6763 DEGs (p &lt; 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\" We can quote that. JSON escaping fine. target_result perhaps \"6763 DEGs\". Need perhaps \"The analysis revealed 6763 differentially expressed genes.\" But report headline number only might mean target_result should simply \"6763 DEGs\". Parent value and unit separate. The evidence whole clause.\n\nCould \"two modules for lncRNAs\" be main finding? Main abstract says \"and finally, two modules for lncRNAs were obtained.\" Yet the study title novel lncRNAs; likely headline numerical result may be \"6763 DEGs\". The wording \"headline numerical result\" likely benchmark asks identify parent quantity. We need choose.\n\nLet's parse all numerics:\n- 6763 DEGs (main analysis result)\n- p cutoff etc\n- two modules\n- 10 hub genes each\n- R version, tool versions, confidence score\nNo count of novel lncRNAs explicitly in provided excerpt.\n\"single numerical result that a replication of registered target has to reproduce.\" \"REGISTERED TARGET: the headline numerical result the paper itself states for its main finding\". This is not a specific named target, so likely abstract's first result. Maybe they expect 6763 DEGs as headline number. Unit \"DEGs\" exact printed.\n\nCould target_result be explanatory string. Required always. We can say \"6763 DEGs\". Evidence exact clause. Need output strict JSON no markdown. Ensure Unicode ≥ allowed. Exact quotation must be exact, contiguous. Let's verify punctuation from source:\n\"Analysis revealed 6763 DEGs (p &lt; 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA). Novel lncRNAs were identified, and to better understand the biological function of the identified lncRNAs, gene modules were constructed using weighted gene coexpression network analysis (WGCNA), and finally, two modules for lncRNAs were obtained.\"\n\nCould quote only sentence 1. It contains number and attribution. Fine.\n\nUnit might be \"DEGs\" exactly. Parent value 6763. number_stated true. target_result perhaps \"6763 DEGs\" (headline number only). Let's formulate.</think>\n\n{\"parent_value\":6763,\"unit\":\"DEGs\",\"evidence\":\"Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\",\"target_result\":\"6763 DEGs\",\"number_stated\":true}", "reading": {"parent_value": 6763, "unit": "DEGs", "evidence": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).", "target_result": "6763 DEGs", "number_stated": true, "source_locator": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58"}, "recorded_at": "2026-10-31T15:24:18.091661+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "6763 differentially expressed genes (DEGs), including differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA), were identified in colorectal cancer samples compared with normal samples.", "minimax_alt": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).", "decisive": false}, "analysis_methods": {"minimax": ["limma", "quantile normalization", "differential expression analysis", "weighted gene coexpression network analysis (WGCNA)"], "minimax_alt": ["limma package in Bioconductor with R 4.3.3 for gene-expression preprocessing", "quantile normalization", "DEG screening using p-value and absolute log-fold-change criteria", "weighted gene coexpression network analysis (WGCNA)", "FunRich GO and KEGG enrichment analysis", "STRING protein-protein interaction network analysis", "Cytoscape and CytoHubba degree-based hub-gene selection", "GEPIA expression validation using TCGA and GTEx data"], "decisive": false}, "statistical_method": {"minimax": "limma", "minimax_alt": "limma (Bioconductor/R), followed by DEG screening using p-value and absolute log-fold-change criteria after quantile normalization", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:d3d8f57f44a452f1ff2fe398ca41485b479b0a179e4ec3db0e1a3a18a1ce4f04", "type": "sep_package", "label": "SEP v1 package for pmid:39949372"}], "activities": [{"id": "activity:conversion:pmid:39949372", "type": "conversion", "used": ["package:d3d8f57f44a452f1ff2fe398ca41485b479b0a179e4ec3db0e1a3a18a1ce4f04"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39949372", "parent_hash": "sha256:4c85323cf4b17502acf951aeecf7468825d268c488dd56d5795ebb11b6927a8a", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39949372 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39949372' does not resolve to a declared asset", "targets"]},"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":"2026-11-04T01:32:28+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}