← All .science files
pmid:40552012
Bioinformatics analysis identifies ZBTB16 as a potential immune biomarker for lung cancer and pan-cancer.
Frontiers in genetics · 2025 doi:10.3389/fgene.2025.1541732
Paper
partial
Experiment
partial
Data
partial
Analysis
absent
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
generator object · 3 fields
paper object · 10 fields
claims array · 1 item
gaps array · 2 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 3 items
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 1 field
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 3 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 17 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
gaps array · 1 item
capability object · 3 fields
readiness object · 8 fields
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 7 fields
providers array · 0 items
target_providers array · 0 items
disagreements array · 0 items
agreement_basis object · 2 fields
decisive_fields array · 4 items
human_critique object · 5 fields
stages array · 7 items
[0] object · 4 fields
[1] object · 4 fields
evidence object · 1 field
provider_errors array · 4 items
[0] object · 4 fields
[1] object · 4 fields
[2] object · 4 fields
[3] object · 4 fields
[2] object · 4 fields
[3] object · 4 fields
[4] object · 4 fields
[5] object · 4 fields
[6] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 1 item
activities array · 1 item
agents array · 1 item
lineage object · 4 fields
gaps array · 14 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40552012", "kind": "science-record", "revision": 2, "content_hash": "sha256:b2255c95a55bdd526fa57e7b3b94e637e9c3897288a3d6263293fb23b17e0afe", "created_at": "2026-11-01T10:25:51Z", "updated_at": "2026-11-01T14:01:42Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Bioinformatics analysis identifies ZBTB16 as a potential immune biomarker for lung cancer and pan-cancer.", "doi": "10.3389/fgene.2025.1541732", "pmid": "40552012", "authors": null, "journal": "Frontiers in genetics", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "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:40552012"], "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:40552012", "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:40552012' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40552012", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2025.1541732", "sha256": "sha256:52384cff3fdb7ffe125de420f9462ba30fd66433ab5b95fb405777e8e169fcd4", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2025.1541732", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40552012:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f94d8c6206f4d85548bbb55ff86c3811fb6940ef7e2c01064528b90bc9f0ab39", "bytes": 946, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T1", "version": null, "note": "A total of 116 differentially expressed genes (DEGs).", "structure": {"pmcid": "PMC12183232", "section_index": 16, "section_title": "Identification of DEGs", "row_count": 3, "column_count": 2}, "table": {"label": "TABLE 1", "caption": "A total of 116 differentially expressed genes (DEGs).", "rows": [["DEGs", "Gene"], ["upregulated", "COL11A1 MMP12 SPP1 DSP SULF1 S100A2 KIAA0101 HIST1H2BD COL10A1 LAD1 ZWINT CDC20 PPAP2C THBS2 PAICS TOP2A"], ["downregulated", "FABP4 WIF1 CLDN5 AGER C7 FHL1 ZBTB16 MFAP4 DES CLIC5 ADIRF VWF GPX3 TNNC1 ADH1B AGTR1 TCF21 CHRDL1 ABCA8 LDB2 CDH5 FCN1 AQP1 RAMP2 PTPRB EDNRB CA4 GPM6A AQP4 LPL FCN3 ACKR1 AOC3 GPM6B DLC1 CFD CAV1 SRPX FAM107A GNG11 CD93 NR4A3 ANXA3 FXYD1 KIAA1462 EMP2 FBLN5 ADAMTSL3 FEZ1 ENG ID4 SVEP1 LDLR SMAD6 WISP2 COX7A1 SLC6A4 SPOCK2 NEDD9 ADRB2 C14orf132 TGFBR2 MYH10 TIE1 LRRC32 FOXF1 SLIT2 SPARCL1 PECAM1 DPYSL2 FBLN1 LMO2 SGCE LTBP4 ALOX5AP KAL1 FAM189A2 CAV2 THBD EFEMP1 VSIG4 MMP19 TMEM47 CALCRL RAMP3 HBEGF RASSF2 KLF4 HEG1 WFS1 PROS1 GMFG PPP1R15A CA2 FRY TACC1 MACF1 PMP22 FERMT2 ICAM2"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:40552012:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:939f0ead8fbf6c19f5685da1338238e0c22b738909b46b75d074c126cfee2543", "bytes": 938, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#T2", "version": null, "note": "Relationship between ZBTB16 expression and clinicopathological features in lung cancer patients.", "structure": {"pmcid": "PMC12183232", "section_index": 20, "section_title": "Validation of TCGA and HPA databases", "row_count": 17, "column_count": 4}, "table": {"label": "TABLE 2", "caption": "Relationship between ZBTB16 expression and clinicopathological features in lung cancer patients.", "rows": [["Variables", "Low expression of ZBTB16", "High expression of ZBTB16", "P"], ["n", "520", "521", ""], ["Pathologic T stage, n (%)", "", "", "<0.001"], ["T1", "114 (11%)", "176 (17%)", ""], ["T2", "310 (29.9%)", "276 (26.6%)", ""], ["T3&T4", "95 (9.2%)", "67 (6.5%)", ""], ["Pathologic N stage, n (%)", "", "", "0.066"], ["N0", "321 (31.5%)", "349 (34.2%)", ""], ["N1", "129 (12.7%)", "99 (9.7%)", ""], ["N2&N3", "64 (6.3%)", "57 (5.6%)", ""], ["Age, n (%)", "", "", "0.398"], ["≤65", "234 (23.1%)", "214 (21.1%)", ""], [">65", "280 (27.6%)", "285 (28.1%)", ""], ["Pathologic stage, n (%)", "", "", "0.003"], ["Stage I", "244 (23.7%)", "297 (28.9%)", ""], ["Stage II", "163 (15.8%)", "124 (12.1%)", ""], ["Stage III&Stage IV", "107 (10.4%)", "94 (9.1%)", ""]], "row_count": 17, "column_count": 4, "numeric_cells": 32, "header_rows": 1, "locator": "section[20]/table-wrap[1]#T2"}}], "gaps": ["asset:source:pmid:40552012 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:40552012", "asset:table:pmid:40552012:1", "asset:table:pmid:40552012:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40552012"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "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": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"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", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:bbbc14508f11cb6b6c391a9146ea63c3298e2356d349bd4162c4d88285b2ac56", "type": "sep_package", "label": "SEP v1 package for pmid:40552012"}], "activities": [{"id": "activity:conversion:pmid:40552012", "type": "conversion", "used": ["package:bbbc14508f11cb6b6c391a9146ea63c3298e2356d349bd4162c4d88285b2ac56"], "agent": "agent:corpus-assay-engine"}], "agents": [{"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:40552012", "parent_hash": "sha256:14156cc0ac1ff47df14c29920cdd4f8b210a084546ecea66aefa35bacd804208", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40552012 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "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:40552012' does not resolve to a declared asset", "targets"]}