← All .science files
pmid:40591190
Development and validation of a prognostic model for efferocytosis-associated genes in cervical squamous cell carcinoma.
Discover oncology · 2025 doi:10.1007/s12672-025-02901-9
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 · 1 item
[0] array · 2 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 1 item
[0] array · 2 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:40591190", "kind": "science-record", "revision": 2, "content_hash": "sha256:fa223168433123872e0f2addd0de6ed2f5c3f12537adfc035b2ecff51813a84d", "created_at": "2026-11-01T10:25:51Z", "updated_at": "2026-11-01T14:01:43Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Development and validation of a prognostic model for efferocytosis-associated genes in cervical squamous cell carcinoma.", "doi": "10.1007/s12672-025-02901-9", "pmid": "40591190", "authors": null, "journal": "Discover oncology", "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:40591190"], "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:40591190", "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:40591190' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40591190", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-025-02901-9", "sha256": "sha256:09e9ebca553ac2ea5cfcb782e3965c83e6f7e0267b0c7cacd2a1dbf0c4ad79dd", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-025-02901-9", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40591190:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bf27ca8ed7e454ede58b00772ebe977616aad5697c5c8d27860ba45acc23121c", "bytes": 658, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab1", "version": null, "note": "The list of 71 efferocytosis-related genes (ERGs)", "structure": {"pmcid": "PMC12214117", "section_index": 14, "section_title": "Acquisition and enrichment analysis of PER-DEGs", "row_count": 1, "column_count": 2}, "table": {"label": "Table 1", "caption": "The list of 71 efferocytosis-related genes (ERGs)", "rows": [["ERGs", "P2RY2 PGE2 PANX1 STAB2 ADGRB1 TIM4 TYRO3 MERTK AXL ELMO1 ELMO2 ELMO3 DOCK1 DOCK2 DOCK3 DOCK4 DOCK5 RAC1 CD47 SIRPA SLC2A1 SLC16A2 SLC66A1 ADAM17 ADAM10 DNASE1 DNASE1L1 DNASE2 PPARG TIMD4 HAVCR2 ADAM9 MBTPS1 HIF1A ARNT EPO TNF TNFRSF1A LRP1 ABCA1 HMBG1 CX3CL1 CX3CR1 CXCR4 P2RY12 P2RY6 P2RX7 SLC26A6 SLC35A4 SLC46A1 SLC7A7 SLC14A1 PPARA NR1H4 SLC25A1 SLC25A10 SLC20A1 UCP2 CPT1A DNM1L SLC12A4 SLC16A1 SLC6A6 SLC4A7 WNK1 OSR1 SPAK PDK1 PDK4 ARG1 ODC1"]], "row_count": 1, "column_count": 2, "numeric_cells": 1, "header_rows": 0, "locator": "section[14]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:40591190:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7f899feacadef39cebd67be4f6e00ed7f3cb067d6c2da72576523a57ea5f7024", "bytes": 2269, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab2", "version": null, "note": "The list of 332 prognosis-efferocytosis related DEGs (PER-DEGs)", "structure": {"pmcid": "PMC12214117", "section_index": 14, "section_title": "Acquisition and enrichment analysis of PER-DEGs", "row_count": 1, "column_count": 2}, "table": {"label": "Table 2", "caption": "The list of 332 prognosis-efferocytosis related DEGs (PER-DEGs)", "rows": [["PER-DEGs", "SLC2A1 NDRG1 NDUFA4L2 SLC6A8 VEGFA BNIP3 CSTB IGFBP3 ALDOA FAM83A GJB2 ANGPTL4 MXD1 SERPINB1 BNIP3L TGFB1 PYGL ADM GJB6 SFN KRT17 POLR2L UPP1 RHCG ITGA5 PERP RPL35 PLAUR MT1X CDKN1A FSCN1 ENO1 HSP90AB1 MKNK2 RPS2 PTMA NDUFB2 RPS26 ATP1B1 BZW1 HK2 RPLP2 HMGB1 IL1RN HSP90AA1 S100A10 HMGN2 TPM4 CDCP1 NME1 MRPS12 TMPRSS4 EIF5A SERINC2 SERPINB5 DLG1 GPI TMEM158 PGAM1 RPS27A DSC2 MRPL12 NET1 ERH S100A2 TIMM8B AHNAK2 SRM RPL22 DNAJB6 SLC16A1 ZFP36 IRF6 RPL32 FOSL1 ITGB1 CYCS HSPD1 PSMB2 FAU RPS15 TMEM91 RPS12 RPL8 LINC00520 TXNIP EZR HNRNPA2B1 CD55 SNRPF RPS29 PPIA RPLP1 TMEM45A TGM1 RPS25 TMEM160 SLIRP CYB5R1 LSM7 SEC61G RPL38 RPS17 SERPINB13 AK4 COX6B1 PDK1 COX6C TOMM40 MIR210HG MRPS21 ARNTL2 RPSA SNRPE ISOC2 MRPL52 DHRS3 ASB2 SYNJ2 FERMT1 NDUFS6 SLCO4A1 LIMA1 MRPS34 TRMT112 RPL27 ADAM8 CCT5 RPL14 ISG15 MAP3K13 SRP14 SKIL RPL13 GJB3 NAMPT NCL DCXR PHLDB2 ZNF385A RPS5 LSM4 DSG3 SOD2 CD68 RPS18 EIF3K APRT TUBA1B MRPL4 PIM1 HNRNPA3 PPP4R1 ACAP2 NDUFS8 UQCR11 CEBPB SNRPD1 EEF1B2 HNRNPA1 SRSF7 MRPL3 COA4 RPL12 SET TIMM13 GADD45GIP1 EGLN1 ADAM9 CNN3 DSC3 POLR2F CHCHD2 ZNF593 CCT3 KRT16 CEACAM5 PSMB3 NDUFB7 EHD2 S100A9 NAA38 PPP1CB C1QBP UQCRH EHD4 STMN1 B3GNT8 IL36G RAI14 RIOK3 TGFA CYC1 SERTAD1 CTHRC1 SSBP1 ARL8B ANKLE2 CDKN3 SOWAHC MRPS15 NHP2 EIF4EBP1 KRT6B FNDC3B TPD52 IQGAP1 NDUFB10 CAV2 PTTG1 SDF2L1 CDH1 EHF RPL21 COX5B CAV1 MRPL55 HCAR3 DENND2C TRIB1 ITPA MRPL20 RPS10 YBX1 KCMF1 MRPL36 COX8A CDH3 ANXA5 AREG RBMX SRSF3 HBEGF DNPH1 PPARD TMEM30B NPC1 DDX39A CENPF CKS1B CDC20 FBL PRDX6 ARHGAP5 SYNE2 CKS2 RALA GNA15 MDK UQCRQ VCL MAD1L1 WDR83OS SERPINB2 NAA10 EID1 ELL2 ISCU AKR1B10 GPR68 DUSP7 SULT2B1 CA2 EIF3G NDUFA2 AKR1C3 SRSF2 LYPD3 KRT6A FOS HCAR2 PYCARD EXOC3 JTB TP63 ZFP36L1 P3H2 CFD DAPK3 PDLIM5 MARK3 TMPO EEF1D SPRR1B ANP32B CP UBE2S HSPG2 PSMB4 CALM3 ITGAV TOP2A PPP1R13L SNRNP70 NUSAP1 EGR1 KLF3 CHCHD10 NUCKS1 NASP ID3 PCNA CCT4 BGN RPL9 DDX5 S100A4 CLEC2B SLC20A1 CTSL LURAP1L PRELID1 ITPKC GABRP CALM2 HMGB2 SRGAP3 IVL LGALS7 HOPX ITGAE THBD TSC22D3 ARL6IP1 KRT1 KRT6C ARL6IP5 HSPA6 CNFN APOBEC3G ID2 MT2A"]], "row_count": 1, "column_count": 2, "numeric_cells": 1, "header_rows": 0, "locator": "section[14]/table-wrap[2]#Tab2"}}], "gaps": ["asset:source:pmid:40591190 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:40591190", "asset:table:pmid:40591190:1", "asset:table:pmid:40591190:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40591190"]}, "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:b627d88414a547664e9f90a54572fd03ab189f63bceed4725d65502b2c5330e1", "type": "sep_package", "label": "SEP v1 package for pmid:40591190"}], "activities": [{"id": "activity:conversion:pmid:40591190", "type": "conversion", "used": ["package:b627d88414a547664e9f90a54572fd03ab189f63bceed4725d65502b2c5330e1"], "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:40591190", "parent_hash": "sha256:55990a8e714293d0113b3c82a8318bf7a9feb7d7bd9682ab2ebf91f599385d70", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40591190 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:40591190' does not resolve to a declared asset", "targets"]}