← All .science files
pmid:40995431
ZC3H18 regulates alternative splicing and related genes in cervical cancer.
Frontiers in genetics · 2025 doi:10.3389/fgene.2025.1621238
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
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 · 1 item
[0] object · 15 fields
structure object · 1 field
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 · 1 item
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 · 2 items
[0] object · 7 fields
[1] object · 7 fields
target_providers array · 0 items
disagreements object · 4 fields
target_result object · 3 fields
physical_methods object · 3 fields
minimax array · 2 items
minimax_alt array · 2 items
analysis_methods object · 3 fields
minimax array · 8 items
minimax_alt array · 6 items
statistical_method object · 3 fields
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 · 2 items
[0] object · 4 fields
[1] 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 · 2 items
provenance object · 7 fields
entities array · 1 item
activities array · 1 item
agents array · 3 items
lineage object · 4 fields
gaps array · 13 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40995431", "kind": "science-record", "revision": 1, "content_hash": "sha256:79b03c43ba13943456ac794c7cfd6dd94b86e4e76a19ad32c8f08cf1220438b9", "created_at": "2026-11-01T10:25:53Z", "updated_at": "2026-11-01T10:25:53Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "ZC3H18 regulates alternative splicing and related genes in cervical cancer.", "doi": "10.3389/fgene.2025.1621238", "pmid": "40995431", "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:40995431"], "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:40995431", "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:40995431' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40995431", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2025.1621238", "sha256": "sha256:190e21123fbe49e0b78e626603b101a3b1ddaf6946427614ab6953fb0d48e056", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2025.1621238", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40995431 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:40995431"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40995431"]}, "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": "055fb76efdb217d5e6d795922215e953097e4b63ef4946e589f1167bc97d640a", "source_hash": "190e21123fbe49e0b78e626603b101a3b1ddaf6946427614ab6953fb0d48e056", "raw_response_sha256": "sha256:a3fec9bb805de606417dd9005e4d662e4f1bb8f77af655d16133255232062041", "raw_response_chars": 4510}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "d67c7802e92362cdfde2b1b36bed7ad055654953c003f2899f37b973f203322e", "source_hash": "190e21123fbe49e0b78e626603b101a3b1ddaf6946427614ab6953fb0d48e056", "raw_response_sha256": "sha256:d7adbac51b51fe22c7b22c4ca0e9dc0e2ef7c0206fa9b020812bae8d9ed8b31c", "raw_response_chars": 65484}], "target_providers": [], "agreement": false, "disagreements": {"target_result": {"minimax": "ZC3H18 was involved in the regulation of 1,830 alternative splicing events (ASEs).", "minimax_alt": "ZC3H18 was found to be involved in the regulation of 1,830 ASEs.", "decisive": false}, "physical_methods": {"minimax": ["In vitro ZC3H18 knockdown experiments in HeLa cells", "In vitro validation of ZC3H18-regulated alternative splicing events"], "minimax_alt": ["in vitro experiments", "knockdown of ZC3H18 in HeLa cells"], "decisive": false}, "analysis_methods": {"minimax": ["ABLas pipeline", "Fisher’s exact test", "Student’s t-test", "DESeq2", "Principal component analysis", "Gene Ontology and KEGG enrichment analysis", "Reactome pathway enrichment analysis", "Intersection of GEO- and TCGA-identified ZC3H18-regulated genes"], "minimax_alt": ["ABLas pipeline for defining and quantifying ASEs and RASEs", "RPM normalization", "sogen in-house visualization script", "GEO–TCGA result integration and intersection", "KOBAS 2.0 GO and KEGG enrichment analysis", "hypergeometric tests with Benjamini–Hochberg FDR control"], "decisive": false}, "statistical_method": {"minimax": "Fisher’s exact test", "minimax_alt": "Fisher’s exact test and Student’s t-test", "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": [{"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"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:706d9449a8a42b59867d1d572813753f12437cd6aa186fa1d733c56a66b5cc63", "type": "sep_package", "label": "SEP v1 package for pmid:40995431"}], "activities": [{"id": "activity:conversion:pmid:40995431", "type": "conversion", "used": ["package:706d9449a8a42b59867d1d572813753f12437cd6aa186fa1d733c56a66b5cc63"], "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": "5e9a47ea-e73f-4aa9-8895-90af67470ff3", "parent_hash": "706d9449a8a42b59867d1d572813753f12437cd6aa186fa1d733c56a66b5cc63", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40995431 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:40995431' does not resolve to a declared asset", "targets"]}