← All .science files
pmid:26697373
Function analysis of proteins encoded by ORFs 1 to 8 of porcine circovirus-like virus P1 by microarray assay.
Libin Wen · Fengzhi Wang · Dan Zhang · Kongwang He
Genomics data · 2015 doi:10.1016/j.gdata.2015.09.017
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
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
paper object · 10 fields
authors array · 4 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 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 · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
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 · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 60 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 7 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697373", "kind": "science-record", "revision": 6, "content_hash": "sha256:ca038aa0af0ac039e9049fed01d9d3dbc9971c3a42f89425d1fa0c99934f431c", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:20:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Function analysis of proteins encoded by ORFs 1 to 8 of porcine circovirus-like virus P1 by microarray assay.", "doi": "10.1016/j.gdata.2015.09.017", "pmid": "26697373", "authors": ["Libin Wen", "Fengzhi Wang", "Dan Zhang", "Kongwang He"], "journal": "Genomics data", "year": 2015, "abstract": "Porcine circovirus-like agent P1 is a newly discovered virus containing a single-strand circular genome. The genome of P1 is a DNA molecule of 648 nucleotides which contains eight open reading frames (ORFs) that probably encode potential proteins or polypeptides. Thus it is very important to clarify these proteins' function. Here we provide the methods and analysis of microarray data in detail to characterize the transcriptome profile of P1 with and without the ORF. The relevant microarray data sets have been deposited in Gene Expression Omnibus (GEO) database under accession number GSE71945.", "claims": [{"id": "claim-method", "statement": "In a comparison analysis, a two class unpaired method in the Significant Analysis of Microarray software (SAM, version 3.02) was applied to identify significantly differentially expressed genes between TEST and CONTROL groups. Q value was set to ﹤0.05 and transcripts were filtered on the basis of ≥ 1.2-fold difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697373", "locator": "sections[6] \"Microarray data analysis\" paragraph 2", "quote": "In a comparison analysis, a two class unpaired method in the Significant Analysis of Microarray software (SAM, version 3.02) was applied to identify significantly differentially expressed genes between TEST and CONTROL groups. Q value was set to ﹤0.05 and transcripts were filtered on the basis of ≥ 1.2-fold difference."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray CEL files, normalized data and experimental information have been deposited in NCBI's Gene Expression Omnibus database under accession number GSE71945.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697373", "locator": "sections[6] \"Microarray data analysis\" paragraph 3", "quote": "The microarray CEL files, normalized data and experimental information have been deposited in NCBI's Gene Expression Omnibus database under accession number GSE71945."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:26697373"], "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:GSE71945"], "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:GSE71945"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26697373", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.09.017", "sha256": "sha256:27c6ee1f4f88e5d7c1dc6aa868c4885502b78a459da4333566ed7f98c1b34b91", "bytes": 7504, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.09.017", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4664753", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE71945", "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=GSE71945", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71945", "version": null, "note": "The microarray CEL files, normalized data and experimental information have been deposited in NCBI's Gene Expression Omnibus database under accession number GSE71945.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray CEL files, normalized data and experimental information have been deposited in NCBI's Gene Expression Omnibus database under accession number GSE71945.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1847728", "GSM1847729", "GSM1847730", "GSM1847731", "GSM1847732", "GSM1847733", "GSM1847734", "GSM1847735", "GSM1847736", "GSM1847737", "GSM1847738", "GSM1847739", "GSM1847740", "GSM1847741", "GSM1847742", "GSM1847743", "GSM1847744", "GSM1847745", "GSM1847746", "GSM1847747", "GSM1847748", "GSM1847749", "GSM1847750", "GSM1847751", "GSM1847752", "GSM1847753", "GSM1847754", "GSM1847755", "GSM1847756", "GSM1847757", "GSM1847758", "GSM1847759", "GSM1847760", "GSM1847761", "GSM1847762", "GSM1847763", "GSM1847764", "GSM1847765", "GSM1847766", "GSM1847767", "GSM1847768", "GSM1847769", "GSM1847770", "GSM1847771", "GSM1847772", "GSM1847773", "GSM1847774", "GSM1847775", "GSM1847776", "GSM1847777", "GSM1847778", "GSM1847779", "GSM1847780", "GSM1847781", "GSM1847782", "GSM1847783", "GSM1847784", "GSM1847785", "GSM1847786", "GSM1847787"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "18699", "taxon": "Sus scrofa", "title": "Expression data from porcine kidney cell (PK15) transfected by the plasmids", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE71945 not downloaded", "asset:data:geo:GSE71945 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Significant Analysis of Microarray (SAM), version 3.02, using a two-class unpaired method; hypergeometric distribution for functional enrichment analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In a comparison analysis, a two class unpaired method in the Significant Analysis of Microarray software (SAM, version 3.02) was applied to identify significantly differentially expressed genes between TEST and CONTROL groups. Q value was set to ﹤0.05 and transcripts were filtered on the basis of ≥ 1.2-fold difference."}}], "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 (Significant Analysis of Microarray (SAM), version 3.02, using a two-class unpaired method; hypergeometric distribution for functional enrichment analysis), 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": ["GSE71945"], "resolved_accessions": ["GSE71945"], "statements": ["The microarray CEL files, normalized data and experimental information have been deposited in NCBI's Gene Expression Omnibus database under accession number GSE71945."], "basis": "The paper names GSE71945 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26697373", "data:geo:GSE71945"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE71945"]}, "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": "2026-10-31T18:26:52Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 20462, "completion_tokens": 3501, "cached_tokens": 6168}}, "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:26697373", "type": "paper", "label": "pmid:26697373"}, {"id": "source:pmid:26697373", "type": "manuscript", "label": "PMID 26697373 full text"}, {"id": "data:geo:GSE71945", "type": "dataset", "label": "GEO GSE71945"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26697373", "type": "paper", "label": "pmid:26697373"}, {"id": "source:pmid:26697373", "type": "manuscript", "label": "PMID 26697373 full text"}, {"id": "data:geo:GSE71945", "type": "dataset", "label": "GEO GSE71945"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26697373", "type": "extraction", "used": ["source:pmid:26697373"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE71945", "type": "accession_resolution", "used": ["data:geo:GSE71945"], "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:26697373", "parent_hash": "sha256:975f84371b99bca9bc41221c440b70e449fe3dfc73ba1e87972d9164d279620e", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE71945 licence not read", "asset:data:geo:GSE71945 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["to 8 of porcine circovirus-like virus P1 by microarray assay.", "Here we provide the methods and analysis of microarray data in detail to characterize the transcrip", "of P1 with and without the ORF. The relevant microarray data sets have been deposited in Gene Expres", "of the viral proteins of P1 were studied by microarray assay."], "order_basis": "paper_text_order:48", "id": "assay:1"}]}