Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:31384647

Transcriptomic data during seed maturation in dormant and non-dormant genotypes of wheat (Triticum aestivum L.).

Yuji Yamasaki · Mark C Jordan · Belay T Ayele

Data in brief · 2019 doi:10.1016/j.dib.2019.104254

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

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
id
pmid:31384647
kind
science-record
content_hash
sha256:994914ea138914d25bf85dacc7c18c05bc268dc4edd8bc09dbf1d0d159dd238b
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:48Z
updated_at
2026-11-01T22:44:07Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Transcriptomic data during seed maturation in dormant and non-dormant genotypes of wheat (Triticum aestivum L.).
doi
10.1016/j.dib.2019.104254
pmid
31384647
authors array · 3 items
[0]
Yuji Yamasaki
[1]
Mark C Jordan
[2]
Belay T Ayele
journal
Data in brief
year
2019
abstract
The present data profiles a large scale transcriptome changes in seed tissues (embryo and endosperm) during maturation in dormant and non-dormant genotypes of hexaploid wheat. Seed dormancy is an adaptive trait that has a significant influence on the incidence of preharvest sprouting, which is referred to as the germination of grains on the spike prior to harvest, in wheat. Given that preharvest sprouting causes a substantial yield and quality losses, elucidation of the molecular features that regulate seed dormancy has a paramount significance in the development of preharvest sprouting resistant wheat cultivars. The data presented here was produced from total RNA/mRNA samples isolated from developing seeds of dormant and non-dormant wheat genotypes using the Affymetrix GeneChip Wheat Genome Array. The raw and normalized formats of these data are available in Gene Expression Ominbus (GEO), NCBI's gene expression data repository, with accession number GSE83077.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31384647
locator
sections[8] "Data analysis" paragraph 2
quote
The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31384647
locator
sections[1] "table-wrap" paragraph 1
quote
Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
steps array · 3 items
[0] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:31384647
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE83077
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE83077
outputs array · 1 item
[0]
the replicated result and its comparison
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
state
partial
assets array · 3 items
[0] object · 15 fields
id
source:pmid:31384647
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2019.104254
sha256
sha256:e2ce47f09e60410f134104c877e51adb0be4cc4b9166d07b02ccdc5017a008e0
bytes
10501
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2019.104254
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC6661463
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE83077
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=GSE83077
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE83077
version
null
note
Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077
access_statement_kind
data_availability_statement
sample_accessions array · 34 items
[0]
GSM2192573
[1]
GSM2192574
[2]
GSM2192575
[3]
GSM2192576
[4]
GSM2192577
[5]
GSM2192578
[6]
GSM2192579
[7]
GSM2192580
[8]
GSM2192581
[9]
GSM2192582
[10]
GSM2192583
[11]
GSM2192584
[12]
GSM2192585
[13]
GSM2192586
[14]
GSM2192587
[15]
GSM2192588
[16]
GSM2192589
[17]
GSM2192590
[18]
GSM2192591
[19]
GSM2192592
[20]
GSM2192593
[21]
GSM2192594
[22]
GSM2192595
[23]
GSM2192596
[24]
GSM2192597
[25]
GSM2192598
[26]
GSM2192599
[27]
GSM2192600
[28]
GSM2192601
[29]
GSM2192602
[30]
GSM2192603
[31]
GSM2192604
[32]
GSM2192605
[33]
GSM2192606
sample_count
34
group_sizes
null
group_sizes_basis
null
platform
3802
taxon
Triticum aestivum
title
Tissue specific expression data from maturing wheat seeds (20-50 DAA) of two genotypes
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:31384647:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:c89ea73149329cc019babc33be6a5d03ec3e25b0895a1a7b1a215712ac54ac41
bytes
520
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[3]/table-wrap[1]#tbl1
version
null
note
Reproducibility of transcriptomic data from the independent replicates of 20 DAA embryo samples derived from AC Domain genotype.
structure object · 5 fields
pmcid
PMC6661463
section_index
3
section_title
Data
row_count
7
column_count
4
table object · 8 fields
label
Table 1
caption
Reproducibility of transcriptomic data from the independent replicates of 20 DAA embryo samples derived from AC Domain genotype.
rows array · 7 items
[0] array · 4 items
[0]
Genotype
[1]
Embryo
[2]
Replicates
[3]
R2 value
[1] array · 4 items
[0]
AC Domain
[1]
20 DAAa
[2]
Repb #1 vs. Rep #2
[3]
0.99
[2] array · 2 items
[0]
Rep #1 vs. Rep #3
[1]
0.99
[3] array · 2 items
[0]
Rep #1 vs. Rep #4
[1]
0.96
[4] array · 2 items
[0]
Rep #2 vs. Rep #3
[1]
0.97
[5] array · 2 items
[0]
Rep #2 vs. Rep #4
[1]
0.97
[6] array · 2 items
[0]
Rep #3 vs. Rep #4
[1]
0.97
locator
section[3]/table-wrap[1]#tbl1
gaps array · 2 items
[0]
asset:data:geo:GSE83077 not downloaded
[1]
asset:data:geo:GSE83077 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed.
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova.
capability object · 4 fields
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 object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE83077
resolved_accessions array · 1 item
[0]
GSE83077
statements array · 1 item
[0]
Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077
basis
The paper names GSE83077 in Gene Expression Ominbus (GEO), NCBI's gene expression data repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 3 items
[0]
source:pmid:31384647
[1]
data:geo:GSE83077
[2]
asset:table:pmid:31384647:1
steps array · 1 item
[0]
run_analysis
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
[0]
data:geo:GSE83077
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:15:40Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
9169
completion_tokens
1119
cached_tokens
784
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:31384647
type
paper
label
pmid:31384647
[1] object · 3 fields
id
source:pmid:31384647
type
manuscript
label
PMID 31384647 full text
[2] object · 3 fields
id
data:geo:GSE83077
type
dataset
label
GEO GSE83077
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:31384647
type
paper
label
pmid:31384647
[1] object · 3 fields
id
source:pmid:31384647
type
manuscript
label
PMID 31384647 full text
[2] object · 3 fields
id
data:geo:GSE83077
type
dataset
label
GEO GSE83077
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-31384647
type
extraction
used array · 1 item
[0]
source:pmid:31384647
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE83077
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE83077
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
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 object · 4 fields
parent_id
pmid:31384647
parent_hash
sha256:798cfda40cd4a783dd53751c0441b04a2da711d5c1eb098214e4c3a609d0dbe0
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:GSE83077 licence not read
[1]
asset:data:geo:GSE83077 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
nt and non-dormant wheat genotypes using the Affymetrix GeneChip Wheat Genome Array. The raw and nor
[1]
ding to the manufacturer's instructions. The microarray experimental procedures of the endosperm tis
[2]
spermic carbohydrate or starch interference. Microarray experimental procedure The total RNA or mRNA
[3]
Kit and the GeneChip Sample Cleanup Module (Affymetrix). Assessment of the quality of the labelled
order_basis
paper_text_order:838
id
assay:1
[1] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed.
order_basis
consumes_earlier_output
id
assay:2
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31384647", "kind": "science-record", "revision": 8, "content_hash": "sha256:994914ea138914d25bf85dacc7c18c05bc268dc4edd8bc09dbf1d0d159dd238b", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:44:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic data during seed maturation in dormant and non-dormant genotypes of wheat (Triticum aestivum L.).", "doi": "10.1016/j.dib.2019.104254", "pmid": "31384647", "authors": ["Yuji Yamasaki", "Mark C Jordan", "Belay T Ayele"], "journal": "Data in brief", "year": 2019, "abstract": "The present data profiles a large scale transcriptome changes in seed tissues (embryo and endosperm) during maturation in dormant and non-dormant genotypes of hexaploid wheat. Seed dormancy is an adaptive trait that has a significant influence on the incidence of preharvest sprouting, which is referred to as the germination of grains on the spike prior to harvest, in wheat. Given that preharvest sprouting causes a substantial yield and quality losses, elucidation of the molecular features that regulate seed dormancy has a paramount significance in the development of preharvest sprouting resistant wheat cultivars. The data presented here was produced from total RNA/mRNA samples isolated from developing seeds of dormant and non-dormant wheat genotypes using the Affymetrix GeneChip Wheat Genome Array. The raw and normalized formats of these data are available in Gene Expression Ominbus (GEO), NCBI's gene expression data repository, with accession number GSE83077.", "claims": [{"id": "claim-method", "statement": "The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31384647", "locator": "sections[8] \"Data analysis\" paragraph 2", "quote": "The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31384647", "locator": "sections[1] \"table-wrap\" paragraph 1", "quote": "Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31384647"], "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:GSE83077"], "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:GSE83077"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31384647", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2019.104254", "sha256": "sha256:e2ce47f09e60410f134104c877e51adb0be4cc4b9166d07b02ccdc5017a008e0", "bytes": 10501, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2019.104254", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6661463", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE83077", "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=GSE83077", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE83077", "version": null, "note": "Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2192573", "GSM2192574", "GSM2192575", "GSM2192576", "GSM2192577", "GSM2192578", "GSM2192579", "GSM2192580", "GSM2192581", "GSM2192582", "GSM2192583", "GSM2192584", "GSM2192585", "GSM2192586", "GSM2192587", "GSM2192588", "GSM2192589", "GSM2192590", "GSM2192591", "GSM2192592", "GSM2192593", "GSM2192594", "GSM2192595", "GSM2192596", "GSM2192597", "GSM2192598", "GSM2192599", "GSM2192600", "GSM2192601", "GSM2192602", "GSM2192603", "GSM2192604", "GSM2192605", "GSM2192606"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "3802", "taxon": "Triticum aestivum", "title": "Tissue specific expression data from maturing wheat seeds (20-50 DAA) of two genotypes", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31384647:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c89ea73149329cc019babc33be6a5d03ec3e25b0895a1a7b1a215712ac54ac41", "bytes": 520, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl1", "version": null, "note": "Reproducibility of transcriptomic data from the independent replicates of 20 DAA embryo samples derived from AC Domain genotype.", "structure": {"pmcid": "PMC6661463", "section_index": 3, "section_title": "Data", "row_count": 7, "column_count": 4}, "table": {"label": "Table 1", "caption": "Reproducibility of transcriptomic data from the independent replicates of 20 DAA embryo samples derived from AC Domain genotype.", "rows": [["Genotype", "Embryo", "Replicates", "R2 value"], ["AC Domain", "20 DAAa", "Repb #1 vs. Rep #2", "0.99"], ["Rep #1 vs. Rep #3", "0.99"], ["Rep #1 vs. Rep #4", "0.96"], ["Rep #2 vs. Rep #3", "0.97"], ["Rep #2 vs. Rep #4", "0.97"], ["Rep #3 vs. Rep #4", "0.97"]], "row_count": 7, "column_count": 4, "numeric_cells": 13, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl1"}}], "gaps": ["asset:data:geo:GSE83077 not downloaded", "asset:data:geo:GSE83077 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed."}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE83077"], "resolved_accessions": ["GSE83077"], "statements": ["Raw and normalized data are available in Gene Expression Ominbus (GEO) database of NCBI with accession number GSE83077"], "basis": "The paper names GSE83077 in Gene Expression Ominbus (GEO), NCBI's gene expression data repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:31384647", "data:geo:GSE83077", "asset:table:pmid:31384647:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE83077"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:40Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 9169, "completion_tokens": 1119, "cached_tokens": 784}}, "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:31384647", "type": "paper", "label": "pmid:31384647"}, {"id": "source:pmid:31384647", "type": "manuscript", "label": "PMID 31384647 full text"}, {"id": "data:geo:GSE83077", "type": "dataset", "label": "GEO GSE83077"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31384647", "type": "paper", "label": "pmid:31384647"}, {"id": "source:pmid:31384647", "type": "manuscript", "label": "PMID 31384647 full text"}, {"id": "data:geo:GSE83077", "type": "dataset", "label": "GEO GSE83077"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31384647", "type": "extraction", "used": ["source:pmid:31384647"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE83077", "type": "accession_resolution", "used": ["data:geo:GSE83077"], "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:31384647", "parent_hash": "sha256:798cfda40cd4a783dd53751c0441b04a2da711d5c1eb098214e4c3a609d0dbe0", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE83077 licence not read", "asset:data:geo:GSE83077 not downloaded", "execution.not_run", "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": ["nt and non-dormant wheat genotypes using the Affymetrix GeneChip Wheat Genome Array. The raw and nor", "ding to the manufacturer's instructions. The microarray experimental procedures of the endosperm tis", "spermic carbohydrate or starch interference. Microarray experimental procedure The total RNA or mRNA", "Kit and the GeneChip Sample Cleanup Module (Affymetrix). Assessment of the quality of the labelled"], "order_basis": "paper_text_order:838", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The probesets that are differentially expressed between dormant and non-dormant seed tissues were identified using FlexArray software [7] by analysis of variance, and probesets with two or more fold changes at probability level of 0.05 or less were considered differentially expressed."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}