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

pmid:26981390

Genome wide expression after different doses of irradiation of a three-dimensional (3D) model of oral mucosal.

Maria P Lambros · Michael K DeSalvo · Hari Chandana Mulamalla · Jonathan Moreno · Lavanya Kondapalli

Genomics data · 2016 doi:10.1016/j.gdata.2015.12.013

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
id
pmid:26981390
kind
science-record
content_hash
sha256:af8e55791cf9e844668fce546f569613b13b233ab2bdf6465ff0822d7d1cc683
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:17Z
updated_at
2026-11-01T21:20:28Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Genome wide expression after different doses of irradiation of a three-dimensional (3D) model of oral mucosal.
doi
10.1016/j.gdata.2015.12.013
pmid
26981390
authors array · 5 items
[0]
Maria P Lambros
[1]
Michael K DeSalvo
[2]
Hari Chandana Mulamalla
[3]
Jonathan Moreno
[4]
Lavanya Kondapalli
journal
Genomics data
year
2016
abstract
We evaluated a three-dimensional (3D) human oral cell culture that consisted of two types of cells, oral keratinocytes and fibroblasts as a model of oral mucositis which is a debilitating adverse effect of chemotherapy and radiation treatment. The 3D cell culture model was irradiated with 12 or 2 Gy, and total RNA was collected 6 h after irradiation to compare global gene expression profiles via microarray analysis. Here we provide detailed methods and analysis on these microarray data, which have been deposited in Gene Expression Omnibus (GEO): GSE62395.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26981390
locator
sections[6] "Microarray data pre-processing and statistical analysis" paragraph 3
quote
Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26981390
locator
sections[2] "Direct link to deposited data" paragraph 2
quote
The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The paper used Rosetta Resolver error-model-based hypothesis tests, which account for fold change and expression level, and directs readers to the source microarray data at GEO accession GSE62395.
kind
qualitative
target
null
evidence array · 3 items
[0] object · 3 fields
asset
source:pmid:26981390
locator
sections[0] "Abstract" paragraph 1
quote
Here we provide detailed methods and analysis on these microarray data, which have been deposited in Gene Expression Omnibus (GEO): GSE62395.
[1] object · 3 fields
asset
source:pmid:26981390
locator
sections[6] "Microarray data pre-processing and statistical analysis" paragraph 3
quote
Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level.
[2] object · 3 fields
asset
source:pmid:26981390
locator
sections[2] "Direct link to deposited data" paragraph 2
quote
The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
The paper used Rosetta Resolver error-model-based hypothesis tests, which account for fold change and expression level, and directs readers to the source microarray data at GEO accession GSE62395.
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:26981390
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:GSE62395
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:GSE62395
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:26981390
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.gdata.2015.12.013
sha256
sha256:5d389e343c14a22a6f03bcf5d020e72caaa480d9485ded09461585351661ca43
bytes
9109
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.gdata.2015.12.013
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
PMC4778614
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE62395
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=GSE62395
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE62395
version
null
note
The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.
access_statement_kind
data_availability_statement
sample_accessions array · 3 items
[0]
GSM1526513
[1]
GSM1526514
[2]
GSM1526515
sample_count
3
group_sizes
null
group_sizes_basis
null
platform
19298
taxon
Homo sapiens
title
Radiation Effects on a 3-Dimensional Model of Oral Mucositis
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:26981390:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:38cb8c4c77c6ef358dce575e95138ab7efb19954a8f12d959b96a7232b11b414
bytes
881
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[1]/table-wrap[1]#t0015
version
null
note
null
structure object · 5 fields
pmcid
PMC4778614
section_index
1
section_title
p
row_count
9
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 9 items
[0] array · 1 item
[0]
Specifications
[1] array · 2 items
[0]
Organism/cell line/tissue
[1]
Human primary oral keratinocytes and fibroblasts grown in 3D culture
[2] array · 2 items
[0]
Sex
[1]
Male
[3] array · 2 items
[0]
Sequencer or array type
[1]
Phalanx Human OneArray v4.3 (GPL19298)
[4] array · 2 items
[0]
Data format
[1]
Raw and processed
[5] array · 2 items
[0]
Experimental factors
[1]
Control (non-irradiated) compared to: (1) irradiated with 12 Gy; (2) irradiated with 2 Gy
[6] array · 2 items
[0]
Experimental features
[1]
3D oral tissues were exposed to gamma irradiation at 12 Gy or 2 Gy. After irradiation, the tissues were incubated for 6 h at 37 °C with 5% CO2. Subsequently, some of the tissues were used for the extraction of total RNA, and others were placed in 10% formalin for histopathological studies.
[7] array · 2 items
[0]
Consent
[1]
N/A
[8] array · 2 items
[0]
Sample source location
[1]
Pomona, CA
locator
section[1]/table-wrap[1]#t0015
gaps array · 2 items
[0]
asset:data:geo:GSE62395 not downloaded
[1]
asset:data:geo:GSE62395 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Error-model-based hypothesis tests
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Error-model-based hypothesis tests), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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]
GSE62395
resolved_accessions array · 1 item
[0]
GSE62395
statements array · 1 item
[0]
The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.
basis
The paper names GSE62395 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
[0]
source:pmid:26981390
[1]
data:geo:GSE62395
[2]
asset:table:pmid:26981390:1
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:GSE62395
gaps array · 1 item
[0]
method:not_determinable
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
2026-10-31T18:27:42Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
20192
completion_tokens
2725
cached_tokens
6176
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:26981390
type
paper
label
pmid:26981390
[1] object · 3 fields
id
source:pmid:26981390
type
manuscript
label
PMID 26981390 full text
[2] object · 3 fields
id
data:geo:GSE62395
type
dataset
label
GEO GSE62395
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:26981390
type
paper
label
pmid:26981390
[1] object · 3 fields
id
source:pmid:26981390
type
manuscript
label
PMID 26981390 full text
[2] object · 3 fields
id
data:geo:GSE62395
type
dataset
label
GEO GSE62395
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-26981390
type
extraction
used array · 1 item
[0]
source:pmid:26981390
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE62395
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE62395
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:26981390
parent_hash
sha256:52de1f0e2bfe5d5df6122de0edcaecac5d0c2fc9c404754770e27b50a87ab5bb
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE62395 licence not read
[1]
asset:data:geo:GSE62395 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 1 item
[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 · 3 items
[0]
compare global gene expression profiles via microarray analysis. Here we provide detailed methods a
[1]
ovide detailed methods and analysis on these microarray data, which have been deposited in Gene Expr
[2]
Experimental design, materials and methods Microarray data pre-processing and statistical analysis
order_basis
paper_text_order:466
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981390", "kind": "science-record", "revision": 6, "content_hash": "sha256:af8e55791cf9e844668fce546f569613b13b233ab2bdf6465ff0822d7d1cc683", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T21:20:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome wide expression after different doses of irradiation of a three-dimensional (3D) model of oral mucosal.", "doi": "10.1016/j.gdata.2015.12.013", "pmid": "26981390", "authors": ["Maria P Lambros", "Michael K DeSalvo", "Hari Chandana Mulamalla", "Jonathan Moreno", "Lavanya Kondapalli"], "journal": "Genomics data", "year": 2016, "abstract": "We evaluated a three-dimensional (3D) human oral cell culture that consisted of two types of cells, oral keratinocytes and fibroblasts as a model of oral mucositis which is a debilitating adverse effect of chemotherapy and radiation treatment. The 3D cell culture model was irradiated with 12 or 2 Gy, and total RNA was collected 6 h after irradiation to compare global gene expression profiles via microarray analysis. Here we provide detailed methods and analysis on these microarray data, which have been deposited in Gene Expression Omnibus (GEO): GSE62395.", "claims": [{"id": "claim-method", "statement": "Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981390", "locator": "sections[6] \"Microarray data pre-processing and statistical analysis\" paragraph 3", "quote": "Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981390", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used Rosetta Resolver error-model-based hypothesis tests, which account for fold change and expression level, and directs readers to the source microarray data at GEO accession GSE62395.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981390", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide detailed methods and analysis on these microarray data, which have been deposited in Gene Expression Omnibus (GEO): GSE62395."}, {"asset": "source:pmid:26981390", "locator": "sections[6] \"Microarray data pre-processing and statistical analysis\" paragraph 3", "quote": "Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level."}, {"asset": "source:pmid:26981390", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used Rosetta Resolver error-model-based hypothesis tests, which account for fold change and expression level, and directs readers to the source microarray data at GEO accession GSE62395.", "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:26981390"], "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:GSE62395"], "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:GSE62395"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26981390", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.12.013", "sha256": "sha256:5d389e343c14a22a6f03bcf5d020e72caaa480d9485ded09461585351661ca43", "bytes": 9109, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.12.013", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4778614", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62395", "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=GSE62395", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62395", "version": null, "note": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1526513", "GSM1526514", "GSM1526515"], "sample_count": 3, "group_sizes": null, "group_sizes_basis": null, "platform": "19298", "taxon": "Homo sapiens", "title": "Radiation Effects on a 3-Dimensional Model of Oral Mucositis", "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:26981390:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:38cb8c4c77c6ef358dce575e95138ab7efb19954a8f12d959b96a7232b11b414", "bytes": 881, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC4778614", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Human primary oral keratinocytes and fibroblasts grown in 3D culture"], ["Sex", "Male"], ["Sequencer or array type", "Phalanx Human OneArray v4.3 (GPL19298)"], ["Data format", "Raw and processed"], ["Experimental factors", "Control (non-irradiated) compared to: (1) irradiated with 12 Gy; (2) irradiated with 2 Gy"], ["Experimental features", "3D oral tissues were exposed to gamma irradiation at 12 Gy or 2 Gy. After irradiation, the tissues were incubated for 6 h at 37 °C with 5% CO2. Subsequently, some of the tissues were used for the extraction of total RNA, and others were placed in 10% formalin for histopathological studies."], ["Consent", "N/A"], ["Sample source location", "Pomona, CA"]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0015"}}], "gaps": ["asset:data:geo:GSE62395 not downloaded", "asset:data:geo:GSE62395 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Error-model-based hypothesis tests", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Rather than focusing solely on fold changes, Rosetta Resolver uses error-model-based hypothesis tests, which account for both fold change and expression level."}}], "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 (Error-model-based hypothesis tests), 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": ["GSE62395"], "resolved_accessions": ["GSE62395"], "statements": ["The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62395."], "basis": "The paper names GSE62395 in 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:26981390", "data:geo:GSE62395", "asset:table:pmid:26981390:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62395"]}, "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": "2026-10-31T18:27:42Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 20192, "completion_tokens": 2725, "cached_tokens": 6176}}, "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:26981390", "type": "paper", "label": "pmid:26981390"}, {"id": "source:pmid:26981390", "type": "manuscript", "label": "PMID 26981390 full text"}, {"id": "data:geo:GSE62395", "type": "dataset", "label": "GEO GSE62395"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26981390", "type": "paper", "label": "pmid:26981390"}, {"id": "source:pmid:26981390", "type": "manuscript", "label": "PMID 26981390 full text"}, {"id": "data:geo:GSE62395", "type": "dataset", "label": "GEO GSE62395"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26981390", "type": "extraction", "used": ["source:pmid:26981390"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62395", "type": "accession_resolution", "used": ["data:geo:GSE62395"], "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:26981390", "parent_hash": "sha256:52de1f0e2bfe5d5df6122de0edcaecac5d0c2fc9c404754770e27b50a87ab5bb", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE62395 licence not read", "asset:data:geo:GSE62395 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": ["compare global gene expression profiles via microarray analysis. Here we provide detailed methods a", "ovide detailed methods and analysis on these microarray data, which have been deposited in Gene Expr", "Experimental design, materials and methods Microarray data pre-processing and statistical analysis"], "order_basis": "paper_text_order:466", "id": "assay:1"}]}