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

pmid:35804190

Mitoribosome insufficiency in β cells is associated with type 2 diabetes-like islet failure.

Hyun Jung Hong · Kyong Hye Joung · Yong Kyung Kim · Min Jeong Choi · Seul Gi Kang · Jung Tae Kim · Yea Eun Kang · Joon Young Chang · Joon Ho Moon · Sangmi Jun · Hyun-Joo Ro · Yujeong Lee · Hyeongseok Kim · Jae-Hyung Park · Baeki E Kang · Yunju Jo · Heejung Choi · Dongryeol Ryu · Chul-Ho Lee · Hail Kim · Kyu-Sang Park · Hyun Jin Kim · Minho Shong

Experimental & molecular medicine · 2022 doi:10.1038/s12276-022-00797-x

Paper

complete

Experiment

partial

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:35804190
kind
science-record
content_hash
sha256:34c1dbbcef27b1017ea1e48c2b12a19edc9f7996103b16386fe84204f466a654
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T18:14:51Z
updated_at
2026-11-01T22:49:30Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Mitoribosome insufficiency in β cells is associated with type 2 diabetes-like islet failure.
doi
10.1038/s12276-022-00797-x
pmid
35804190
authors array · 23 items
[0]
Hyun Jung Hong
[1]
Kyong Hye Joung
[2]
Yong Kyung Kim
[3]
Min Jeong Choi
[4]
Seul Gi Kang
[5]
Jung Tae Kim
[6]
Yea Eun Kang
[7]
Joon Young Chang
[8]
Joon Ho Moon
[9]
Sangmi Jun
[10]
Hyun-Joo Ro
[11]
Yujeong Lee
[12]
Hyeongseok Kim
[13]
Jae-Hyung Park
[14]
Baeki E Kang
[15]
Yunju Jo
[16]
Heejung Choi
[17]
Dongryeol Ryu
[18]
Chul-Ho Lee
[19]
Hail Kim
[20]
Kyu-Sang Park
[21]
Hyun Jin Kim
[22]
Minho Shong
journal
Experimental & molecular medicine
year
2022
abstract
Genetic variations in mitoribosomal subunits and mitochondrial transcription factors are related to type 2 diabetes. However, the role of islet mitoribosomes in the development of type 2 diabetes has not been determined. We investigated the effects of the mitoribosomal gene on β-cell function and glucose homeostasis. Mitoribosomal gene expression was analyzed in datasets from the NCBI GEO website (GSE25724, GSE76894, and GSE76895) and the European Nucleotide Archive (ERP017126), which contain the transcriptomes of type 2 diabetic and nondiabetic organ donors. We found deregulation of most mitoribosomal genes in islets from individuals with type 2 diabetes, including partial downregulation of CRIF1. The phenotypes of haploinsufficiency in a single mitoribosomal gene were examined using β-cell-specific Crif1 (Mrpl59) heterozygous-deficient mice. Crif1beta+/- mice had normal glucose tolerance, but their islets showed a loss of first-phase glucose-stimulated insulin secretion. They also showed increased β-cell mass associated with higher expression of Reg family genes. However, Crif1beta+/- mice showed earlier islet failure in response to high-fat feeding, which was exacerbated by aging. Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35804190
locator
sections[13] "Statistical analysis" paragraph 2
quote
We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35804190
locator
sections[30] "notes" paragraph 1
quote
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35804190
locator
sections[0] "Abstract" paragraph 1
quote
Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans.
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:35804190
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:GSE151708
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
blocked
blocked_on
method:student_t
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:GSE151708
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 · 1 item
[0]
step:run_analysis blocked on method:student_t
data object · 3 fields
state
partial
assets array · 6 items
[0] object · 15 fields
id
source:pmid:35804190
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1038/s12276-022-00797-x
sha256
sha256:03336fc6187f76e7cac23fd724c41af58a7093dc6ea46e2971003c2e5faf33cd
bytes
48176
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1038/s12276-022-00797-x
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
PMC9355985
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE151708
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=GSE151708
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE151708
version
null
note
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 6 items
[0]
GSM4588616
[1]
GSM4588617
[2]
GSM4588618
[3]
GSM4588619
[4]
GSM4588620
[5]
GSM4588621
sample_count
6
group_sizes
null
group_sizes_basis
null
platform
24247
taxon
Mus musculus
title
β cell specific Crif1 haploinsufficiency effect.
resolution_checked_at
2026-11-01T18:06:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE159984
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=GSE159984
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE159984
version
null
note
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 131 items
[0]
GSM4852033
[1]
GSM4852034
[2]
GSM4852035
[3]
GSM4852036
[4]
GSM4852037
[5]
GSM4852038
[6]
GSM4852039
[7]
GSM4852040
[8]
GSM4852041
[9]
GSM4852042
[10]
GSM4852043
[11]
GSM4852044
[12]
GSM4852045
[13]
GSM4852046
[14]
GSM4852047
[15]
GSM4852048
[16]
GSM4852049
[17]
GSM4852050
[18]
GSM4852051
[19]
GSM4852052
[20]
GSM4852053
[21]
GSM4852054
[22]
GSM4852055
[23]
GSM4852056
[24]
GSM4852057
[25]
GSM4852058
[26]
GSM4852059
[27]
GSM4852060
[28]
GSM4852061
[29]
GSM4852062
[30]
GSM4852063
[31]
GSM4852064
[32]
GSM4852065
[33]
GSM4852066
[34]
GSM4852067
[35]
GSM4852068
[36]
GSM4852069
[37]
GSM4852070
[38]
GSM4852071
[39]
GSM4852072
[40]
GSM4852073
[41]
GSM4852074
[42]
GSM4852075
[43]
GSM4852076
[44]
GSM4852077
[45]
GSM4852078
[46]
GSM4852079
[47]
GSM4852080
[48]
GSM4852081
[49]
GSM4852082
[50]
GSM4852083
[51]
GSM4852084
[52]
GSM4852085
[53]
GSM4852086
[54]
GSM4852087
[55]
GSM4852088
[56]
GSM4852089
[57]
GSM4852090
[58]
GSM4852091
[59]
GSM4852092
[60]
GSM4852093
[61]
GSM4852094
[62]
GSM4852095
[63]
GSM4852096
[64]
GSM4852097
[65]
GSM4852098
[66]
GSM4852099
[67]
GSM4852100
[68]
GSM4852101
[69]
GSM4852102
[70]
GSM4852103
[71]
GSM4852104
[72]
GSM4852105
[73]
GSM4852106
[74]
GSM4852107
[75]
GSM4852108
[76]
GSM4852109
[77]
GSM4852110
[78]
GSM4852111
[79]
GSM4852112
[80]
GSM4852113
[81]
GSM4852114
[82]
GSM4852115
[83]
GSM4852116
[84]
GSM4852117
[85]
GSM4852118
[86]
GSM4852119
[87]
GSM4852120
[88]
GSM4852121
[89]
GSM4852122
[90]
GSM4852123
[91]
GSM4852124
[92]
GSM4852125
[93]
GSM4852126
[94]
GSM4852127
[95]
GSM4852128
[96]
GSM4852129
[97]
GSM4852130
[98]
GSM4852131
[99]
GSM4852132
[100]
GSM4852133
[101]
GSM4852134
[102]
GSM4852135
[103]
GSM4852136
[104]
GSM4852137
[105]
GSM4852138
[106]
GSM4852139
[107]
GSM4852140
[108]
GSM4852141
[109]
GSM4852142
[110]
GSM4852143
[111]
GSM4852144
[112]
GSM4852145
[113]
GSM4852146
[114]
GSM4852147
[115]
GSM4852148
[116]
GSM4852149
[117]
GSM4852150
[118]
GSM4852151
[119]
GSM4852152
[120]
GSM4852153
[121]
GSM4852154
[122]
GSM4852155
[123]
GSM4852156
[124]
GSM4852157
[125]
GSM4852158
[126]
GSM4852159
[127]
GSM4852160
[128]
GSM4852161
[129]
GSM4852162
[130]
GSM4852163
sample_count
131
group_sizes
null
group_sizes_basis
null
platform
9115;16791
taxon
Homo sapiens
title
Persistent or Transient Human β-cell Dysfunction Induced by Metabolic Stress Associated with Specific Signatures and Shared Gene Expression of Type 2 Diabetes
resolution_checked_at
2026-11-01T18:06:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:GSE25724
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=GSE25724
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE25724
version
null
note
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 13 items
[0]
GSM631755
[1]
GSM631756
[2]
GSM631757
[3]
GSM631758
[4]
GSM631759
[5]
GSM631760
[6]
GSM631761
[7]
GSM631762
[8]
GSM631763
[9]
GSM631764
[10]
GSM631765
[11]
GSM631766
[12]
GSM631767
sample_count
13
group_sizes
null
group_sizes_basis
null
platform
96
taxon
Homo sapiens
title
Expression data from type 2 diabetic and non-diabetic isolated human islets
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[4] object · 15 fields
id
data:geo:GSE76894
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=GSE76894
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE76894
version
null
note
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 103 items
[0]
GSM2040049
[1]
GSM2040050
[2]
GSM2040051
[3]
GSM2040052
[4]
GSM2040053
[5]
GSM2040054
[6]
GSM2040055
[7]
GSM2040056
[8]
GSM2040057
[9]
GSM2040058
[10]
GSM2040059
[11]
GSM2040060
[12]
GSM2040061
[13]
GSM2040062
[14]
GSM2040063
[15]
GSM2040064
[16]
GSM2040065
[17]
GSM2040066
[18]
GSM2040067
[19]
GSM2040068
[20]
GSM2040069
[21]
GSM2040070
[22]
GSM2040071
[23]
GSM2040072
[24]
GSM2040073
[25]
GSM2040074
[26]
GSM2040075
[27]
GSM2040076
[28]
GSM2040077
[29]
GSM2040078
[30]
GSM2040079
[31]
GSM2040080
[32]
GSM2040081
[33]
GSM2040082
[34]
GSM2040083
[35]
GSM2040084
[36]
GSM2040085
[37]
GSM2040086
[38]
GSM2040087
[39]
GSM2040088
[40]
GSM2040089
[41]
GSM2040090
[42]
GSM2040091
[43]
GSM2040092
[44]
GSM2040093
[45]
GSM2040094
[46]
GSM2040095
[47]
GSM2040096
[48]
GSM2040097
[49]
GSM2040098
[50]
GSM2040099
[51]
GSM2040100
[52]
GSM2040101
[53]
GSM2040102
[54]
GSM2040103
[55]
GSM2040104
[56]
GSM2040105
[57]
GSM2040106
[58]
GSM2040107
[59]
GSM2040108
[60]
GSM2040109
[61]
GSM2040110
[62]
GSM2040111
[63]
GSM2040112
[64]
GSM2040113
[65]
GSM2040114
[66]
GSM2040115
[67]
GSM2040116
[68]
GSM2040117
[69]
GSM2040118
[70]
GSM2040119
[71]
GSM2040120
[72]
GSM2040121
[73]
GSM2040122
[74]
GSM2040123
[75]
GSM2040124
[76]
GSM2040125
[77]
GSM2040126
[78]
GSM2040127
[79]
GSM2040128
[80]
GSM2040129
[81]
GSM2040130
[82]
GSM2040131
[83]
GSM2040132
[84]
GSM2040133
[85]
GSM2040134
[86]
GSM2040135
[87]
GSM2040136
[88]
GSM2040137
[89]
GSM2040138
[90]
GSM2040139
[91]
GSM2040140
[92]
GSM2040141
[93]
GSM2040142
[94]
GSM2040143
[95]
GSM2040144
[96]
GSM2040145
[97]
GSM2040146
[98]
GSM2040147
[99]
GSM2040148
[100]
GSM2040149
[101]
GSM2040150
[102]
GSM2040151
sample_count
103
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [organ donor cohort]
resolution_checked_at
2026-11-01T18:06:44Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[5] object · 15 fields
id
data:geo:GSE76895
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=GSE76895
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE76895
version
null
note
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 103 items
[0]
GSM2040152
[1]
GSM2040153
[2]
GSM2040154
[3]
GSM2040155
[4]
GSM2040156
[5]
GSM2040157
[6]
GSM2040158
[7]
GSM2040159
[8]
GSM2040160
[9]
GSM2040161
[10]
GSM2040162
[11]
GSM2040163
[12]
GSM2040164
[13]
GSM2040165
[14]
GSM2040166
[15]
GSM2040167
[16]
GSM2040168
[17]
GSM2040169
[18]
GSM2040170
[19]
GSM2040171
[20]
GSM2040172
[21]
GSM2040173
[22]
GSM2040174
[23]
GSM2040175
[24]
GSM2040176
[25]
GSM2040177
[26]
GSM2040178
[27]
GSM2040179
[28]
GSM2040180
[29]
GSM2040181
[30]
GSM2040182
[31]
GSM2040183
[32]
GSM2040184
[33]
GSM2040185
[34]
GSM2040186
[35]
GSM2040187
[36]
GSM2040188
[37]
GSM2040189
[38]
GSM2040190
[39]
GSM2040191
[40]
GSM2040192
[41]
GSM2040193
[42]
GSM2040194
[43]
GSM2040195
[44]
GSM2040196
[45]
GSM2040197
[46]
GSM2040198
[47]
GSM2040199
[48]
GSM2040200
[49]
GSM2040201
[50]
GSM2040202
[51]
GSM2040203
[52]
GSM2040204
[53]
GSM2040205
[54]
GSM2040206
[55]
GSM2040207
[56]
GSM2040208
[57]
GSM2040209
[58]
GSM2040210
[59]
GSM2040211
[60]
GSM2040212
[61]
GSM2040213
[62]
GSM2040214
[63]
GSM2040215
[64]
GSM2040216
[65]
GSM2040217
[66]
GSM2040218
[67]
GSM2040219
[68]
GSM2040220
[69]
GSM2040221
[70]
GSM2040222
[71]
GSM2040223
[72]
GSM2040224
[73]
GSM2040225
[74]
GSM2040226
[75]
GSM2040227
[76]
GSM2040228
[77]
GSM2040229
[78]
GSM2040230
[79]
GSM2040231
[80]
GSM2040232
[81]
GSM2040233
[82]
GSM2040234
[83]
GSM2040235
[84]
GSM2040236
[85]
GSM2040237
[86]
GSM2040238
[87]
GSM2040239
[88]
GSM2040240
[89]
GSM2040241
[90]
GSM2040242
[91]
GSM2040243
[92]
GSM2040244
[93]
GSM2040245
[94]
GSM2040246
[95]
GSM2040247
[96]
GSM2040248
[97]
GSM2040249
[98]
GSM2040250
[99]
GSM2040251
[100]
GSM2040252
[101]
GSM2040253
[102]
GSM2040254
sample_count
103
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [partially pancreatectomized patient cohort]
resolution_checked_at
2026-11-01T18:06:44Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 10 items
[0]
asset:data:geo:GSE151708 not downloaded
[1]
asset:data:geo:GSE151708 licence not read
[2]
asset:data:geo:GSE159984 not downloaded
[3]
asset:data:geo:GSE159984 licence not read
[4]
asset:data:geo:GSE25724 not downloaded
[5]
asset:data:geo:GSE25724 licence not read
[6]
asset:data:geo:GSE76894 not downloaded
[7]
asset:data:geo:GSE76894 licence not read
[8]
asset:data:geo:GSE76895 not downloaded
[9]
asset:data:geo:GSE76895 licence not read
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
student_t_test
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups.
[1] object · 10 fields
id
method-2
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
0.8
band
high
quote
ANOVA
targets array · 0 items
gaps array · 1 item
[0]
method.student_t
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
false
required_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test.
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 · 5 items
[0]
GSE25724
[1]
GSE76895
[2]
GSE76894
[3]
GSE159984
[4]
GSE151708
resolved_accessions array · 5 items
[0]
GSE25724
[1]
GSE76895
[2]
GSE76894
[3]
GSE159984
[4]
GSE151708
statements array · 1 item
[0]
All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.
basis
The paper names GSE25724, GSE76895, GSE76894, GSE159984, GSE151708 in NCBI 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 · 2 items
[0]
source:pmid:35804190
[1]
data:geo:GSE151708
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
student_t
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE151708
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
2026-11-01T17:54:10Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
13891
completion_tokens
1960
cached_tokens
128
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:35804190
type
paper
label
pmid:35804190
[1] object · 3 fields
id
source:pmid:35804190
type
manuscript
label
PMID 35804190 full text
[2] object · 3 fields
id
data:geo:GSE151708
type
dataset
label
GEO GSE151708
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:35804190
type
paper
label
pmid:35804190
[1] object · 3 fields
id
source:pmid:35804190
type
manuscript
label
PMID 35804190 full text
[2] object · 3 fields
id
data:geo:GSE151708
type
dataset
label
GEO GSE151708
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-35804190
type
extraction
used array · 1 item
[0]
source:pmid:35804190
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE151708
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE151708
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:35804190
parent_hash
sha256:be900525974e1eee72cf0a1eee143fdfa64017ad51a531da0b093806559376cf
fork_of
null
gaps array · 16 items
[0]
asset:data:geo:GSE151708 licence not read
[1]
asset:data:geo:GSE151708 not downloaded
[2]
asset:data:geo:GSE159984 licence not read
[3]
asset:data:geo:GSE159984 not downloaded
[4]
asset:data:geo:GSE25724 licence not read
[5]
asset:data:geo:GSE25724 not downloaded
[6]
asset:data:geo:GSE76894 licence not read
[7]
asset:data:geo:GSE76894 not downloaded
[8]
asset:data:geo:GSE76895 licence not read
[9]
asset:data:geo:GSE76895 not downloaded
[10]
execution.not_run
[11]
method.student_t
[12]
review.human_critique
[13]
review.independent_reader
[14]
review.machine_critique
[15]
step:run_analysis blocked on method:student_t
assays array · 3 items
[0] object · 11 fields
role
data_generation
definition_id
rna_seq
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]
otide Archive (ERP017126), which contain the transcriptomes of type 2 diabetic and nondiabetic organ don
[1]
for the care and use of laboratory animals. RNA-sequencing, data processing, and analysis RNA sequencin
[2]
NA-sequencing, data processing, and analysis RNA sequencing was performed using Crif1beta+/− and Crif1be
[3]
lementary Information). The raw data for the RNA sequencing reported in this paper have been deposited t
order_basis
paper_text_order:550
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
animal_model
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]
nformation). Animals Floxed Crif1 (Crif1f/f) mice were mated with Ins2-Cre transgenic mice to gener
[1]
1 heterozygous mice (Crif1beta+/−). Crif1f/f mice were generated as described previously15. Ins2-Cr
[2]
erotonin16. In all experiments, Cre-positive mice were used as a control. All mice were maintained
[3]
re-positive mice were used as a control. All mice were maintained in a controlled environment (12-h
order_basis
paper_text_order:2103
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups.
order_basis
consumes_earlier_output
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35804190", "kind": "science-record", "revision": 5, "content_hash": "sha256:34c1dbbcef27b1017ea1e48c2b12a19edc9f7996103b16386fe84204f466a654", "created_at": "2026-11-01T18:14:51Z", "updated_at": "2026-11-01T22:49:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Mitoribosome insufficiency in β cells is associated with type 2 diabetes-like islet failure.", "doi": "10.1038/s12276-022-00797-x", "pmid": "35804190", "authors": ["Hyun Jung Hong", "Kyong Hye Joung", "Yong Kyung Kim", "Min Jeong Choi", "Seul Gi Kang", "Jung Tae Kim", "Yea Eun Kang", "Joon Young Chang", "Joon Ho Moon", "Sangmi Jun", "Hyun-Joo Ro", "Yujeong Lee", "Hyeongseok Kim", "Jae-Hyung Park", "Baeki E Kang", "Yunju Jo", "Heejung Choi", "Dongryeol Ryu", "Chul-Ho Lee", "Hail Kim", "Kyu-Sang Park", "Hyun Jin Kim", "Minho Shong"], "journal": "Experimental & molecular medicine", "year": 2022, "abstract": "Genetic variations in mitoribosomal subunits and mitochondrial transcription factors are related to type 2 diabetes. However, the role of islet mitoribosomes in the development of type 2 diabetes has not been determined. We investigated the effects of the mitoribosomal gene on β-cell function and glucose homeostasis. Mitoribosomal gene expression was analyzed in datasets from the NCBI GEO website (GSE25724, GSE76894, and GSE76895) and the European Nucleotide Archive (ERP017126), which contain the transcriptomes of type 2 diabetic and nondiabetic organ donors. We found deregulation of most mitoribosomal genes in islets from individuals with type 2 diabetes, including partial downregulation of CRIF1. The phenotypes of haploinsufficiency in a single mitoribosomal gene were examined using β-cell-specific Crif1 (Mrpl59) heterozygous-deficient mice. Crif1beta+/- mice had normal glucose tolerance, but their islets showed a loss of first-phase glucose-stimulated insulin secretion. They also showed increased β-cell mass associated with higher expression of Reg family genes. However, Crif1beta+/- mice showed earlier islet failure in response to high-fat feeding, which was exacerbated by aging. Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans.", "claims": [{"id": "claim-method", "statement": "We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35804190", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35804190", "locator": "sections[30] \"notes\" paragraph 1", "quote": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35804190", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans.", "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:35804190"], "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:GSE151708"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE151708"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35804190", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s12276-022-00797-x", "sha256": "sha256:03336fc6187f76e7cac23fd724c41af58a7093dc6ea46e2971003c2e5faf33cd", "bytes": 48176, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s12276-022-00797-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9355985", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE151708", "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=GSE151708", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE151708", "version": null, "note": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4588616", "GSM4588617", "GSM4588618", "GSM4588619", "GSM4588620", "GSM4588621"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "24247", "taxon": "Mus musculus", "title": "β cell specific Crif1 haploinsufficiency effect.", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE159984", "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=GSE159984", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE159984", "version": null, "note": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4852033", "GSM4852034", "GSM4852035", "GSM4852036", "GSM4852037", "GSM4852038", "GSM4852039", "GSM4852040", "GSM4852041", "GSM4852042", "GSM4852043", "GSM4852044", "GSM4852045", "GSM4852046", "GSM4852047", "GSM4852048", "GSM4852049", "GSM4852050", "GSM4852051", "GSM4852052", "GSM4852053", "GSM4852054", "GSM4852055", "GSM4852056", "GSM4852057", "GSM4852058", "GSM4852059", "GSM4852060", "GSM4852061", "GSM4852062", "GSM4852063", "GSM4852064", "GSM4852065", "GSM4852066", "GSM4852067", "GSM4852068", "GSM4852069", "GSM4852070", "GSM4852071", "GSM4852072", "GSM4852073", "GSM4852074", "GSM4852075", "GSM4852076", "GSM4852077", "GSM4852078", "GSM4852079", "GSM4852080", "GSM4852081", "GSM4852082", "GSM4852083", "GSM4852084", "GSM4852085", "GSM4852086", "GSM4852087", "GSM4852088", "GSM4852089", "GSM4852090", "GSM4852091", "GSM4852092", "GSM4852093", "GSM4852094", "GSM4852095", "GSM4852096", "GSM4852097", "GSM4852098", "GSM4852099", "GSM4852100", "GSM4852101", "GSM4852102", "GSM4852103", "GSM4852104", "GSM4852105", "GSM4852106", "GSM4852107", "GSM4852108", "GSM4852109", "GSM4852110", "GSM4852111", "GSM4852112", "GSM4852113", "GSM4852114", "GSM4852115", "GSM4852116", "GSM4852117", "GSM4852118", "GSM4852119", "GSM4852120", "GSM4852121", "GSM4852122", "GSM4852123", "GSM4852124", "GSM4852125", "GSM4852126", "GSM4852127", "GSM4852128", "GSM4852129", "GSM4852130", "GSM4852131", "GSM4852132", "GSM4852133", "GSM4852134", "GSM4852135", "GSM4852136", "GSM4852137", "GSM4852138", "GSM4852139", "GSM4852140", "GSM4852141", "GSM4852142", "GSM4852143", "GSM4852144", "GSM4852145", "GSM4852146", "GSM4852147", "GSM4852148", "GSM4852149", "GSM4852150", "GSM4852151", "GSM4852152", "GSM4852153", "GSM4852154", "GSM4852155", "GSM4852156", "GSM4852157", "GSM4852158", "GSM4852159", "GSM4852160", "GSM4852161", "GSM4852162", "GSM4852163"], "sample_count": 131, "group_sizes": null, "group_sizes_basis": null, "platform": "9115;16791", "taxon": "Homo sapiens", "title": "Persistent or Transient Human β-cell Dysfunction Induced by Metabolic Stress Associated with Specific Signatures and Shared Gene Expression of Type 2 Diabetes", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25724", "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=GSE25724", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25724", "version": null, "note": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM631755", "GSM631756", "GSM631757", "GSM631758", "GSM631759", "GSM631760", "GSM631761", "GSM631762", "GSM631763", "GSM631764", "GSM631765", "GSM631766", "GSM631767"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from type 2 diabetic and non-diabetic isolated human islets", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE76894", "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=GSE76894", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76894", "version": null, "note": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2040049", "GSM2040050", "GSM2040051", "GSM2040052", "GSM2040053", "GSM2040054", "GSM2040055", "GSM2040056", "GSM2040057", "GSM2040058", "GSM2040059", "GSM2040060", "GSM2040061", "GSM2040062", "GSM2040063", "GSM2040064", "GSM2040065", "GSM2040066", "GSM2040067", "GSM2040068", "GSM2040069", "GSM2040070", "GSM2040071", "GSM2040072", "GSM2040073", "GSM2040074", "GSM2040075", "GSM2040076", "GSM2040077", "GSM2040078", "GSM2040079", "GSM2040080", "GSM2040081", "GSM2040082", "GSM2040083", "GSM2040084", "GSM2040085", "GSM2040086", "GSM2040087", "GSM2040088", "GSM2040089", "GSM2040090", "GSM2040091", "GSM2040092", "GSM2040093", "GSM2040094", "GSM2040095", "GSM2040096", "GSM2040097", "GSM2040098", "GSM2040099", "GSM2040100", "GSM2040101", "GSM2040102", "GSM2040103", "GSM2040104", "GSM2040105", "GSM2040106", "GSM2040107", "GSM2040108", "GSM2040109", "GSM2040110", "GSM2040111", "GSM2040112", "GSM2040113", "GSM2040114", "GSM2040115", "GSM2040116", "GSM2040117", "GSM2040118", "GSM2040119", "GSM2040120", "GSM2040121", "GSM2040122", "GSM2040123", "GSM2040124", "GSM2040125", "GSM2040126", "GSM2040127", "GSM2040128", "GSM2040129", "GSM2040130", "GSM2040131", "GSM2040132", "GSM2040133", "GSM2040134", "GSM2040135", "GSM2040136", "GSM2040137", "GSM2040138", "GSM2040139", "GSM2040140", "GSM2040141", "GSM2040142", "GSM2040143", "GSM2040144", "GSM2040145", "GSM2040146", "GSM2040147", "GSM2040148", "GSM2040149", "GSM2040150", "GSM2040151"], "sample_count": 103, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [organ donor cohort]", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE76895", "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=GSE76895", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76895", "version": null, "note": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2040152", "GSM2040153", "GSM2040154", "GSM2040155", "GSM2040156", "GSM2040157", "GSM2040158", "GSM2040159", "GSM2040160", "GSM2040161", "GSM2040162", "GSM2040163", "GSM2040164", "GSM2040165", "GSM2040166", "GSM2040167", "GSM2040168", "GSM2040169", "GSM2040170", "GSM2040171", "GSM2040172", "GSM2040173", "GSM2040174", "GSM2040175", "GSM2040176", "GSM2040177", "GSM2040178", "GSM2040179", "GSM2040180", "GSM2040181", "GSM2040182", "GSM2040183", "GSM2040184", "GSM2040185", "GSM2040186", "GSM2040187", "GSM2040188", "GSM2040189", "GSM2040190", "GSM2040191", "GSM2040192", "GSM2040193", "GSM2040194", "GSM2040195", "GSM2040196", "GSM2040197", "GSM2040198", "GSM2040199", "GSM2040200", "GSM2040201", "GSM2040202", "GSM2040203", "GSM2040204", "GSM2040205", "GSM2040206", "GSM2040207", "GSM2040208", "GSM2040209", "GSM2040210", "GSM2040211", "GSM2040212", "GSM2040213", "GSM2040214", "GSM2040215", "GSM2040216", "GSM2040217", "GSM2040218", "GSM2040219", "GSM2040220", "GSM2040221", "GSM2040222", "GSM2040223", "GSM2040224", "GSM2040225", "GSM2040226", "GSM2040227", "GSM2040228", "GSM2040229", "GSM2040230", "GSM2040231", "GSM2040232", "GSM2040233", "GSM2040234", "GSM2040235", "GSM2040236", "GSM2040237", "GSM2040238", "GSM2040239", "GSM2040240", "GSM2040241", "GSM2040242", "GSM2040243", "GSM2040244", "GSM2040245", "GSM2040246", "GSM2040247", "GSM2040248", "GSM2040249", "GSM2040250", "GSM2040251", "GSM2040252", "GSM2040253", "GSM2040254"], "sample_count": 103, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [partially pancreatectomized patient cohort]", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE151708 not downloaded", "asset:data:geo:GSE151708 licence not read", "asset:data:geo:GSE159984 not downloaded", "asset:data:geo:GSE159984 licence not read", "asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE76894 not downloaded", "asset:data:geo:GSE76894 licence not read", "asset:data:geo:GSE76895 not downloaded", "asset:data:geo:GSE76895 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "ANOVA"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE25724", "GSE76895", "GSE76894", "GSE159984", "GSE151708"], "resolved_accessions": ["GSE25724", "GSE76895", "GSE76894", "GSE159984", "GSE151708"], "statements": ["All data that support the findings of this study are available from the authors on reasonable request. No applicable resources were generated or analyzed during the current study."], "basis": "The paper names GSE25724, GSE76895, GSE76894, GSE159984, GSE151708 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:35804190", "data:geo:GSE151708"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE151708"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:54:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13891, "completion_tokens": 1960, "cached_tokens": 128}}, "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:35804190", "type": "paper", "label": "pmid:35804190"}, {"id": "source:pmid:35804190", "type": "manuscript", "label": "PMID 35804190 full text"}, {"id": "data:geo:GSE151708", "type": "dataset", "label": "GEO GSE151708"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35804190", "type": "paper", "label": "pmid:35804190"}, {"id": "source:pmid:35804190", "type": "manuscript", "label": "PMID 35804190 full text"}, {"id": "data:geo:GSE151708", "type": "dataset", "label": "GEO GSE151708"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35804190", "type": "extraction", "used": ["source:pmid:35804190"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE151708", "type": "accession_resolution", "used": ["data:geo:GSE151708"], "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:35804190", "parent_hash": "sha256:be900525974e1eee72cf0a1eee143fdfa64017ad51a531da0b093806559376cf", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE151708 licence not read", "asset:data:geo:GSE151708 not downloaded", "asset:data:geo:GSE159984 licence not read", "asset:data:geo:GSE159984 not downloaded", "asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE76894 licence not read", "asset:data:geo:GSE76894 not downloaded", "asset:data:geo:GSE76895 licence not read", "asset:data:geo:GSE76895 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["otide Archive (ERP017126), which contain the transcriptomes of type 2 diabetic and nondiabetic organ don", "for the care and use of laboratory animals. RNA-sequencing, data processing, and analysis RNA sequencin", "NA-sequencing, data processing, and analysis RNA sequencing was performed using Crif1beta+/− and Crif1be", "lementary Information). The raw data for the RNA sequencing reported in this paper have been deposited t"], "order_basis": "paper_text_order:550", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nformation). Animals Floxed Crif1 (Crif1f/f) mice were mated with Ins2-Cre transgenic mice to gener", "1 heterozygous mice (Crif1beta+/−). Crif1f/f mice were generated as described previously15. Ins2-Cr", "erotonin16. In all experiments, Cre-positive mice were used as a control. All mice were maintained", "re-positive mice were used as a control. All mice were maintained in a controlled environment (12-h"], "order_basis": "paper_text_order:2103", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used an unpaired, two-tailed Student’s t test for comparisons between two groups and one-way ANOVA followed by Tukey’s HSD test for multiple comparisons between three or more groups."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}