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

pmid:41430741

TELO2 mediates parabens-induced breast carcinogenesis: a comprehensive network analysis.

BMC pharmacology & toxicology · 2025 doi:10.1186/s40360-025-01072-1

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:41430741
kind
science-record
content_hash
sha256:e19613bfead04e36c990496da15b69f72b49c845c48388610cdc301167e29445
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:54Z
updated_at
2026-11-01T14:01:53Z
generator object · 3 fields
name
corpus-assay-engine
converter
sep_to_sci_v1
source_package_schema
urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
TELO2 mediates parabens-induced breast carcinogenesis: a comprehensive network analysis.
doi
10.1186/s40360-025-01072-1
pmid
41430741
authors
null
journal
BMC pharmacology & toxicology
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
kind
qualitative
state
blocked
target object · 4 fields
value
null
unit
null
tolerance
null
source
null
evidence array · 0 items
gaps array · 2 items
[0]
abstract
[1]
authors
experiment object · 8 fields
state
partial
objective
the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate and its interval from the source
kind
other
state
complete
blocked_on
null
description
The number a replication must land on, and the sentence it came from.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:41430741
outputs array · 1 item
[0]
the published estimate, its unit and its interval
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data behind the published result
kind
data-preparation
state
blocked
blocked_on
data:not_downloaded
description
The published result cannot be recomputed without the data the paper analysed.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the analysis programme
kind
analysis
state
blocked
blocked_on
no owned computational capability is bound to this experiment
description
Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41430741
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 3 items
[0]
step:obtain_source_data blocked on data:not_downloaded
[1]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:41430741' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:41430741
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1186/s40360-025-01072-1
sha256
sha256:ed50bbb9abdf9440805e02ef3368287e62afa12b28a47eb48a67d4c689bcbbdb
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1186/s40360-025-01072-1
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
[1] object · 16 fields
id
asset:table:pmid:41430741:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:38c87736e77a3dd65fe3b864be20434a076582eca00f0b6faaea8a019c47bf04
bytes
2632
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[2]/table-wrap[1]#Tab1
version
null
note
List of databases and software
structure object · 5 fields
pmcid
PMC12837177
section_index
2
section_title
Materials and methods
row_count
32
column_count
2
table object · 8 fields
label
Table 1
caption
List of databases and software
rows array · 32 items
[0] array · 2 items
[0]
Databases
[1]
Database links
[1] array · 2 items
[0]
Public Chemical Database, Pubchem
[1]
https://pubchem.ncbi.nlm.nih.gov/
[2] array · 2 items
[0]
Swiss Target Prediction
[1]
http://www.swisstargetprediction.ch/
[3] array · 2 items
[0]
Universal Protein Resource, UniProt
[1]
https://www.uniprot.org/
[4] array · 2 items
[0]
GeneCards-The Human Gene Database, GeneCards
[1]
https://www.genecards.org/
[5] array · 2 items
[0]
Protein Data Bank, PDB
[1]
http://www.rcsb.org/
[6] array · 2 items
[0]
Xiantao Academic
[1]
https://www.xiantaozi.com/
[7] array · 2 items
[0]
ProTox 3.0 - Prediction Of Toxicity Of Chemicals, ProTox 3.0
[1]
https://tox.charite.de/protox3/index.php?site=home
[8] array · 2 items
[0]
ADMETlab, ADMETlab 3.0
[1]
https://admetlab3.scbdd.com/
[9] array · 2 items
[0]
Super-PRED
[1]
https://prediction.charite.de/
[10] array · 2 items
[0]
Super-Enhancer Archive, SEA
[1]
https://sea.bkslab.org/
[11] array · 2 items
[0]
Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine, BATMAN-TCM
[1]
http://bionet.ncpsb.org.cn/batman-tcm/index.php/Home/document/index
[12] array · 2 items
[0]
Comparative Toxicogenomics Database, CTD
[1]
https://ctdbase.org/
[13] array · 2 items
[0]
Search Tool for Interactions of Chemicals, STITCH
[1]
http://stitch.embl.de/
[14] array · 2 items
[0]
FinnGen
[1]
https://www.finngen.fi/en
[15] array · 2 items
[0]
Genotype-Tissue Expression Project, GTEx
[1]
https://gtexportal.org/home/
[16] array · 2 items
[0]
Genome-Wide Association Studies Catalog, GWAS catalog
[1]
https://www.ebi.ac.uk/gwas/
[17] array · 2 items
[0]
Cell Identification By Estimating Relative Subsets Of RNA Transcripts (x), CIBERSORTx
[1]
https://cibersortx.stanford.edu/
[18] array · 2 items
[0]
Cell Marker Database 2.0, CellMarker 2.0
[1]
http://117.50.127.228/CellMarker/index.html
[19] array · 2 items
[0]
miRNA Target Database, miRDB
[1]
https://mirdb.org/
[20] array · 2 items
[0]
DIANA-MicroT-CDS (microRNA Target Prediction), DIANA-MicroT
[1]
https://dianalab.e-ce.uth.gr/microt_webserver/#/interactions
[21] array · 2 items
[0]
miRWalk - miRNA Target Prediction, miRWalk
[1]
http://129.206.7.150/
[22] array · 2 items
[0]
The Encyclopedia of RNA Interactomes, ENCORI/starBase
[1]
https://rnasysu.com/encori/index.php
[23] array · 2 items
[0]
Search Tool for the Retrieval of Interacting Genes/Proteins, STRING
[1]
https://string-db.org/
[24] array · 2 items
[0]
Human Protein Atlas, HPA
[1]
https://www.proteinatlas.org/
[25] array · 2 items
[0]
National Health and Nutrition Examination Survey, NHANES
[1]
https://www.cdc.gov/nchs/nhanes/
[26] array · 2 items
[0]
Cavity-detection guided Blind Docking 2, CB-dock2
[1]
https://cadd.labshare.cn/cb-dock2/php/index.php
[27] array · 2 items
[0]
RCSB Protein Data Bank, RCSB
[1]
https://www.rcsb.org/
[28] array · 2 items
[0]
The Cancer Genome Atlas Program, TCGA
[1]
https://www.cancer.gov/ccg/research/genome-sequencing/tcga
[29] array · 2 items
[0]
Cytoscape
[1]
Cytoscape Consortium, 3.9.0
[30] array · 2 items
[0]
RStudio
[1]
Public Benefit Corporation, 4.3.3
[31] array · 2 items
[0]
Pymol
[1]
Schrödinger, Limited Liability Company, 2.6
locator
section[2]/table-wrap[1]#Tab1
[2] object · 16 fields
id
asset:table:pmid:41430741:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:16f4e7c851337b3b66d133373d8cdcc8a29a28c48092d1ccb1edd9c164a5cc30
bytes
175
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[17]/table-wrap[1]#Tab2
version
null
note
List of molecular docking
structure object · 5 fields
pmcid
PMC12837177
section_index
17
section_title
Results of molecular docking and dynamics simulations
row_count
0
column_count
0
table object · 8 fields
label
Table 2
caption
List of molecular docking
rows array · 0 items
locator
section[17]/table-wrap[1]#Tab2
[3] object · 16 fields
id
asset:table:pmid:41430741:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:01b85e3f8b175d20bbfb9a51eee85b8ebed2ac634ed24465a986c28858409682
bytes
2265
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[19]/table-wrap[1]#Tab3
version
null
note
List of PBs analysis in breast cancer
structure object · 5 fields
pmcid
PMC12837177
section_index
19
section_title
Results of a cross-sectional analysis
row_count
42
column_count
5
table object · 8 fields
label
Table 3
caption
List of PBs analysis in breast cancer
rows array · 42 items
[0] array · 3 items
[0]
Characteristic
[1]
Breat cancer
[2]
P value2
[1] array · 3 items
[0]
Overall, N = 6847 1
[1]
No, N = 6745 1
[2]
Yes, N = 102 1
[2] array · 5 items
[0]
Age
[1]
48.0 (33.0, 63.0)
[2]
47.0 (33.0, 63.0)
[3]
68.0 (62.0, 79.0)
[4]
< 0.001
[3] array · 5 items
[0]
Gender
[1]
[2]
[3]
[4]
< 0.001
[4] array · 5 items
[0]
Female
[1]
3459 (51%)
[2]
3357 (50%)
[3]
102 (100%)
[4]
[5] array · 5 items
[0]
Male
[1]
3388 (49%)
[2]
3388 (50%)
[3]
0 (0%)
[4]
[6] array · 5 items
[0]
Race
[1]
[2]
[3]
[4]
0.064
[7] array · 5 items
[0]
Mexican American
[1]
1100 (16%)
[2]
1089 (16%)
[3]
11 (11%)
[4]
[8] array · 5 items
[0]
Non-Hispanic Black
[1]
1492 (22%)
[2]
1468 (22%)
[3]
24 (24%)
[4]
[9] array · 5 items
[0]
Non-Hispanic White
[1]
3114 (45%)
[2]
3056 (45%)
[3]
58 (57%)
[4]
[10] array · 5 items
[0]
Other Hispanic
[1]
602 (8.8%)
[2]
597 (8.9%)
[3]
5 (4.9%)
[4]
[11] array · 5 items
[0]
Other Race
[1]
539 (7.9%)
[2]
535 (7.9%)
[3]
4 (3.9%)
[4]
[12] array · 5 items
[0]
Education
[1]
[2]
[3]
[4]
0.4
[13] array · 5 items
[0]
Above high school
[1]
3372 (49%)
[2]
3330 (49%)
[3]
42 (41%)
[4]
[14] array · 5 items
[0]
Below high school
[1]
794 (12%)
[2]
778 (12%)
[3]
16 (16%)
[4]
[15] array · 5 items
[0]
High school
[1]
2673 (39%)
[2]
2629 (39%)
[3]
44 (43%)
[4]
[16] array · 5 items
[0]
Unkown
[1]
8 (0.1%)
[2]
8 (0.1%)
[3]
0 (0%)
[4]
[17] array · 5 items
[0]
Income
[1]
[2]
[3]
[4]
0.7
[18] array · 5 items
[0]
Poverty
[1]
1339 (20%)
[2]
1321 (20%)
[3]
18 (18%)
[4]
[19] array · 5 items
[0]
Richer
[1]
4935 (72%)
[2]
4858 (72%)
[3]
77 (75%)
[4]
[20] array · 5 items
[0]
Unkown
[1]
573 (8.4%)
[2]
566 (8.4%)
[3]
7 (6.9%)
[4]
[21] array · 5 items
[0]
BMI
[1]
28 (24, 32)
[2]
28 (24, 32)
[3]
28 (24, 34)
[4]
0.3
[22] array · 5 items
[0]
Drinker
[1]
[2]
[3]
[4]
0.002
[23] array · 5 items
[0]
No
[1]
1723 (25%)
[2]
1681 (25%)
[3]
42 (41%)
[4]
[24] array · 5 items
[0]
Unkown
[1]
606 (8.9%)
[2]
600 (8.9%)
[3]
6 (5.9%)
[4]
[25] array · 5 items
[0]
Yes
[1]
4518 (66%)
[2]
4464 (66%)
[3]
54 (53%)
[4]
[26] array · 5 items
[0]
Smoker
[1]
[2]
[3]
[4]
0.007
[27] array · 5 items
[0]
No
[1]
4870 (71%)
[2]
4790 (71%)
[3]
80 (78%)
[4]
[28] array · 5 items
[0]
Unkown
[1]
361 (5.3%)
[2]
351 (5.2%)
[3]
10 (9.8%)
[4]
[29] array · 5 items
[0]
Yes
[1]
1616 (24%)
[2]
1604 (24%)
[3]
12 (12%)
[4]
[30] array · 5 items
[0]
Hypertension
[1]
[2]
[3]
[4]
< 0.001
[31] array · 5 items
[0]
No
[1]
4479 (65%)
[2]
4440 (66%)
[3]
39 (38%)
[4]
[32] array · 5 items
[0]
Unkown
[1]
6 (< 0.1%)
[2]
5 (< 0.1%)
[3]
1 (1.0%)
[4]
[33] array · 5 items
[0]
Yes
[1]
2362 (34%)
[2]
2300 (34%)
[3]
62 (61%)
[4]
[34] array · 5 items
[0]
Diabetes
[1]
[2]
[3]
[4]
0.001
[35] array · 5 items
[0]
Diabetes
[1]
1042 (15%)
[2]
1014 (15%)
[3]
28 (27%)
[4]
[36] array · 5 items
[0]
Normal
[1]
3945 (58%)
[2]
3902 (58%)
[3]
43 (42%)
[4]
[37] array · 5 items
[0]
Prediabetes
[1]
1860 (27%)
[2]
1829 (27%)
[3]
31 (30%)
[4]
[38] array · 5 items
[0]
MP
[1]
71 (17, 259)
[2]
71 (17, 258)
[3]
105 (35, 335)
[4]
0.018
[39] array · 5 items
[0]
EP
[1]
1 (1, 7)
[2]
1 (1, 7)
[3]
1 (1, 15)
[4]
0.5
[40] array · 5 items
[0]
PP
[1]
9 (1, 53)
[2]
9 (1, 52)
[3]
21 (4, 81)
[4]
< 0.001
[41] array · 5 items
[0]
BP
[1]
0.1 (0.1, 0.8)
[2]
0.1 (0.1, 0.7)
[3]
0.1 (0.1, 1.7)
[4]
0.049
locator
section[19]/table-wrap[1]#Tab3
gaps array · 1 item
[0]
asset:source:pmid:41430741 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
state
partial
tier
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
[0]
source:pmid:41430741
[1]
asset:table:pmid:41430741:1
[2]
asset:table:pmid:41430741:2
[3]
asset:table:pmid:41430741:3
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:41430741
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 0 items
target_providers array · 0 items
agreement
false
disagreements array · 0 items
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 4 items
[0] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[1] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[3] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 3 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
[2]
review.machine_critique.providers
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 · 1 item
[0] object · 3 fields
id
package:549bcaedbd09e05ea9d6528d21647adbff2cf85c62cb7c10f23de9057446fe71
type
sep_package
label
SEP v1 package for pmid:41430741
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:41430741
type
conversion
used array · 1 item
[0]
package:549bcaedbd09e05ea9d6528d21647adbff2cf85c62cb7c10f23de9057446fe71
agent
agent:corpus-assay-engine
agents array · 1 item
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
source_run_id
run-20261023T122449232913
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:41430741
parent_hash
sha256:2e39e23aedb8b581abb8d2ef85c8d0feebff67b1aa839985fba2f76f4503bfe1
fork_of
null
gaps array · 14 items
[0]
abstract
[1]
asset:source:pmid:41430741 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
review.machine_critique.providers
[10]
step:obtain_source_data blocked on data:not_downloaded
[11]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[12]
step:run_analysis input 'materials:the source data behind the published result in pmid:41430741' does not resolve to a declared asset
[13]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41430741", "kind": "science-record", "revision": 2, "content_hash": "sha256:e19613bfead04e36c990496da15b69f72b49c845c48388610cdc301167e29445", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T14:01:53Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "TELO2 mediates parabens-induced breast carcinogenesis: a comprehensive network analysis.", "doi": "10.1186/s40360-025-01072-1", "pmid": "41430741", "authors": null, "journal": "BMC pharmacology & toxicology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41430741"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41430741", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41430741' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41430741", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40360-025-01072-1", "sha256": "sha256:ed50bbb9abdf9440805e02ef3368287e62afa12b28a47eb48a67d4c689bcbbdb", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40360-025-01072-1", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:41430741:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:38c87736e77a3dd65fe3b864be20434a076582eca00f0b6faaea8a019c47bf04", "bytes": 2632, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#Tab1", "version": null, "note": "List of databases and software", "structure": {"pmcid": "PMC12837177", "section_index": 2, "section_title": "Materials and methods", "row_count": 32, "column_count": 2}, "table": {"label": "Table 1", "caption": "List of databases and software", "rows": [["Databases", "Database links"], ["Public Chemical Database, Pubchem", "https://pubchem.ncbi.nlm.nih.gov/"], ["Swiss Target Prediction", "http://www.swisstargetprediction.ch/"], ["Universal Protein Resource, UniProt", "https://www.uniprot.org/"], ["GeneCards-The Human Gene Database, GeneCards", "https://www.genecards.org/"], ["Protein Data Bank, PDB", "http://www.rcsb.org/"], ["Xiantao Academic", "https://www.xiantaozi.com/"], ["ProTox 3.0 - Prediction Of Toxicity Of Chemicals, ProTox 3.0", "https://tox.charite.de/protox3/index.php?site=home"], ["ADMETlab, ADMETlab 3.0", "https://admetlab3.scbdd.com/"], ["Super-PRED", "https://prediction.charite.de/"], ["Super-Enhancer Archive, SEA", "https://sea.bkslab.org/"], ["Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine, BATMAN-TCM", "http://bionet.ncpsb.org.cn/batman-tcm/index.php/Home/document/index"], ["Comparative Toxicogenomics Database, CTD", "https://ctdbase.org/"], ["Search Tool for Interactions of Chemicals, STITCH", "http://stitch.embl.de/"], ["FinnGen", "https://www.finngen.fi/en"], ["Genotype-Tissue Expression Project, GTEx", "https://gtexportal.org/home/"], ["Genome-Wide Association Studies Catalog, GWAS catalog", "https://www.ebi.ac.uk/gwas/"], ["Cell Identification By Estimating Relative Subsets Of RNA Transcripts (x), CIBERSORTx", "https://cibersortx.stanford.edu/"], ["Cell Marker Database 2.0, CellMarker 2.0", "http://117.50.127.228/CellMarker/index.html"], ["miRNA Target Database, miRDB", "https://mirdb.org/"], ["DIANA-MicroT-CDS (microRNA Target Prediction), DIANA-MicroT", "https://dianalab.e-ce.uth.gr/microt_webserver/#/interactions"], ["miRWalk - miRNA Target Prediction, miRWalk", "http://129.206.7.150/"], ["The Encyclopedia of RNA Interactomes, ENCORI/starBase", "https://rnasysu.com/encori/index.php"], ["Search Tool for the Retrieval of Interacting Genes/Proteins, STRING", "https://string-db.org/"], ["Human Protein Atlas, HPA", "https://www.proteinatlas.org/"], ["National Health and Nutrition Examination Survey, NHANES", "https://www.cdc.gov/nchs/nhanes/"], ["Cavity-detection guided Blind Docking 2, CB-dock2", "https://cadd.labshare.cn/cb-dock2/php/index.php"], ["RCSB Protein Data Bank, RCSB", "https://www.rcsb.org/"], ["The Cancer Genome Atlas Program, TCGA", "https://www.cancer.gov/ccg/research/genome-sequencing/tcga"], ["Cytoscape", "Cytoscape Consortium, 3.9.0"], ["RStudio", "Public Benefit Corporation, 4.3.3"], ["Pymol", "Schrödinger, Limited Liability Company, 2.6"]], "row_count": 32, "column_count": 2, "numeric_cells": 9, "header_rows": 1, "locator": "section[2]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:41430741:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:16f4e7c851337b3b66d133373d8cdcc8a29a28c48092d1ccb1edd9c164a5cc30", "bytes": 175, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab2", "version": null, "note": "List of molecular docking", "structure": {"pmcid": "PMC12837177", "section_index": 17, "section_title": "Results of molecular docking and dynamics simulations", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "List of molecular docking", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[17]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:41430741:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:01b85e3f8b175d20bbfb9a51eee85b8ebed2ac634ed24465a986c28858409682", "bytes": 2265, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#Tab3", "version": null, "note": "List of PBs analysis in breast cancer", "structure": {"pmcid": "PMC12837177", "section_index": 19, "section_title": "Results of a cross-sectional analysis", "row_count": 42, "column_count": 5}, "table": {"label": "Table 3", "caption": "List of PBs analysis in breast cancer", "rows": [["Characteristic", "Breat cancer", "P value2"], ["Overall, N = 6847 1", "No, N = 6745 1", "Yes, N = 102 1"], ["Age", "48.0 (33.0, 63.0)", "47.0 (33.0, 63.0)", "68.0 (62.0, 79.0)", "< 0.001"], ["Gender", "", "", "", "< 0.001"], ["Female", "3459 (51%)", "3357 (50%)", "102 (100%)", ""], ["Male", "3388 (49%)", "3388 (50%)", "0 (0%)", ""], ["Race", "", "", "", "0.064"], ["Mexican American", "1100 (16%)", "1089 (16%)", "11 (11%)", ""], ["Non-Hispanic Black", "1492 (22%)", "1468 (22%)", "24 (24%)", ""], ["Non-Hispanic White", "3114 (45%)", "3056 (45%)", "58 (57%)", ""], ["Other Hispanic", "602 (8.8%)", "597 (8.9%)", "5 (4.9%)", ""], ["Other Race", "539 (7.9%)", "535 (7.9%)", "4 (3.9%)", ""], ["Education", "", "", "", "0.4"], ["Above high school", "3372 (49%)", "3330 (49%)", "42 (41%)", ""], ["Below high school", "794 (12%)", "778 (12%)", "16 (16%)", ""], ["High school", "2673 (39%)", "2629 (39%)", "44 (43%)", ""], ["Unkown", "8 (0.1%)", "8 (0.1%)", "0 (0%)", ""], ["Income", "", "", "", "0.7"], ["Poverty", "1339 (20%)", "1321 (20%)", "18 (18%)", ""], ["Richer", "4935 (72%)", "4858 (72%)", "77 (75%)", ""], ["Unkown", "573 (8.4%)", "566 (8.4%)", "7 (6.9%)", ""], ["BMI", "28 (24, 32)", "28 (24, 32)", "28 (24, 34)", "0.3"], ["Drinker", "", "", "", "0.002"], ["No", "1723 (25%)", "1681 (25%)", "42 (41%)", ""], ["Unkown", "606 (8.9%)", "600 (8.9%)", "6 (5.9%)", ""], ["Yes", "4518 (66%)", "4464 (66%)", "54 (53%)", ""], ["Smoker", "", "", "", "0.007"], ["No", "4870 (71%)", "4790 (71%)", "80 (78%)", ""], ["Unkown", "361 (5.3%)", "351 (5.2%)", "10 (9.8%)", ""], ["Yes", "1616 (24%)", "1604 (24%)", "12 (12%)", ""], ["Hypertension", "", "", "", "< 0.001"], ["No", "4479 (65%)", "4440 (66%)", "39 (38%)", ""], ["Unkown", "6 (< 0.1%)", "5 (< 0.1%)", "1 (1.0%)", ""], ["Yes", "2362 (34%)", "2300 (34%)", "62 (61%)", ""], ["Diabetes", "", "", "", "0.001"], ["Diabetes", "1042 (15%)", "1014 (15%)", "28 (27%)", ""], ["Normal", "3945 (58%)", "3902 (58%)", "43 (42%)", ""], ["Prediabetes", "1860 (27%)", "1829 (27%)", "31 (30%)", ""], ["MP", "71 (17, 259)", "71 (17, 258)", "105 (35, 335)", "0.018"], ["EP", "1 (1, 7)", "1 (1, 7)", "1 (1, 15)", "0.5"], ["PP", "9 (1, 53)", "9 (1, 52)", "21 (4, 81)", "< 0.001"], ["BP", "0.1 (0.1, 0.8)", "0.1 (0.1, 0.7)", "0.1 (0.1, 1.7)", "0.049"]], "row_count": 42, "column_count": 5, "numeric_cells": 113, "header_rows": 2, "locator": "section[19]/table-wrap[1]#Tab3"}}], "gaps": ["asset:source:pmid:41430741 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41430741", "asset:table:pmid:41430741:1", "asset:table:pmid:41430741:2", "asset:table:pmid:41430741:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41430741"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:549bcaedbd09e05ea9d6528d21647adbff2cf85c62cb7c10f23de9057446fe71", "type": "sep_package", "label": "SEP v1 package for pmid:41430741"}], "activities": [{"id": "activity:conversion:pmid:41430741", "type": "conversion", "used": ["package:549bcaedbd09e05ea9d6528d21647adbff2cf85c62cb7c10f23de9057446fe71"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41430741", "parent_hash": "sha256:2e39e23aedb8b581abb8d2ef85c8d0feebff67b1aa839985fba2f76f4503bfe1", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:41430741 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41430741' does not resolve to a declared asset", "targets"]}