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

pmid:40709170

Molecular Basis of Aggressiveness in Pituitary Adenomas and Its Association With the Immune Microenvironment.

International journal of genomics · 2025 doi:10.1155/ijog/9346050

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:40709170
kind
science-record
content_hash
sha256:bdf31e622c129d6c67b217aea938de03c7a1435bb97a10c017fb3ae177708371
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:52Z
updated_at
2026-11-01T10:25:52Z
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
Molecular Basis of Aggressiveness in Pituitary Adenomas and Its Association With the Immune Microenvironment.
doi
10.1155/ijog/9346050
pmid
40709170
authors
null
journal
International journal of genomics
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:40709170
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:40709170
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:40709170' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:40709170
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1155/ijog/9346050
sha256
sha256:2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1155/ijog/9346050
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
gaps array · 1 item
[0]
asset:source:pmid:40709170 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 · 1 item
[0]
source:pmid:40709170
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:40709170
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
cefc8e96a099f1e66945c60de2155f06f94c4cc139f1943c3dc79b9e7db7f613
source_hash
2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3
raw_response_sha256
sha256:7ce1e491dc2de8852fe6bf2754769ba6bd78ada23a798e1c44a4efee39791819
raw_response_chars
4201
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
8406e365d76ad06980da23bdbcb8daf937490d44956302bf50a36b03fe4cff09
source_hash
2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3
raw_response_sha256
sha256:d4ac5ec79986002f33c334254483998d1f30df95fd65441eb8744cebac144048
raw_response_chars
33730
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
2b3c423ff62d0899844d7a829e8f105bcb365224614d9bbd5f26db2599fd3d36
source_hash
2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3
raw_response
{"parent_value":0,"unit":"","evidence":"","target_result":"The paper states that MYH7 was identified as an accurate diagnostic marker for PAs and that the immune infiltration analysis revealed its correlations with stromal score, immune score, and antitumor-cell infiltration, but it gives no numerical diagnostic-performance result for the registered target.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The paper states that MYH7 was identified as an accurate diagnostic marker for PAs and that the immune infiltration analysis revealed its correlations with stromal score, immune score, and antitumor-cell infiltration, but it gives no numerical diagnostic-performance result for the registered target.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:26:22.624747+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
28233702e86807d8265eb47c307748b0fbfc85190b8f906f7e00896aaeb8b88e
source_hash
2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3
raw_response
<think>We need answer JSON only. Need interpret. Registered target headline numerical result paper states for main finding. Source text perhaps no headline numerical performance value. It states counts 521 DEGs, 187 overlapping, top 10; but main finding MYH7 diagnostic marker no numerical diagnostic performance. User says if no number for registered target, false, parent 0, unit/evidence empty, target_result what text does state instead. Need exact perhaps target_result concise. Since "headline numerical result the paper states for its main finding" likely target is paper headline numerical result, perhaps no AUC given. We should say no numerical diagnostic performance stated; identifies MYH7. Need obey evidence empty. JSON valid. Could target_result: "No numerical diagnostic-performance result is stated for the main finding; the text states that MYH7 was identified as an accurate diagnostic marker for PAs." Is that extracting. number_stated false. parent 0. unit "". Evidence "". Ensure no extra.</think> {"parent_value":0,"unit":"","evidence":"","target_result":"No numerical diagnostic-performance result is stated for the main finding; the text states that MYH7 was identified as an accurate diagnostic marker for PAs.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
No numerical diagnostic-performance result is stated for the main finding; the text states that MYH7 was identified as an accurate diagnostic marker for PAs.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:26:15.835063+00:00
agreement
false
disagreements object · 2 fields
analysis_methods object · 3 fields
minimax array · 10 items
[0]
Weighted gene co-expression network analysis (WGCNA)
[1]
limma differential expression analysis
[2]
Protein–protein interaction network analysis
[3]
CytoHubba
[4]
Support vector machine
[5]
Lasso
[6]
ESTIMATE
[7]
Single-sample gene set enrichment analysis (ssGSEA) using the GSVA R package
[8]
Wilcoxon's test
[9]
Pearson correlation
minimax_alt array · 11 items
[0]
WGCNA
[1]
limma
[2]
STRING protein–protein interaction (PPI) network analysis
[3]
Cytoscape
[4]
CytoHubba
[5]
support vector machine (SVM)
[6]
Lasso
[7]
ESTIMATE
[8]
single-sample gene set enrichment analysis (ssGSEA) using GSVA
[9]
Wilcoxon's test
[10]
Pearson correlation
decisive
false
statistical_method object · 3 fields
minimax
Differential expression analysis using the limma R package
minimax_alt
limma differential expression analysis
decisive
true
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 · 0 items
[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 · 2 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
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:36289b4e17d2c31556a58e8294e3c3e6ac348499090118eacd1a44ba0451cc47
type
sep_package
label
SEP v1 package for pmid:40709170
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40709170
type
conversion
used array · 1 item
[0]
package:36289b4e17d2c31556a58e8294e3c3e6ac348499090118eacd1a44ba0451cc47
agent
agent:corpus-assay-engine
agents array · 3 items
[0] object · 3 fields
id
agent:minimax
type
model
label
minimax
[1] object · 3 fields
id
agent:minimax_alt
type
model
label
minimax_alt
[2] 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
93f24f36-d2bb-4dc1-ab02-b1cf3d3b6a6e
parent_hash
36289b4e17d2c31556a58e8294e3c3e6ac348499090118eacd1a44ba0451cc47
fork_of
null
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40709170 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]
step:obtain_source_data blocked on data:not_downloaded
[10]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40709170' does not resolve to a declared asset
[12]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40709170", "kind": "science-record", "revision": 1, "content_hash": "sha256:bdf31e622c129d6c67b217aea938de03c7a1435bb97a10c017fb3ae177708371", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T10:25:52Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Molecular Basis of Aggressiveness in Pituitary Adenomas and Its Association With the Immune Microenvironment.", "doi": "10.1155/ijog/9346050", "pmid": "40709170", "authors": null, "journal": "International journal of genomics", "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:40709170"], "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:40709170", "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:40709170' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40709170", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/ijog/9346050", "sha256": "sha256:2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/ijog/9346050", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40709170 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:40709170"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40709170"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "cefc8e96a099f1e66945c60de2155f06f94c4cc139f1943c3dc79b9e7db7f613", "source_hash": "2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3", "raw_response_sha256": "sha256:7ce1e491dc2de8852fe6bf2754769ba6bd78ada23a798e1c44a4efee39791819", "raw_response_chars": 4201}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "8406e365d76ad06980da23bdbcb8daf937490d44956302bf50a36b03fe4cff09", "source_hash": "2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3", "raw_response_sha256": "sha256:d4ac5ec79986002f33c334254483998d1f30df95fd65441eb8744cebac144048", "raw_response_chars": 33730}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "2b3c423ff62d0899844d7a829e8f105bcb365224614d9bbd5f26db2599fd3d36", "source_hash": "2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that MYH7 was identified as an accurate diagnostic marker for PAs and that the immune infiltration analysis revealed its correlations with stromal score, immune score, and antitumor-cell infiltration, but it gives no numerical diagnostic-performance result for the registered target.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that MYH7 was identified as an accurate diagnostic marker for PAs and that the immune infiltration analysis revealed its correlations with stromal score, immune score, and antitumor-cell infiltration, but it gives no numerical diagnostic-performance result for the registered target.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:26:22.624747+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "28233702e86807d8265eb47c307748b0fbfc85190b8f906f7e00896aaeb8b88e", "source_hash": "2ec6f14adbe7d118b471abf78647ee93a75ff76adde08bcd8027a92917fa73c3", "raw_response": "<think>We need answer JSON only. Need interpret. Registered target headline numerical result paper states for main finding. Source text perhaps no headline numerical performance value. It states counts 521 DEGs, 187 overlapping, top 10; but main finding MYH7 diagnostic marker no numerical diagnostic performance. User says if no number for registered target, false, parent 0, unit/evidence empty, target_result what text does state instead. Need exact perhaps target_result concise. Since \"headline numerical result the paper states for its main finding\" likely target is paper headline numerical result, perhaps no AUC given. We should say no numerical diagnostic performance stated; identifies MYH7. Need obey evidence empty. JSON valid. Could target_result: \"No numerical diagnostic-performance result is stated for the main finding; the text states that MYH7 was identified as an accurate diagnostic marker for PAs.\" Is that extracting. number_stated false. parent 0. unit \"\". Evidence \"\". Ensure no extra.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"No numerical diagnostic-performance result is stated for the main finding; the text states that MYH7 was identified as an accurate diagnostic marker for PAs.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "No numerical diagnostic-performance result is stated for the main finding; the text states that MYH7 was identified as an accurate diagnostic marker for PAs.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:26:15.835063+00:00"}], "agreement": false, "disagreements": {"analysis_methods": {"minimax": ["Weighted gene co-expression network analysis (WGCNA)", "limma differential expression analysis", "Protein–protein interaction network analysis", "CytoHubba", "Support vector machine", "Lasso", "ESTIMATE", "Single-sample gene set enrichment analysis (ssGSEA) using the GSVA R package", "Wilcoxon's test", "Pearson correlation"], "minimax_alt": ["WGCNA", "limma", "STRING protein–protein interaction (PPI) network analysis", "Cytoscape", "CytoHubba", "support vector machine (SVM)", "Lasso", "ESTIMATE", "single-sample gene set enrichment analysis (ssGSEA) using GSVA", "Wilcoxon's test", "Pearson correlation"], "decisive": false}, "statistical_method": {"minimax": "Differential expression analysis using the limma R package", "minimax_alt": "limma differential expression analysis", "decisive": true}}, "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": []}}, {"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"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:36289b4e17d2c31556a58e8294e3c3e6ac348499090118eacd1a44ba0451cc47", "type": "sep_package", "label": "SEP v1 package for pmid:40709170"}], "activities": [{"id": "activity:conversion:pmid:40709170", "type": "conversion", "used": ["package:36289b4e17d2c31556a58e8294e3c3e6ac348499090118eacd1a44ba0451cc47"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"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": "93f24f36-d2bb-4dc1-ab02-b1cf3d3b6a6e", "parent_hash": "36289b4e17d2c31556a58e8294e3c3e6ac348499090118eacd1a44ba0451cc47", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40709170 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "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:40709170' does not resolve to a declared asset", "targets"]}