← All .science files
pmid:38025539
Establishing a novel Fanconi anemia signaling pathway-associated prognostic model and tumor clustering for pediatric acute myeloid leukemia patients.
Lixian Chang · Xuelian Cheng · Xingjie Gao · Yao Zou · Weiping Yuan · Li Zhang · Xiaofan Zhu
Open medicine (Warsaw, Poland) · 2023 doi:10.1515/med-2023-0847
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 7 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 405 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 984 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 104 items
gaps array · 6 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 3 items
resolved_accessions array · 3 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 11 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38025539", "kind": "science-record", "revision": 2, "content_hash": "sha256:42f51fb87c217bd47e284efad62b4f9d6b47c66a967cdfe0d0295a7b03ece94b", "created_at": "2026-11-01T19:02:57Z", "updated_at": "2026-11-01T21:32:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishing a novel Fanconi anemia signaling pathway-associated prognostic model and tumor clustering for pediatric acute myeloid leukemia patients.", "doi": "10.1515/med-2023-0847", "pmid": "38025539", "authors": ["Lixian Chang", "Xuelian Cheng", "Xingjie Gao", "Yao Zou", "Weiping Yuan", "Li Zhang", "Xiaofan Zhu"], "journal": "Open medicine (Warsaw, Poland)", "year": 2023, "abstract": "Considering the connection between the Fanconi anemia (FA) signaling pathway and tumor development, we aim to investigate the links between the FA gene expression and the survival prognosis of acute myeloid leukemia (AML) patients. Our study begins by identifying two distinct clusters of pediatric AML patients. Following the batch matching of the TARGET-AML, TCGA-LAML GSE71014, GSE12417, and GSE37642 cohorts, the samples were divided into a training set and an internal validation set. A Lasso regression modeling analysis was performed to identify five signatures: BRIP1, FANCC, FANCL, MAD2L2, and RFWD3. The AML samples were stratified into high- and low-risk groups by evaluating the risk scores. The AML high-risk patients showed a poorer overall survival prognosis. To predict the survival rates, we developed an FA Nomogram incorporating risk score, gender, age, and French-American-British classification. We further utilized the BEAT-AML cohort for the external validation of FA-associated prognostic models and observed good clinical validity. Additionally, we found a correlation between DNA repair, cell cycle, and peroxide-related metabolic events and FA-related high/low risk or cluster 1/2. In summary, our novel FA-associated prognostic models promise to enhance the prediction of pediatric AML prognosis.", "claims": [{"id": "claim-method", "statement": "We used the “glmnet” R package to conduct a Lasso regression modeling analysis of the training set.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38025539", "locator": "sections[5] \"Lasso regression modeling construction\" paragraph 2", "quote": "We used the “glmnet” R package to conduct a Lasso regression modeling analysis of the training set."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38025539", "locator": "sections[23] \"fn-group\" paragraph 1", "quote": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The AML high-risk patients showed a poorer overall survival prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38025539", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The AML high-risk patients showed a poorer overall survival prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The AML high-risk patients showed a poorer overall survival prognosis.", "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:38025539"], "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:GSE12417"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE12417"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38025539", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1515/med-2023-0847", "sha256": "sha256:fcbba8962796ff93b64d13ffafb591aabb26c7fab665aee5eb22b60a93854989", "bytes": 27786, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1515/med-2023-0847", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10655686", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12417", "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=GSE12417", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12417", "version": null, "note": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM311598", "GSM311599", "GSM311600", "GSM311601", "GSM311602", "GSM311603", "GSM311604", "GSM311605", "GSM311606", "GSM311607", "GSM311608", "GSM311609", "GSM311610", "GSM311611", "GSM311612", "GSM311613", "GSM311614", "GSM311615", "GSM311616", "GSM311617", "GSM311618", "GSM311619", "GSM311620", "GSM311621", "GSM311622", "GSM311623", "GSM311624", "GSM311625", "GSM311626", "GSM311627", "GSM311628", "GSM311629", "GSM311630", "GSM311631", "GSM311632", "GSM311633", "GSM311634", "GSM311635", "GSM311636", "GSM311637", "GSM311638", "GSM311639", "GSM311640", "GSM311641", "GSM311642", "GSM311643", "GSM311644", "GSM311645", "GSM311646", "GSM311647", "GSM311648", "GSM311649", "GSM311650", "GSM311651", "GSM311652", "GSM311653", "GSM311654", "GSM311655", "GSM311656", "GSM311657", "GSM311658", "GSM311659", "GSM311660", "GSM311661", "GSM311662", "GSM311663", "GSM311664", "GSM311665", "GSM311666", "GSM311667", "GSM311668", "GSM311669", "GSM311670", "GSM311671", "GSM311672", "GSM311673", "GSM311674", "GSM311675", "GSM311676", "GSM311677", "GSM311678", "GSM311679", "GSM311680", "GSM311681", "GSM311682", "GSM311683", "GSM311684", "GSM311685", "GSM311686", "GSM311687", "GSM311688", "GSM311689", "GSM311690", "GSM311691", "GSM311692", "GSM311693", "GSM311694", "GSM311695", "GSM311696", "GSM311697", "GSM311698", "GSM311699", "GSM311700", "GSM311701", "GSM311702", "GSM311703", "GSM311704", "GSM311705", "GSM311706", "GSM311707", "GSM311708", "GSM311709", "GSM311710", "GSM311711", "GSM311712", "GSM311713", "GSM311714", "GSM311715", "GSM311716", "GSM311717", "GSM311718", "GSM311719", "GSM311720", "GSM311721", "GSM311722", "GSM311723", "GSM311724", "GSM311725", "GSM311726", "GSM311727", "GSM311728", "GSM311729", "GSM311730", "GSM311731", "GSM311732", "GSM311733", "GSM311734", "GSM311735", "GSM311736", "GSM311737", "GSM311738", "GSM311739", "GSM311740", "GSM311741", "GSM311742", "GSM311743", "GSM311744", "GSM311745", "GSM311746", "GSM311747", "GSM311748", "GSM311749", "GSM311750", "GSM311751", "GSM311752", "GSM311753", "GSM311754", "GSM311755", "GSM311756", "GSM311757", "GSM311758", "GSM311759", "GSM311760", "GSM311761", "GSM311762", "GSM311763", "GSM311764", "GSM311765", "GSM311766", "GSM311767", "GSM311768", "GSM311769", "GSM311770", "GSM311771", "GSM311772", "GSM311773", "GSM311774", "GSM311775", "GSM311776", "GSM311777", "GSM311778", "GSM311779", "GSM311780", "GSM311781", "GSM311782", "GSM311783", "GSM311784", "GSM311785", "GSM311786", "GSM311787", "GSM311788", "GSM311789", "GSM311790", "GSM311791", "GSM311792", "GSM311793", "GSM311794", "GSM311795", "GSM311796", "GSM311797", "GSM311798", "GSM311799", "GSM311800", "GSM311801", "GSM311802", "GSM311803", "GSM311804", "GSM311805", "GSM311806", "GSM311807", "GSM311808", "GSM311809", "GSM311810", "GSM311811", "GSM311812", "GSM311813", "GSM311814", "GSM311815", "GSM311816", "GSM311817", "GSM311818", "GSM311819", "GSM311820", "GSM311821", "GSM311822", "GSM311823", "GSM311824", "GSM311825", "GSM311826", "GSM311827", "GSM311828", "GSM311829", "GSM311830", "GSM311831", "GSM311832", "GSM311833", "GSM311834", "GSM311835", "GSM311836", "GSM311837", "GSM311838", "GSM311839", "GSM311840", "GSM311841", "GSM311842", "GSM311843", "GSM311844", "GSM311845", "GSM311846", "GSM311847", "GSM311848", "GSM311849", "GSM311850", "GSM311851", "GSM311852", "GSM311853", "GSM311854", "GSM311855", "GSM311856", "GSM311857", "GSM311858", "GSM311859", "GSM311860", "GSM311861", "GSM311862", "GSM311863", "GSM311864", "GSM311865", "GSM311866", "GSM311867", "GSM311868", "GSM311869", "GSM311870", "GSM311871", "GSM311872", "GSM311873", "GSM311874", "GSM311875", "GSM311876", "GSM311877", "GSM311878", "GSM311879", "GSM311880", "GSM311881", "GSM311882", "GSM311883", "GSM311884", "GSM311885", "GSM311886", "GSM311887", "GSM311888", "GSM311889", "GSM311890", "GSM311891", "GSM311892", "GSM311893", "GSM311894", "GSM311895", "GSM311896", "GSM311897", "GSM311898", "GSM311899", "GSM311900", "GSM311901", "GSM311902", "GSM311903", "GSM311904", "GSM311905", "GSM311906", "GSM311907", "GSM311908", "GSM311909", "GSM311910", "GSM311911", "GSM311912", "GSM311913", "GSM311914", "GSM311915", "GSM311916", "GSM311917", "GSM311918", "GSM311919", "GSM311920", "GSM311921", "GSM311922", "GSM311923", "GSM316652", "GSM316653", "GSM316654", "GSM316655", "GSM316656", "GSM316657", "GSM316658", "GSM316659", "GSM316660", "GSM316661", "GSM316662", "GSM316663", "GSM316664", "GSM316665", "GSM316666", "GSM316667", "GSM316668", "GSM316669", "GSM316670", "GSM316671", "GSM316672", "GSM316673", "GSM316674", "GSM316675", "GSM316676", "GSM316677", "GSM316678", "GSM316679", "GSM316680", "GSM316681", "GSM316682", "GSM316683", "GSM316684", "GSM316685", "GSM316686", "GSM316687", "GSM316688", "GSM316689", "GSM316690", "GSM316691", "GSM316692", "GSM316693", "GSM316694", "GSM316695", "GSM316696", "GSM316697", "GSM316698", "GSM316699", "GSM316700", "GSM316701", "GSM316702", "GSM316703", "GSM316704", "GSM316705", "GSM316706", "GSM316707", "GSM316708", "GSM316709", "GSM316710", "GSM316711", "GSM316712", "GSM316713", "GSM316714", "GSM316715", "GSM316716", "GSM316717", "GSM316718", "GSM316719", "GSM316720", "GSM316721", "GSM316722", "GSM316723", "GSM316724", "GSM316725", "GSM316726", "GSM316727", "GSM316728", "GSM316729", "GSM316730"], "sample_count": 405, "group_sizes": null, "group_sizes_basis": null, "platform": "570;96;97", "taxon": "Homo sapiens", "title": "Prognostic gene signature for normal karyotype AML", "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:GSE37642", "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=GSE37642", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37642", "version": null, "note": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM923596", "GSM923597", "GSM923598", "GSM923599", "GSM923600", "GSM923601", "GSM923602", "GSM923603", "GSM923604", "GSM923605", "GSM923606", "GSM923607", "GSM923608", "GSM923609", "GSM923610", "GSM923611", "GSM923612", "GSM923613", "GSM923614", "GSM923615", "GSM923616", "GSM923617", "GSM923618", "GSM923619", "GSM923620", "GSM923621", "GSM923622", "GSM923623", "GSM923624", "GSM923625", "GSM923626", "GSM923627", "GSM923628", "GSM923629", "GSM923630", "GSM923631", "GSM923632", "GSM923633", "GSM923634", "GSM923635", "GSM923636", "GSM923637", "GSM923638", "GSM923639", "GSM923640", "GSM923641", "GSM923642", "GSM923643", "GSM923644", "GSM923645", "GSM923646", "GSM923647", "GSM923648", "GSM923649", "GSM923650", "GSM923651", "GSM923652", "GSM923653", "GSM923654", "GSM923655", "GSM923656", "GSM923657", "GSM923658", "GSM923659", "GSM923660", "GSM923661", "GSM923662", "GSM923663", "GSM923664", "GSM923665", "GSM923666", "GSM923667", "GSM923668", "GSM923669", "GSM923670", "GSM923671", "GSM923672", "GSM923673", "GSM923674", "GSM923675", "GSM923676", "GSM923677", "GSM923678", "GSM923679", "GSM923680", "GSM923681", "GSM923682", "GSM923683", "GSM923684", "GSM923685", "GSM923686", "GSM923687", "GSM923688", "GSM923689", "GSM923690", "GSM923691", "GSM923692", "GSM923693", "GSM923694", "GSM923695", "GSM923696", "GSM923697", "GSM923698", "GSM923699", "GSM923700", "GSM923701", "GSM923702", "GSM923703", "GSM923704", "GSM923705", "GSM923706", "GSM923707", "GSM923708", "GSM923709", "GSM923710", "GSM923711", "GSM923712", "GSM923713", "GSM923714", "GSM923715", "GSM923716", "GSM923717", "GSM923718", "GSM923719", "GSM923720", "GSM923721", "GSM923722", "GSM923723", "GSM923724", "GSM923725", "GSM923726", "GSM923727", "GSM923728", "GSM923729", "GSM923730", "GSM923731", "GSM923732", "GSM923733", "GSM923734", "GSM923735", "GSM923736", "GSM923737", "GSM923738", "GSM923739", "GSM923740", "GSM923741", "GSM923742", "GSM923743", "GSM923744", "GSM923745", "GSM923746", "GSM923747", "GSM923748", "GSM923749", "GSM923750", "GSM923751", "GSM923752", "GSM923753", "GSM923754", "GSM923755", "GSM923756", "GSM923757", "GSM923758", "GSM923759", "GSM923760", "GSM923761", "GSM923762", "GSM923763", "GSM923764", "GSM923765", "GSM923766", "GSM923767", "GSM923768", "GSM923769", "GSM923770", "GSM923771", "GSM923772", "GSM923773", "GSM923774", "GSM923775", "GSM923776", "GSM923777", "GSM923778", "GSM923779", "GSM923780", "GSM923781", "GSM923782", "GSM923783", "GSM923784", "GSM923785", "GSM923786", "GSM923787", "GSM923788", "GSM923789", "GSM923790", "GSM923791", "GSM923792", "GSM923793", "GSM923794", "GSM923795", "GSM923796", "GSM923797", "GSM923798", "GSM923799", "GSM923800", "GSM923801", "GSM923802", "GSM923803", "GSM923804", "GSM923805", "GSM923806", "GSM923807", "GSM923808", "GSM923809", "GSM923810", "GSM923811", "GSM923812", "GSM923813", "GSM923814", "GSM923815", "GSM923816", "GSM923817", "GSM923818", "GSM923819", "GSM923820", "GSM923821", "GSM923822", "GSM923823", "GSM923824", "GSM923825", "GSM923826", "GSM923827", "GSM923828", "GSM923829", "GSM923830", "GSM923831", "GSM923832", "GSM923833", "GSM923834", "GSM923835", "GSM923836", "GSM923837", "GSM923838", "GSM923839", "GSM923840", "GSM923841", "GSM923842", "GSM923843", "GSM923844", "GSM923845", "GSM923846", "GSM923847", "GSM923848", "GSM923849", "GSM923850", "GSM923851", "GSM923852", "GSM923853", "GSM923854", "GSM923855", "GSM923856", "GSM923857", "GSM923858", "GSM923859", "GSM923860", "GSM923861", "GSM923862", "GSM923863", "GSM923864", "GSM923865", "GSM923866", "GSM923867", "GSM923868", "GSM923869", "GSM923870", "GSM923871", "GSM923872", "GSM923873", "GSM923874", "GSM923875", "GSM923876", "GSM923877", "GSM923878", "GSM923879", "GSM923880", "GSM923881", "GSM923882", "GSM923883", "GSM923884", "GSM923885", "GSM923886", "GSM923887", "GSM923888", "GSM923889", "GSM923890", "GSM923891", "GSM923892", "GSM923893", "GSM923894", "GSM923895", "GSM923896", "GSM923897", "GSM923898", "GSM923899", "GSM923900", "GSM923901", "GSM923902", "GSM923903", "GSM923904", "GSM923905", "GSM923906", "GSM923907", "GSM923908", "GSM923909", "GSM923910", "GSM923911", "GSM923912", "GSM923913", "GSM923914", "GSM923915", "GSM923916", "GSM923917", "GSM923918", "GSM923919", "GSM923920", "GSM923921", "GSM923922", "GSM923923", "GSM923924", "GSM923925", "GSM923926", "GSM923927", "GSM923928", "GSM923929", "GSM923930", "GSM923931", "GSM923932", "GSM923933", "GSM923934", "GSM923935", "GSM923936", "GSM923937", "GSM923938", "GSM923939", "GSM923940", "GSM923941", "GSM923942", "GSM923943", "GSM923944", "GSM923945", "GSM923946", "GSM923947", "GSM923948", "GSM923949", "GSM923950", "GSM923951", "GSM923952", "GSM923953", "GSM923954", "GSM923955", "GSM923956", "GSM923957", "GSM923958", "GSM923959", "GSM923960", "GSM923961", "GSM923962", "GSM923963", "GSM923964", "GSM923965", "GSM923966", "GSM923967", "GSM923968", "GSM923969", "GSM923970", "GSM923971", "GSM923972", "GSM923973", "GSM923974", "GSM923975", "GSM923976", "GSM923977", "GSM923978", "GSM923979", "GSM923980", "GSM923981", "GSM923982", "GSM923983", "GSM923984", "GSM923985", "GSM923986", "GSM923987", "GSM923988", "GSM923989", "GSM923990", "GSM923991", "GSM923992", "GSM923993", "GSM923994", "GSM923995", "GSM923996", "GSM923997", "GSM923998", "GSM923999", "GSM924000", "GSM924001", "GSM924002", "GSM924003", "GSM924004", "GSM924005", "GSM924006", "GSM924007", "GSM924008", "GSM924009", "GSM924010", "GSM924011", "GSM924012", "GSM924013", "GSM924014", "GSM924015", "GSM924016", "GSM924017", "GSM924018", "GSM924019", "GSM924020", "GSM924021", "GSM924022", "GSM924023", "GSM924024", "GSM924025", "GSM924026", "GSM924027", "GSM924028", "GSM924029", "GSM924030", "GSM924031", "GSM924032", "GSM924033", "GSM924034", "GSM924035", "GSM924036", "GSM924037", "GSM924038", "GSM924039", "GSM924040", "GSM924041", "GSM924042", "GSM924043", "GSM924044", "GSM924045", "GSM924046", "GSM924047", "GSM924048", "GSM924049", "GSM924050", "GSM924051", "GSM924052", "GSM924053", "GSM924054", "GSM924055", "GSM924056", "GSM924057", "GSM924058", "GSM924059", "GSM924060", "GSM924061", "GSM924062", "GSM924063", "GSM924064", "GSM924065", "GSM924066", "GSM924067", "GSM924068", "GSM924069", "GSM924070", "GSM924071", "GSM924072", "GSM924073", "GSM924074", "GSM924075", "GSM924076", "GSM924077", "GSM924078", "GSM924079", "GSM924080", "GSM924081", "GSM924082", "GSM924083", "GSM924084", "GSM924085", "GSM924086", "GSM924087", "GSM924088", "GSM924089", "GSM924090", "GSM924091", "GSM924092", "GSM924093", "GSM924094", "GSM924095", "GSM924096", "GSM924097", "GSM924098", "GSM924099", "GSM924100", "GSM924101", "GSM924102", "GSM924103", "GSM924104", "GSM924105", "GSM924106", "GSM924107", "GSM924108", "GSM924109", "GSM924110", "GSM924111", "GSM924112", "GSM924113", "GSM924114", "GSM924115", "GSM924116", "GSM924117", "GSM924118", "GSM924119", "GSM924120", "GSM924121", "GSM924122", "GSM924123", "GSM924124", "GSM924125", "GSM924126", "GSM924127", "GSM924128", "GSM924129", "GSM924130", "GSM924131", "GSM924132", "GSM924133", "GSM924134", "GSM924135", "GSM924136", "GSM924137", "GSM924138", "GSM924139", "GSM924140", "GSM924141", "GSM924142", "GSM924143", "GSM924144", "GSM924145", "GSM924146", "GSM924147", "GSM924148", "GSM924149", "GSM924150", "GSM924151", "GSM924152", "GSM924153", "GSM924154", "GSM924155", "GSM924156", "GSM924157", "GSM924158", "GSM924159", "GSM924160", "GSM924161", "GSM924162", "GSM924163", "GSM924164", "GSM924165", "GSM924166", "GSM924167", "GSM924168", "GSM924169", "GSM924170", "GSM924171", "GSM924172", "GSM924173", "GSM924174", "GSM924175", "GSM924176", "GSM924177", "GSM924178", "GSM924179", "GSM924180", "GSM924181", "GSM924182", "GSM924183", "GSM924184", "GSM924185", "GSM924186", "GSM924187", "GSM924188", "GSM924189", "GSM924190", "GSM924191", "GSM924192", "GSM924193", "GSM924194", "GSM924195", "GSM924196", "GSM924197", "GSM924198", "GSM924199", "GSM924200", "GSM924201", "GSM924202", "GSM924203", "GSM924204", "GSM924205", "GSM924206", "GSM924207", "GSM924208", "GSM924209", "GSM924210", "GSM924211", "GSM924212", "GSM924213", "GSM924214", "GSM924215", "GSM924216", "GSM924217", "GSM924218", "GSM924219", "GSM924220", "GSM924221", "GSM924222", "GSM924223", "GSM924224", "GSM924225", "GSM924226", "GSM924227", "GSM924228", "GSM924229", "GSM924230", "GSM924231", "GSM924232", "GSM924233", "GSM924234", "GSM924235", "GSM924236", "GSM924237", "GSM924238", "GSM924239", "GSM924240", "GSM924241", "GSM924242", "GSM924243", "GSM924244", "GSM924245", "GSM924246", "GSM924247", "GSM924248", "GSM924249", "GSM924250", "GSM924251", "GSM924252", "GSM924253", "GSM924254", "GSM924255", "GSM924256", "GSM924257", "GSM924258", "GSM924259", "GSM924260", "GSM924261", "GSM924262", "GSM924263", "GSM924264", "GSM924265", "GSM924266", "GSM924267", "GSM924268", "GSM924269", "GSM924270", "GSM924271", "GSM924272", "GSM924273", "GSM924274", "GSM924275", "GSM924276", "GSM924277", "GSM924278", "GSM924279", "GSM924280", "GSM924281", "GSM924282", "GSM924283", "GSM924284", "GSM924285", "GSM924286", "GSM924287", "GSM924288", "GSM924289", "GSM924290", "GSM924291", "GSM924292", "GSM924293", "GSM924294", "GSM924295", "GSM924296", "GSM924297", "GSM924298", "GSM924299", "GSM924300", "GSM924301", "GSM924302", "GSM924303", "GSM924304", "GSM924305", "GSM924306", "GSM924307", "GSM924308", "GSM924309", "GSM924310", "GSM924311", "GSM924312", "GSM924313", "GSM924314", "GSM924315", "GSM924316", "GSM924317", "GSM924318", "GSM924319", "GSM924320", "GSM924321", "GSM924322", "GSM924323", "GSM924324", "GSM924325", "GSM924326", "GSM924327", "GSM924328", "GSM924329", "GSM924330", "GSM924331", "GSM924332", "GSM924333", "GSM924334", "GSM924335", "GSM924336", "GSM924337", "GSM924338", "GSM924339", "GSM924340", "GSM924341", "GSM924342", "GSM924343", "GSM924344", "GSM924345", "GSM924346", "GSM924347", "GSM924348", "GSM924349", "GSM924350", "GSM924351", "GSM924352", "GSM924353", "GSM924354", "GSM924355", "GSM924356", "GSM924357", "GSM924358", "GSM924359", "GSM924360", "GSM924361", "GSM924362", "GSM924363", "GSM924364", "GSM924365", "GSM924366", "GSM924367", "GSM924368", "GSM924369", "GSM924370", "GSM924371", "GSM924372", "GSM924373", "GSM924374", "GSM924375", "GSM924376", "GSM924377", "GSM924378", "GSM924379", "GSM924380", "GSM924381", "GSM924382", "GSM924383", "GSM924384", "GSM924385", "GSM924386", "GSM924387", "GSM924388", "GSM924389", "GSM924390", "GSM924391", "GSM924392", "GSM924393", "GSM924394", "GSM924395", "GSM924396", "GSM924397", "GSM924398", "GSM924399", "GSM924400", "GSM924401", "GSM924402", "GSM924403", "GSM924404", "GSM924405", "GSM924406", "GSM924407", "GSM924408", "GSM924409", "GSM924410", "GSM924411", "GSM924412", "GSM924413", "GSM924414", "GSM924415", "GSM924416", "GSM924417", "GSM924418", "GSM924419", "GSM924420", "GSM924421", "GSM924422", "GSM924423", "GSM924424", "GSM924425", "GSM924426", "GSM924427", "GSM924428", "GSM924429", "GSM924430", "GSM924431", "GSM924432", "GSM924433", "GSM924434", "GSM924435", "GSM924436", "GSM924437", "GSM924438", "GSM924439", "GSM924440", "GSM924441", "GSM924442", "GSM924443", "GSM924444", "GSM924445", "GSM924446", "GSM924447", "GSM924448", "GSM924449", "GSM924450", "GSM924451", "GSM924452", "GSM924453", "GSM924454", "GSM924455", "GSM924456", "GSM924457", "GSM924458", "GSM924459", "GSM924460", "GSM924461", "GSM924462", "GSM924463", "GSM924464", "GSM924465", "GSM924466", "GSM924467", "GSM924468", "GSM924469", "GSM924470", "GSM924471", "GSM924472", "GSM924473", "GSM924474", "GSM924475", "GSM924476", "GSM924477", "GSM924478", "GSM924479", "GSM924480", "GSM924481", "GSM924482", "GSM924483", "GSM924484", "GSM924485", "GSM924486", "GSM924487", "GSM924488", "GSM924489", "GSM924490", "GSM924491", "GSM924492", "GSM924493", "GSM924494", "GSM924495", "GSM924496", "GSM924497", "GSM924498", "GSM924499", "GSM924500", "GSM924501", "GSM924502", "GSM924503", "GSM924504", "GSM924505", "GSM924506", "GSM924507", "GSM924508", "GSM924509", "GSM924510", "GSM924511", "GSM924512", "GSM924513", "GSM924514", "GSM924515", "GSM924516", "GSM924517", "GSM924518", "GSM924519", "GSM924520", "GSM924521", "GSM924522", "GSM924523", "GSM924524", "GSM924525", "GSM924526", "GSM924527", "GSM924528", "GSM924529", "GSM924530", "GSM924531", "GSM924532", "GSM924533", "GSM924534", "GSM924535", "GSM924536", "GSM924537", "GSM924538", "GSM924539", "GSM924540", "GSM924541", "GSM924542", "GSM924543", "GSM924544", "GSM924545", "GSM924546", "GSM924547", "GSM924548", "GSM924549", "GSM924550", "GSM924551", "GSM924552", "GSM924553", "GSM924554", "GSM924555", "GSM924556", "GSM924557", "GSM924558", "GSM924559", "GSM924560", "GSM924561", "GSM924562", "GSM924563", "GSM924564", "GSM924565", "GSM924566", "GSM924567", "GSM924568", "GSM924569", "GSM924570", "GSM924571", "GSM924572", "GSM924573", "GSM924574", "GSM924575", "GSM924576", "GSM924577", "GSM924578", "GSM924579"], "sample_count": 984, "group_sizes": null, "group_sizes_basis": null, "platform": "570;96;97", "taxon": "Homo sapiens", "title": "Prognostic gene signature for AML", "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:GSE71014", "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=GSE71014", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71014", "version": null, "note": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1825455", "GSM1825456", "GSM1825457", "GSM1825458", "GSM1825459", "GSM1825460", "GSM1825461", "GSM1825462", "GSM1825463", "GSM1825464", "GSM1825465", "GSM1825466", "GSM1825467", "GSM1825468", "GSM1825469", "GSM1825470", "GSM1825471", "GSM1825472", "GSM1825473", "GSM1825474", "GSM1825475", "GSM1825476", "GSM1825477", "GSM1825478", "GSM1825479", "GSM1825480", "GSM1825481", "GSM1825482", "GSM1825483", "GSM1825484", "GSM1825485", "GSM1825486", "GSM1825487", "GSM1825488", "GSM1825489", "GSM1825490", "GSM1825491", "GSM1825492", "GSM1825493", "GSM1825494", "GSM1825495", "GSM1825496", "GSM1825497", "GSM1825498", "GSM1825499", "GSM1825500", "GSM1825501", "GSM1825502", "GSM1825503", "GSM1825504", "GSM1825505", "GSM1825506", "GSM1825507", "GSM1825508", "GSM1825509", "GSM1825510", "GSM1825511", "GSM1825512", "GSM1825513", "GSM1825514", "GSM1825515", "GSM1825516", "GSM1825517", "GSM1825518", "GSM1825519", "GSM1825520", "GSM1825521", "GSM1825522", "GSM1825523", "GSM1825524", "GSM1825525", "GSM1825526", "GSM1825527", "GSM1825528", "GSM1825529", "GSM1825530", "GSM1825531", "GSM1825532", "GSM1825533", "GSM1825534", "GSM1825535", "GSM1825536", "GSM1825537", "GSM1825538", "GSM1825539", "GSM1825540", "GSM1825541", "GSM1825542", "GSM1825543", "GSM1825544", "GSM1825545", "GSM1825546", "GSM1825547", "GSM1825548", "GSM1825549", "GSM1825550", "GSM1825551", "GSM1825552", "GSM1825553", "GSM1825554", "GSM1825555", "GSM1825556", "GSM1825557", "GSM1825558"], "sample_count": 104, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "An mRNA Expression Signature for Prognostication in De Novo Acute Myeloid Leukemia Patients with Normal Karyotype", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE12417 not downloaded", "asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE37642 not downloaded", "asset:data:geo:GSE37642 licence not read", "asset:data:geo:GSE71014 not downloaded", "asset:data:geo:GSE71014 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Lasso regression modeling analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used the “glmnet” R package to conduct a Lasso regression modeling analysis of the training set."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Lasso regression modeling analysis), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE71014", "GSE37642", "GSE12417"], "resolved_accessions": ["GSE71014", "GSE37642", "GSE12417"], "statements": ["Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE71014, GSE37642, GSE12417 in gene expression omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38025539", "data:geo:GSE12417"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12417"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:00:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8058, "completion_tokens": 1738, "cached_tokens": 264}}, "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:38025539", "type": "paper", "label": "pmid:38025539"}, {"id": "source:pmid:38025539", "type": "manuscript", "label": "PMID 38025539 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38025539", "type": "paper", "label": "pmid:38025539"}, {"id": "source:pmid:38025539", "type": "manuscript", "label": "PMID 38025539 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38025539", "type": "extraction", "used": ["source:pmid:38025539"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12417", "type": "accession_resolution", "used": ["data:geo:GSE12417"], "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:38025539", "parent_hash": "sha256:8afd6045efa123261b5fc2346e798da10d294e31294488a89e7b3139bbc8dc11", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE12417 not downloaded", "asset:data:geo:GSE37642 licence not read", "asset:data:geo:GSE37642 not downloaded", "asset:data:geo:GSE71014 licence not read", "asset:data:geo:GSE71014 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}