← All .science files
pmid:35045818
Revealing potential diagnostic gene biomarkers of septic shock based on machine learning analysis.
Yonghua Fan · Qiufeng Han · Jinfeng Li · Gaige Ye · Xianjing Zhang · Tengxiao Xu · Huaqing Li
BMC infectious diseases · 2022 doi:10.1186/s12879-022-07056-4
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
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
evidence array · 1 item
[0] object · 3 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 · 7 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 227 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 103 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 130 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 123 items
[5] object · 15 fields
structure object · 15 fields
sample_accessions array · 802 items
[6] object · 15 fields
structure object · 15 fields
sample_accessions array · 124 items
gaps array · 12 items
analysis object · 4 fields
methods array · 5 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[4] object · 10 fields
dsl_operations array · 6 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
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 · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 6 items
resolved_accessions array · 6 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 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 · 0 items
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 · 17 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35045818", "kind": "science-record", "revision": 5, "content_hash": "sha256:aff28937f1afe9f0ad079ee1bed61054c5d9c485ff82085027102ff87b633ba7", "created_at": "2026-11-01T17:36:46Z", "updated_at": "2026-11-01T22:48:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Revealing potential diagnostic gene biomarkers of septic shock based on machine learning analysis.", "doi": "10.1186/s12879-022-07056-4", "pmid": "35045818", "authors": ["Yonghua Fan", "Qiufeng Han", "Jinfeng Li", "Gaige Ye", "Xianjing Zhang", "Tengxiao Xu", "Huaqing Li"], "journal": "BMC infectious diseases", "year": 2022, "abstract": "BACKGROUND: Sepsis is an inflammatory response caused by infection with pathogenic microorganisms. The body shock caused by it is called septic shock. In view of this, we aimed to identify potential diagnostic gene biomarkers of the disease.\nMATERIAL AND METHODS: Firstly, mRNAs expression data sets of septic shock were retrieved and downloaded from the GEO (Gene Expression Omnibus) database for differential expression analysis. Functional enrichment analysis was then used to identify the biological function of DEmRNAs (differentially expressed mRNAs). Machine learning analysis was used to determine the diagnostic gene biomarkers for septic shock. Thirdly, RT-PCR (real-time polymerase chain reaction) verification was performed. Lastly, GSE65682 data set was utilized to further perform diagnostic and prognostic analysis of identified superlative diagnostic gene biomarkers.\nRESULTS: A total of 843 DEmRNAs, including 458 up-regulated and 385 down-regulated DEmRNAs were obtained in septic shock. 15 superlative diagnostic gene biomarkers (such as RAB13, KIF1B, CLEC5A, FCER1A, CACNA2D3, DUSP3, HMGN3, MGST1 and ARHGEF18) for septic shock were identified by machine learning analysis. RF (random forests), SVM (support vector machine) and DT (decision tree) models were used to construct classification models. The accuracy of the DT, SVM and RF models were very high. Interestingly, the RF model had the highest accuracy. It is worth mentioning that ARHGEF18 and FCER1A were related to survival. CACNA2D3 and DUSP3 participated in MAPK signaling pathway to regulate septic shock.\nCONCLUSION: Identified diagnostic gene biomarkers may be helpful in the diagnosis and therapy of patients with septic shock.", "claims": [{"id": "claim-method", "statement": "In this study, Limma and metaMA packages were executed for identification of the DEmRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35045818", "locator": "sections[4] \"Identification of DEmRNAs (differentially expressed mRNAs)\" paragraph 2", "quote": "In this study, Limma and metaMA packages were executed for identification of the DEmRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35045818", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Machine-learning analysis identified 15 diagnostic gene biomarkers for septic shock.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35045818", "locator": "sections[13] \"Identification of superlative diagnostic gene biomarkers\" paragraph 2", "quote": "Therefore, the first 15 DEmRNAs (KLRF1, UPP1, RAB13, KIF1B, CLEC5A, NARF, DUSP3, FCER1A, CACNA2D3, HMGN3, ECRP, HDAC4, LHFPL2, MGST1 and ARHGEF18) were selected as the superlative diagnostic gene biomarkers."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Machine-learning analysis identified 15 diagnostic gene biomarkers for septic shock.", "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:35045818"], "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:GSE13904"], "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:GSE13904"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35045818", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12879-022-07056-4", "sha256": "sha256:cf4875aae0291286d3e762608c2958e1f3b25b5799473f62749cec93f5ed3ec0", "bytes": 47617, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12879-022-07056-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8772133", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13904", "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=GSE13904", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13904", "version": null, "note": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM350139", "GSM350140", "GSM350141", "GSM350142", "GSM350143", "GSM350144", "GSM350145", "GSM350146", "GSM350147", "GSM350148", "GSM350149", "GSM350150", "GSM350151", "GSM350152", "GSM350153", "GSM350154", "GSM350155", "GSM350156", "GSM350157", "GSM350158", "GSM350159", "GSM350160", "GSM350161", "GSM350162", "GSM350163", "GSM350164", "GSM350165", "GSM350166", "GSM350167", "GSM350168", "GSM350169", "GSM350170", "GSM350171", "GSM350172", "GSM350173", "GSM350174", "GSM350175", "GSM350176", "GSM350177", "GSM350178", "GSM350179", "GSM350180", "GSM350181", "GSM350182", "GSM350183", "GSM350184", "GSM350185", "GSM350186", "GSM350187", "GSM350188", "GSM350189", "GSM350190", "GSM350191", "GSM350192", "GSM350193", "GSM350194", "GSM350195", "GSM350196", "GSM350197", "GSM350198", "GSM350199", "GSM350200", "GSM350201", "GSM350202", "GSM350203", "GSM350204", "GSM350205", "GSM350206", "GSM350207", "GSM350208", "GSM350209", "GSM350210", "GSM350211", "GSM350212", "GSM350213", "GSM350214", "GSM350215", "GSM350216", "GSM350217", "GSM350218", "GSM350219", "GSM350220", "GSM350221", "GSM350222", "GSM350223", "GSM350224", "GSM350225", "GSM350226", "GSM350227", "GSM350228", "GSM350229", "GSM350230", "GSM350231", "GSM350232", "GSM350233", "GSM350234", "GSM350235", "GSM350236", "GSM350237", "GSM350238", "GSM350239", "GSM350240", "GSM350241", "GSM350242", "GSM350243", "GSM350244", "GSM350245", "GSM350246", "GSM350247", "GSM350248", "GSM350249", "GSM350250", "GSM350251", "GSM350252", "GSM350253", "GSM350254", "GSM350255", "GSM350256", "GSM350257", "GSM350258", "GSM350259", "GSM350260", "GSM350261", "GSM350262", "GSM350263", "GSM350264", "GSM350265", "GSM350266", "GSM350267", "GSM350268", "GSM350269", "GSM350270", "GSM350271", "GSM350272", "GSM350273", "GSM350274", "GSM350275", "GSM350276", "GSM350277", "GSM350278", "GSM350279", "GSM350280", "GSM350281", "GSM350282", "GSM350283", "GSM350284", "GSM350285", "GSM350286", "GSM350287", "GSM350288", "GSM350289", "GSM350290", "GSM350291", "GSM350292", "GSM350293", "GSM350294", "GSM350295", "GSM350296", "GSM350297", "GSM350298", "GSM350299", "GSM350300", "GSM350301", "GSM350302", "GSM350303", "GSM350304", "GSM350305", "GSM350306", "GSM350307", "GSM350308", "GSM350309", "GSM350310", "GSM350311", "GSM350312", "GSM350313", "GSM350314", "GSM350315", "GSM350316", "GSM350317", "GSM350318", "GSM350319", "GSM350320", "GSM350321", "GSM350322", "GSM350323", "GSM350324", "GSM350325", "GSM350326", "GSM350327", "GSM350328", "GSM350329", "GSM350330", "GSM350331", "GSM350332", "GSM350333", "GSM350334", "GSM350335", "GSM350336", "GSM350337", "GSM350338", "GSM350339", "GSM350340", "GSM350341", "GSM350342", "GSM350343", "GSM350344", "GSM350345", "GSM350346", "GSM350347", "GSM350348", "GSM350349", "GSM350350", "GSM350351", "GSM350352", "GSM350353", "GSM350354", "GSM350355", "GSM350356", "GSM350357", "GSM350358", "GSM350359", "GSM350360", "GSM350361", "GSM350362", "GSM350363", "GSM350364", "GSM350365"], "sample_count": 227, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum", "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:GSE26378", "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=GSE26378", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26378", "version": null, "note": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM647527", "GSM647528", "GSM647529", "GSM647530", "GSM647531", "GSM647532", "GSM647533", "GSM647534", "GSM647535", "GSM647536", "GSM647537", "GSM647538", "GSM647539", "GSM647540", "GSM647541", "GSM647542", "GSM647543", "GSM647544", "GSM647545", "GSM647546", "GSM647547", "GSM647548", "GSM647549", "GSM647550", "GSM647551", "GSM647552", "GSM647553", "GSM647554", "GSM647555", "GSM647556", "GSM647557", "GSM647558", "GSM647559", "GSM647560", "GSM647561", "GSM647562", "GSM647563", "GSM647564", "GSM647565", "GSM647566", "GSM647567", "GSM647568", "GSM647569", "GSM647570", "GSM647571", "GSM647572", "GSM647573", "GSM647574", "GSM647575", "GSM647576", "GSM647577", "GSM647578", "GSM647579", "GSM647580", "GSM647581", "GSM647582", "GSM647583", "GSM647584", "GSM647585", "GSM647586", "GSM647587", "GSM647588", "GSM647589", "GSM647590", "GSM647591", "GSM647592", "GSM647593", "GSM647594", "GSM647595", "GSM647596", "GSM647597", "GSM647598", "GSM647599", "GSM647600", "GSM647601", "GSM647602", "GSM647603", "GSM647604", "GSM647605", "GSM647606", "GSM647607", "GSM647608", "GSM647609", "GSM647610", "GSM647611", "GSM647612", "GSM647613", "GSM647614", "GSM647615", "GSM647616", "GSM647617", "GSM647618", "GSM647619", "GSM647620", "GSM647621", "GSM647622", "GSM647623", "GSM647624", "GSM647625", "GSM647626", "GSM647627", "GSM647628", "GSM647629"], "sample_count": 103, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from validation cohort of children with septic shock", "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:GSE26440", "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=GSE26440", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26440", "version": null, "note": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM648590", "GSM648591", "GSM648592", "GSM648593", "GSM648594", "GSM648595", "GSM648596", "GSM648597", "GSM648598", "GSM648599", "GSM648600", "GSM648601", "GSM648602", "GSM648603", "GSM648604", "GSM648605", "GSM648606", "GSM648607", "GSM648608", "GSM648609", "GSM648610", "GSM648611", "GSM648612", "GSM648613", "GSM648614", "GSM648615", "GSM648616", "GSM648617", "GSM648618", "GSM648619", "GSM648620", "GSM648621", "GSM648622", "GSM648623", "GSM648624", "GSM648625", "GSM648626", "GSM648627", "GSM648628", "GSM648629", "GSM648630", "GSM648631", "GSM648632", "GSM648633", "GSM648634", "GSM648635", "GSM648636", "GSM648637", "GSM648638", "GSM648639", "GSM648640", "GSM648641", "GSM648642", "GSM648643", "GSM648644", "GSM648645", "GSM648646", "GSM648647", "GSM648648", "GSM648649", "GSM648650", "GSM648651", "GSM648652", "GSM648653", "GSM648654", "GSM648655", "GSM648656", "GSM648657", "GSM648658", "GSM648659", "GSM648660", "GSM648661", "GSM648662", "GSM648663", "GSM648664", "GSM648665", "GSM648666", "GSM648667", "GSM648668", "GSM648669", "GSM648670", "GSM648671", "GSM648672", "GSM648673", "GSM648674", "GSM648675", "GSM648676", "GSM648677", "GSM648678", "GSM648679", "GSM648680", "GSM648681", "GSM648682", "GSM648683", "GSM648684", "GSM648685", "GSM648686", "GSM648687", "GSM648688", "GSM648689", "GSM648690", "GSM648691", "GSM648692", "GSM648693", "GSM648694", "GSM648695", "GSM648696", "GSM648697", "GSM648698", "GSM648699", "GSM648700", "GSM648701", "GSM648702", "GSM648703", "GSM648704", "GSM648705", "GSM648706", "GSM648707", "GSM648708", "GSM648709", "GSM648710", "GSM648711", "GSM648712", "GSM648713", "GSM648714", "GSM648715", "GSM648716", "GSM648717", "GSM648718", "GSM648719"], "sample_count": 130, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data for derivation of septic shock subgroups", "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:GSE4607", "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=GSE4607", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE4607", "version": null, "note": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM102961", "GSM102962", "GSM102963", "GSM102964", "GSM102965", "GSM102966", "GSM102967", "GSM102968", "GSM102969", "GSM102970", "GSM102971", "GSM102972", "GSM102973", "GSM102974", "GSM102975", "GSM102976", "GSM102977", "GSM102978", "GSM102979", "GSM102980", "GSM102981", "GSM102982", "GSM102983", "GSM102984", "GSM102985", "GSM102986", "GSM102987", "GSM102988", "GSM102989", "GSM102990", "GSM102991", "GSM102992", "GSM102993", "GSM102994", "GSM102995", "GSM102996", "GSM102997", "GSM102998", "GSM102999", "GSM103000", "GSM103001", "GSM103002", "GSM103003", "GSM103004", "GSM103005", "GSM103006", "GSM103007", "GSM103008", "GSM103009", "GSM103010", "GSM103011", "GSM103012", "GSM103013", "GSM103014", "GSM103015", "GSM103016", "GSM103017", "GSM103018", "GSM103019", "GSM103020", "GSM103021", "GSM103022", "GSM103023", "GSM103024", "GSM103025", "GSM103026", "GSM103027", "GSM103028", "GSM103029", "GSM103030", "GSM103031", "GSM103032", "GSM103033", "GSM103034", "GSM103035", "GSM103036", "GSM103037", "GSM103038", "GSM103039", "GSM103040", "GSM103041", "GSM103042", "GSM103043", "GSM103044", "GSM103045", "GSM103046", "GSM103047", "GSM103048", "GSM103049", "GSM103050", "GSM103051", "GSM103052", "GSM103053", "GSM103054", "GSM103055", "GSM103056", "GSM103057", "GSM103058", "GSM103059", "GSM103060", "GSM103061", "GSM103062", "GSM103063", "GSM103064", "GSM103065", "GSM103066", "GSM103067", "GSM103068", "GSM103069", "GSM103070", "GSM103071", "GSM103072", "GSM103073", "GSM103074", "GSM103075", "GSM103076", "GSM103077", "GSM103078", "GSM103079", "GSM103080", "GSM103081", "GSM103082", "GSM103083"], "sample_count": 123, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Systemic inflammatory response syndrome and septic shock", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65682", "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=GSE65682", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65682", "version": null, "note": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1602801", "GSM1602802", "GSM1602803", "GSM1602804", "GSM1602805", "GSM1602806", "GSM1602807", "GSM1602808", "GSM1602809", "GSM1602810", "GSM1602811", "GSM1602812", "GSM1602813", "GSM1602814", "GSM1602815", "GSM1602816", "GSM1602817", "GSM1602818", "GSM1602819", "GSM1602820", "GSM1602821", "GSM1602822", "GSM1602823", "GSM1602824", "GSM1602825", "GSM1602826", "GSM1602827", "GSM1602828", "GSM1602829", "GSM1602830", "GSM1602831", "GSM1602832", "GSM1602833", "GSM1602834", "GSM1602835", "GSM1602836", "GSM1602837", "GSM1602838", "GSM1602839", "GSM1602840", "GSM1602841", "GSM1602842", "GSM1602843", "GSM1602844", "GSM1602845", "GSM1602846", "GSM1602847", "GSM1602848", "GSM1602849", "GSM1602850", "GSM1602851", "GSM1602852", "GSM1602853", "GSM1602854", "GSM1602855", "GSM1602856", "GSM1602857", "GSM1602858", "GSM1602859", "GSM1602860", "GSM1602861", "GSM1602862", "GSM1602863", "GSM1602864", "GSM1602865", "GSM1602866", "GSM1602867", "GSM1602868", "GSM1602869", "GSM1602870", "GSM1602871", "GSM1602872", "GSM1602873", "GSM1602874", "GSM1602875", "GSM1602876", "GSM1602877", "GSM1602878", "GSM1602879", "GSM1602880", "GSM1602881", "GSM1602882", "GSM1602883", "GSM1602884", "GSM1602885", "GSM1602886", "GSM1602887", "GSM1602888", "GSM1602889", "GSM1602890", "GSM1602891", "GSM1602892", "GSM1602893", "GSM1602894", "GSM1602895", "GSM1602896", "GSM1602897", "GSM1602898", "GSM1602899", "GSM1602900", "GSM1602901", "GSM1602902", "GSM1602903", "GSM1602904", "GSM1602905", "GSM1602906", "GSM1602907", "GSM1602908", "GSM1602909", "GSM1602910", "GSM1602911", "GSM1602912", "GSM1602913", "GSM1602914", "GSM1602915", "GSM1602916", "GSM1602917", "GSM1602918", "GSM1602919", "GSM1602920", "GSM1602921", "GSM1602922", "GSM1602923", "GSM1602924", "GSM1602925", "GSM1602926", "GSM1602927", "GSM1602928", "GSM1602929", "GSM1602930", "GSM1602931", "GSM1602932", "GSM1602933", "GSM1602934", "GSM1602935", "GSM1602936", "GSM1602937", "GSM1602938", "GSM1602939", "GSM1602940", "GSM1602941", "GSM1602942", "GSM1602943", "GSM1602944", "GSM1602945", "GSM1602946", "GSM1602947", "GSM1602948", "GSM1602949", "GSM1602950", "GSM1602951", "GSM1602952", "GSM1602953", "GSM1602954", "GSM1602955", "GSM1602956", "GSM1602957", "GSM1602958", "GSM1602959", "GSM1602960", "GSM1602961", "GSM1602962", "GSM1602963", "GSM1602964", "GSM1602965", "GSM1602966", "GSM1602967", "GSM1602968", "GSM1602969", "GSM1602970", "GSM1602971", "GSM1602972", "GSM1602973", "GSM1602974", "GSM1602975", "GSM1602976", "GSM1691861", "GSM1691862", "GSM1691863", "GSM1691864", "GSM1691865", "GSM1691866", "GSM1691867", "GSM1691868", "GSM1691869", "GSM1691870", "GSM1691871", "GSM1691873", "GSM1691874", "GSM1691875", "GSM1691876", "GSM1691877", "GSM1691878", "GSM1691879", "GSM1691880", "GSM1691881", "GSM1691882", "GSM1691883", "GSM1691884", "GSM1691885", "GSM1691886", "GSM1691887", "GSM1691888", "GSM1691889", "GSM1691890", "GSM1691891", "GSM1691892", "GSM1691893", "GSM1691894", "GSM1691895", "GSM1691896", "GSM1691897", "GSM1691898", "GSM1691899", "GSM1691900", "GSM1691901", "GSM1691902", "GSM1691903", "GSM1691904", "GSM1691905", "GSM1691906", "GSM1691907", "GSM1691908", "GSM1691909", "GSM1691910", "GSM1691911", "GSM1691912", "GSM1691913", "GSM1691914", "GSM1691915", "GSM1691916", "GSM1691917", "GSM1691918", "GSM1691919", "GSM1691920", "GSM1691921", "GSM1691922", "GSM1691923", "GSM1691924", "GSM1691925", "GSM1691926", "GSM1691927", "GSM1691928", "GSM1691929", "GSM1691930", "GSM1691932", "GSM1691933", "GSM1691934", "GSM1691935", "GSM1691936", "GSM1691937", "GSM1691938", "GSM1691939", "GSM1691940", "GSM1691941", "GSM1691942", "GSM1691943", "GSM1691944", "GSM1691945", "GSM1691946", "GSM1691947", "GSM1691948", "GSM1691949", "GSM1691950", "GSM1691951", "GSM1691952", "GSM1691953", "GSM1691954", "GSM1691955", "GSM1691957", "GSM1691958", "GSM1691959", "GSM1691960", "GSM1691961", "GSM1691962", "GSM1691963", "GSM1691964", "GSM1691965", "GSM1691966", "GSM1691967", "GSM1691968", "GSM1691969", "GSM1691970", "GSM1691971", "GSM1691972", "GSM1691973", "GSM1691974", "GSM1691975", "GSM1691976", "GSM1691977", "GSM1691978", "GSM1691979", "GSM1691980", "GSM1691981", "GSM1691982", "GSM1691983", "GSM1691984", "GSM1691985", "GSM1691986", "GSM1691987", "GSM1691988", "GSM1691989", "GSM1691990", "GSM1691991", "GSM1691992", "GSM1691993", "GSM1691994", "GSM1691995", "GSM1691996", "GSM1691997", "GSM1691998", "GSM1691999", "GSM1692000", "GSM1692001", "GSM1692002", "GSM1692003", "GSM1692004", "GSM1692005", "GSM1692006", "GSM1692007", "GSM1692008", "GSM1692009", "GSM1692010", "GSM1692011", "GSM1692012", "GSM1692015", "GSM1692016", "GSM1692017", "GSM1692018", "GSM1692019", "GSM1692020", "GSM1692021", "GSM1692022", "GSM1692023", "GSM1692024", "GSM1692025", "GSM1692026", "GSM1692027", "GSM1692028", "GSM1692029", "GSM1692030", "GSM1692032", "GSM1692033", "GSM1692034", "GSM1692035", "GSM1692036", "GSM1692037", "GSM1692038", "GSM1692039", "GSM1692040", "GSM1692041", "GSM1692042", "GSM1692043", "GSM1692044", "GSM1692045", "GSM1692046", "GSM1692047", "GSM1692048", "GSM1692049", "GSM1692050", "GSM1692051", "GSM1692052", "GSM1692053", "GSM1692054", "GSM1692055", "GSM1692056", "GSM1692057", "GSM1692058", "GSM1692059", "GSM1692060", "GSM1692061", "GSM1692062", "GSM1692063", "GSM1692064", "GSM1692065", "GSM1692066", "GSM1692067", "GSM1692068", "GSM1692069", "GSM1692070", "GSM1692071", "GSM1692072", "GSM1692073", "GSM1692074", "GSM1692075", "GSM1692077", "GSM1692078", "GSM1692079", "GSM1692080", "GSM1692081", "GSM1692082", "GSM1692083", "GSM1692084", "GSM1692085", "GSM1692086", "GSM1692087", "GSM1692088", "GSM1692089", "GSM1692090", "GSM1692091", "GSM1692092", "GSM1692093", "GSM1692094", "GSM1692095", "GSM1692096", "GSM1692097", "GSM1692098", "GSM1692099", "GSM1692100", "GSM1692101", "GSM1692102", "GSM1692103", "GSM1692104", "GSM1692105", "GSM1692106", "GSM1692107", "GSM1692108", "GSM1692109", "GSM1692110", "GSM1692111", "GSM1692112", "GSM1692114", "GSM1692115", "GSM1692116", "GSM1692117", "GSM1692118", "GSM1692119", "GSM1692120", "GSM1692121", "GSM1692122", "GSM1692123", "GSM1692124", "GSM1692125", "GSM1692126", "GSM1692127", "GSM1692128", "GSM1692129", "GSM1692130", "GSM1692131", "GSM1692132", "GSM1692133", "GSM1692135", "GSM1692136", "GSM1692137", "GSM1692138", "GSM1692139", "GSM1692140", "GSM1692141", "GSM1692142", "GSM1692143", "GSM1692144", "GSM1692145", "GSM1692146", "GSM1692147", "GSM1692148", "GSM1692149", "GSM1692150", "GSM1692151", "GSM1692152", "GSM1692153", "GSM1692154", "GSM1692155", "GSM1692156", "GSM1692157", "GSM1692158", "GSM1692159", "GSM1692160", "GSM1692161", "GSM1692162", "GSM1692163", "GSM1692164", "GSM1692165", "GSM1692166", "GSM1692167", "GSM1692168", "GSM1692169", "GSM1692170", "GSM1692171", "GSM1692172", "GSM1692173", "GSM1692174", "GSM1692175", "GSM1692176", "GSM1692177", "GSM1692178", "GSM1692179", "GSM1692180", "GSM1692181", "GSM1692182", "GSM1692183", "GSM1692184", "GSM1692185", "GSM1692186", "GSM1692187", "GSM1692188", "GSM1692189", "GSM1692190", "GSM1692191", "GSM1692192", "GSM1692193", "GSM1692194", "GSM1692195", "GSM1692196", "GSM1692197", "GSM1692198", "GSM1692199", "GSM1692200", "GSM1692201", "GSM1692202", "GSM1692203", "GSM1692204", "GSM1692205", "GSM1692206", "GSM1692207", "GSM1692208", "GSM1692209", "GSM1692210", "GSM1692211", "GSM1692212", "GSM1692213", "GSM1692214", "GSM1692215", "GSM1692216", "GSM1692217", "GSM1692218", "GSM1692219", "GSM1692220", "GSM1692221", "GSM1692222", "GSM1692223", "GSM1692224", "GSM1692225", "GSM1692226", "GSM1692227", "GSM1692228", "GSM1692229", "GSM1692230", "GSM1692231", "GSM1692232", "GSM1692233", "GSM1692234", "GSM1692235", "GSM1692237", "GSM1692238", "GSM1692239", "GSM1692240", "GSM1692241", "GSM1692242", "GSM1692243", "GSM1692244", "GSM1692245", "GSM1692246", "GSM1692247", "GSM1692248", "GSM1692249", "GSM1692250", "GSM1692251", "GSM1692252", "GSM1692253", "GSM1692254", "GSM1692255", "GSM1692256", "GSM1692257", "GSM1692258", "GSM1692259", "GSM1692260", "GSM1692261", "GSM1692262", "GSM1692263", "GSM1692264", "GSM1692265", "GSM1692266", "GSM1692267", "GSM1692268", "GSM1692269", "GSM1692270", "GSM1692271", "GSM1692272", "GSM1692273", "GSM1692274", "GSM1692275", "GSM1692276", "GSM1692277", "GSM1692278", "GSM1692279", "GSM1692280", "GSM1692281", "GSM1692282", "GSM1692283", "GSM1692284", "GSM1692286", "GSM1692287", "GSM1692288", "GSM1692289", "GSM1692290", "GSM1692291", "GSM1692292", "GSM1692293", "GSM1692294", "GSM1692295", "GSM1692296", "GSM1692297", "GSM1692298", "GSM1692299", "GSM1692300", "GSM1692301", "GSM1692302", "GSM1692303", "GSM1692304", "GSM1692305", "GSM1692306", "GSM1692307", "GSM1692308", "GSM1692309", "GSM1692310", "GSM1692311", "GSM1692312", "GSM1692313", "GSM1692314", "GSM1692315", "GSM1692316", "GSM1692317", "GSM1692318", "GSM1692319", "GSM1692320", "GSM1692321", "GSM1692322", "GSM1692323", "GSM1692324", "GSM1692326", "GSM1692327", "GSM1692328", "GSM1692329", "GSM1692330", "GSM1692331", "GSM1692332", "GSM1692333", "GSM1692334", "GSM1692335", "GSM1692336", "GSM1692337", "GSM1692338", "GSM1692339", "GSM1692340", "GSM1692341", "GSM1692342", "GSM1692343", "GSM1692344", "GSM1692345", "GSM1692346", "GSM1692347", "GSM1692348", "GSM1692349", "GSM1692350", "GSM1692352", "GSM1692353", "GSM1692354", "GSM1692355", "GSM1692356", "GSM1692357", "GSM1692358", "GSM1692359", "GSM1692360", "GSM1692361", "GSM1692362", "GSM1692363", "GSM1692364", "GSM1692365", "GSM1692366", "GSM1692367", "GSM1692368", "GSM1692369", "GSM1692370", "GSM1692371", "GSM1692372", "GSM1692373", "GSM1692374", "GSM1692375", "GSM1692376", "GSM1692377", "GSM1692378", "GSM1692379", "GSM1692380", "GSM1692381", "GSM1692382", "GSM1692383", "GSM1692384", "GSM1692385", "GSM1692386", "GSM1692387", "GSM1692388", "GSM1692389", "GSM1692390", "GSM1692391", "GSM1692392", "GSM1692393", "GSM1692394", "GSM1692395", "GSM1692396", "GSM1692397", "GSM1692398", "GSM1692399", "GSM1692400", "GSM1692402", "GSM1692404", "GSM1692405", "GSM1692406", "GSM1692407", "GSM1692408", "GSM1692409", "GSM1692410", "GSM1692411", "GSM1692412", "GSM1692413", "GSM1692414", "GSM1692415", "GSM1692416", "GSM1692417", "GSM1692418", "GSM1692419", "GSM1692420", "GSM1692421", "GSM1692422", "GSM1692423", "GSM1692424", "GSM1692425", "GSM1692426", "GSM1692427", "GSM1692428", "GSM1692429", "GSM1692430", "GSM1692431", "GSM1692432", "GSM1692433", "GSM1692434", "GSM1692435", "GSM1692436", "GSM1692437", "GSM1692438", "GSM1692439", "GSM1692440", "GSM1692441", "GSM1692442", "GSM1692443", "GSM1692444", "GSM1692445", "GSM1692446", "GSM1692447", "GSM1692448", "GSM1692449", "GSM1692450", "GSM1692451", "GSM1692452", "GSM1692453", "GSM1692454", "GSM1692455", "GSM1692456", "GSM1692457", "GSM1692458", "GSM1692459", "GSM1692460", "GSM1692461", "GSM1692462", "GSM1692463", "GSM1692465", "GSM1692466", "GSM1692467", "GSM1692468", "GSM1692469", "GSM1692470", "GSM1692471", "GSM1692472", "GSM1692473", "GSM1692474", "GSM1692475", "GSM1692476", "GSM1692477", "GSM1692478", "GSM1692479", "GSM1692480", "GSM1692481", "GSM1692482", "GSM1692483", "GSM1692484", "GSM1692485", "GSM1692487", "GSM1692488", "GSM1692489", "GSM1692490", "GSM1692491", "GSM1692492", "GSM1692493", "GSM1692494", "GSM1692495", "GSM1692496", "GSM1692497", "GSM1692498", "GSM1692499", "GSM1692501", "GSM1692502", "GSM1692503", "GSM1692504"], "sample_count": 802, "group_sizes": null, "group_sizes_basis": null, "platform": "13667", "taxon": "Homo sapiens", "title": "Genome-wide blood transcriptional profiling in critically ill patients - MARS consortium", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE95233", "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=GSE95233", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95233", "version": null, "note": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2500349", "GSM2500350", "GSM2500351", "GSM2500352", "GSM2500353", "GSM2500354", "GSM2500355", "GSM2500356", "GSM2500357", "GSM2500358", "GSM2500359", "GSM2500360", "GSM2500361", "GSM2500362", "GSM2500363", "GSM2500364", "GSM2500365", "GSM2500366", "GSM2500367", "GSM2500368", "GSM2500369", "GSM2500370", "GSM2500371", "GSM2500372", "GSM2500373", "GSM2500374", "GSM2500375", "GSM2500376", "GSM2500377", "GSM2500378", "GSM2500379", "GSM2500380", "GSM2500381", "GSM2500382", "GSM2500383", "GSM2500384", "GSM2500385", "GSM2500386", "GSM2500387", "GSM2500388", "GSM2500389", "GSM2500390", "GSM2500391", "GSM2500392", "GSM2500393", "GSM2500394", "GSM2500395", "GSM2500396", "GSM2500397", "GSM2500398", "GSM2500399", "GSM2500400", "GSM2500401", "GSM2500402", "GSM2500403", "GSM2500404", "GSM2500405", "GSM2500406", "GSM2500407", "GSM2500408", "GSM2500409", "GSM2500410", "GSM2500411", "GSM2500412", "GSM2500413", "GSM2500414", "GSM2500415", "GSM2500416", "GSM2500417", "GSM2500418", "GSM2500419", "GSM2500420", "GSM2500421", "GSM2500422", "GSM2500423", "GSM2500424", "GSM2500425", "GSM2500426", "GSM2500427", "GSM2500428", "GSM2500429", "GSM2500430", "GSM2500431", "GSM2500432", "GSM2500433", "GSM2500434", "GSM2500435", "GSM2500436", "GSM2500437", "GSM2500438", "GSM2500439", "GSM2500440", "GSM2500441", "GSM2500442", "GSM2500443", "GSM2500444", "GSM2500445", "GSM2500446", "GSM2500447", "GSM2500448", "GSM2500449", "GSM2500450", "GSM2500451", "GSM2500452", "GSM2500453", "GSM2500454", "GSM2500455", "GSM2500456", "GSM2500457", "GSM2500458", "GSM2500459", "GSM2500460", "GSM2500461", "GSM2500462", "GSM2500463", "GSM2500464", "GSM2500465", "GSM2500466", "GSM2500467", "GSM2500468", "GSM2500469", "GSM2500470", "GSM2500471", "GSM2500472"], "sample_count": 124, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Fractalkine receptor CX3CR1 and leukocyte Ig-like receptor B2 LILRB2 are prognostic biomarkers in septic shock", "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:GSE13904 not downloaded", "asset:data:geo:GSE13904 licence not read", "asset:data:geo:GSE26378 not downloaded", "asset:data:geo:GSE26378 licence not read", "asset:data:geo:GSE26440 not downloaded", "asset:data:geo:GSE26440 licence not read", "asset:data:geo:GSE4607 not downloaded", "asset:data:geo:GSE4607 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE95233 not downloaded", "asset:data:geo:GSE95233 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this study, Limma and metaMA packages were executed for identification of the DEmRNAs."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "SVM"}}, {"id": "method-4", "family": "machine_learning", "specific": "decision_tree", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "decision tree"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE4607", "GSE13904", "GSE26378", "GSE26440", "GSE65682", "GSE95233"], "resolved_accessions": ["GSE4607", "GSE13904", "GSE26378", "GSE26440", "GSE65682", "GSE95233"], "statements": ["All data generated or analyzed during this study are included in this published article. The data sets (GSE4607, GSE13904, GSE26378, GSE26440, GSE65682 and GSE95233) analysed during the current study are available in the GEO (Gene Expression Omnibus) database, persistent accessible web link to database is https://www.ncbi.nlm.nih.gov/geo/."], "basis": "The paper names GSE4607, GSE13904, GSE26378, GSE26440, GSE65682, GSE95233 in GEO (Gene Expression Omnibus) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35045818", "data:geo:GSE13904"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13904"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:15:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14803, "completion_tokens": 2028, "cached_tokens": 256}}, "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:35045818", "type": "paper", "label": "pmid:35045818"}, {"id": "source:pmid:35045818", "type": "manuscript", "label": "PMID 35045818 full text"}, {"id": "data:geo:GSE13904", "type": "dataset", "label": "GEO GSE13904"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35045818", "type": "paper", "label": "pmid:35045818"}, {"id": "source:pmid:35045818", "type": "manuscript", "label": "PMID 35045818 full text"}, {"id": "data:geo:GSE13904", "type": "dataset", "label": "GEO GSE13904"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35045818", "type": "extraction", "used": ["source:pmid:35045818"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13904", "type": "accession_resolution", "used": ["data:geo:GSE13904"], "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:35045818", "parent_hash": "sha256:d13de1a2355cafe349b07a832ff79332051941f81088d35453a1974c75409609", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE13904 licence not read", "asset:data:geo:GSE13904 not downloaded", "asset:data:geo:GSE26378 licence not read", "asset:data:geo:GSE26378 not downloaded", "asset:data:geo:GSE26440 licence not read", "asset:data:geo:GSE26440 not downloaded", "asset:data:geo:GSE4607 licence not read", "asset:data:geo:GSE4607 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE95233 licence not read", "asset:data:geo:GSE95233 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["In this study, Limma and metaMA packages were executed for identification of the DEmRNAs."], "order_basis": "analysis_only", "id": "assay:1"}]}