Apelin (APLN) is a biomarker contributing to the diagnosis and prognosis of hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39227683", "kind": "science-record", "revision": 3, "content_hash": "sha256:d07e749aebaeeb43ff52687a1441371cbdc6c5ab4492f2be8ba8955029bc075a", "created_at": "2026-11-01T20:29:21Z", "updated_at": "2026-11-01T22:12:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Apelin (APLN) is a biomarker contributing to the diagnosis and prognosis of hepatocellular carcinoma.", "doi": "10.1038/s41598-024-71495-z", "pmid": "39227683", "authors": ["Xi Mao", "Xiaoya Zhu", "Tong Pan", "Zehui Liu", "Pingping Shangguan", "Yi Zhang", "Yingle Liu", "Xiwen Jiang", "Qi Zhang"], "journal": "Scientific reports", "year": 2024, "abstract": "Liver cancer, classified as a malignant hepatic tumor, can be divided into two categories: primary, originating within the liver, and secondary, resulting from metastasis to the liver from other organs. Hepatocellular carcinoma (HCC) is the main form of primary liver cancer and the third leading cause of cancer-related deaths. The diagnosis and prognosis of HCC using current methods still face numerous challenges. This study aims to develop novel diagnostic and prognostic models while identifying new biomarkers for improved HCC treatment. Diagnostic and prognostic models for HCC were constructed using traditional binary classification methods and machine learning algorithms based on the TCGA database (Downloaded in August 2023). The mechanisms by which APLN (Apelin) affects HCC were investigated using single-cell sequencing data sourced from the GEO database (GSE149614). The diagnostic models yielded by various algorithms could effectively distinguished HCC samples from normal ones. The prognostic model, composed of four genes, was constructed using LASSO and Cox regression algorithms, demonstrating good performance in predicting the three-year survival rate of HCC patients. The HCC biomarker Apelin (APLN) was identified in this study. APLN in liver cancer tissues mainly comes from endothelial cells and is associated with the carcinogenesis of these cells. APLN expression is significantly upregulated in liver cancer tissues, marking it as a viable indicator of endothelial cell malignancy in HCC. Furthermore, APLN expression was determined to be an independent predictor of tumor endothelial cell carcinogenesis, unaffected by its modifications such as single nucleotide variation, copy number variation, and methylation. Additionally, liver cancers characterized by high APLN expression are likely to progress rapidly after T2 stage. Our study presents diagnostic and prognostic models for HCC with appreciably improved accuracy and reliability compared to previous reports. APLN is a reliable HCC biomarker and contributes to the establishment of our models.", "claims": [{"id": "claim-method", "statement": "The prognostic model, composed of four genes, was constructed using LASSO and Cox regression algorithms, demonstrating good performance in predicting the three-year survival rate of HCC patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39227683", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The prognostic model, composed of four genes, was constructed using LASSO and Cox regression algorithms, demonstrating good performance in predicting the three-year survival rate of HCC patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39227683", "locator": "sections[27] \"Data availability\" paragraph 2", "quote": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:39227683"], "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:GSE102079"], "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:GSE102079"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39227683", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-71495-z", "sha256": "sha256:d0aab101cde1aef983a97182ac8bf9eb25a7d9de849384109138e6355551200c", "bytes": 52643, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-71495-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11371925", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102079", "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=GSE102079", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102079", "version": null, "note": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2723148", "GSM2723149", "GSM2723150", "GSM2723151", "GSM2723152", "GSM2723153", "GSM2723154", "GSM2723155", "GSM2723156", "GSM2723157", "GSM2723158", "GSM2723159", "GSM2723160", "GSM2723161", "GSM2723162", "GSM2723163", "GSM2723164", "GSM2723165", "GSM2723166", "GSM2723167", "GSM2723168", "GSM2723169", "GSM2723170", "GSM2723171", "GSM2723172", "GSM2723173", "GSM2723174", "GSM2723175", "GSM2723176", "GSM2723177", "GSM2723178", "GSM2723179", "GSM2723180", "GSM2723181", "GSM2723182", "GSM2723183", "GSM2723184", "GSM2723185", "GSM2723186", "GSM2723187", "GSM2723188", "GSM2723189", "GSM2723190", "GSM2723191", "GSM2723192", "GSM2723193", "GSM2723194", "GSM2723195", "GSM2723196", "GSM2723197", "GSM2723198", "GSM2723199", "GSM2723200", "GSM2723201", "GSM2723202", "GSM2723203", "GSM2723204", "GSM2723205", "GSM2723206", "GSM2723207", "GSM2723208", "GSM2723209", "GSM2723210", "GSM2723211", "GSM2723212", "GSM2723213", "GSM2723214", "GSM2723215", "GSM2723216", "GSM2723217", "GSM2723218", "GSM2723219", "GSM2723220", "GSM2723221", "GSM2723222", "GSM2723223", "GSM2723224", "GSM2723225", "GSM2723226", "GSM2723227", "GSM2723228", "GSM2723229", "GSM2723230", "GSM2723231", "GSM2723232", "GSM2723233", "GSM2723234", "GSM2723235", "GSM2723236", "GSM2723237", "GSM2723238", "GSM2723239", "GSM2723240", "GSM2723241", "GSM2723242", "GSM2723243", "GSM2723244", "GSM2723245", "GSM2723246", "GSM2723247", "GSM2723248", "GSM2723249", "GSM2723250", "GSM2723251", "GSM2723252", "GSM2723253", "GSM2723254", "GSM2723255", "GSM2723256", "GSM2723257", "GSM2723258", "GSM2723259", "GSM2723260", "GSM2723261", "GSM2723262", "GSM2723263", "GSM2723264", "GSM2723265", "GSM2723266", "GSM2723267", "GSM2723268", "GSM2723269", "GSM2723270", "GSM2723271", "GSM2723272", "GSM2723273", "GSM2723274", "GSM2723275", "GSM2723276", "GSM2723277", "GSM2723278", "GSM2723279", "GSM2723280", "GSM2723281", "GSM2723282", "GSM2723283", "GSM2723284", "GSM2723285", "GSM2723286", "GSM2723287", "GSM2723288", "GSM2723289", "GSM2723290", "GSM2723291", "GSM2723292", "GSM2723293", "GSM2723294", "GSM2723295", "GSM2723296", "GSM2723297", "GSM2723298", "GSM2723299", "GSM2723300", "GSM2723301", "GSM2723302", "GSM2723303", "GSM2723304", "GSM2723305", "GSM2723306", "GSM2723307", "GSM2723308", "GSM2723309", "GSM2723310", "GSM2723311", "GSM2723312", "GSM2723313", "GSM2723314", "GSM2723315", "GSM2723316", "GSM2723317", "GSM2723318", "GSM2723319", "GSM2723320", "GSM2723321", "GSM2723322", "GSM2723323", "GSM2723324", "GSM2723325", "GSM2723326", "GSM2723327", "GSM2723328", "GSM2723329", "GSM2723330", "GSM2723331", "GSM2723332", "GSM2723333", "GSM2723334", "GSM2723335", "GSM2723336", "GSM2723337", "GSM2723338", "GSM2723339", "GSM2723340", "GSM2723341", "GSM2723342", "GSM2723343", "GSM2723344", "GSM2723345", "GSM2723346", "GSM2723347", "GSM2723348", "GSM2723349", "GSM2723350", "GSM2723351", "GSM2723352", "GSM2723353", "GSM2723354", "GSM2723355", "GSM2723356", "GSM2723357", "GSM2723358", "GSM2723359", "GSM2723360", "GSM2723361", "GSM2723362", "GSM2723363", "GSM2723364", "GSM2723365", "GSM2723366", "GSM2723367", "GSM2723368", "GSM2723369", "GSM2723370", "GSM2723371", "GSM2723372", "GSM2723373", "GSM2723374", "GSM2723375", "GSM2723376", "GSM2723377", "GSM2723378", "GSM2723379", "GSM2723380", "GSM2723381", "GSM2723382", "GSM2723383", "GSM2723384", "GSM2723385", "GSM2723386", "GSM2723387", "GSM2723388", "GSM2723389", "GSM2723390", "GSM2723391", "GSM2723392", "GSM2723393", "GSM2723394", "GSM2723395", "GSM2723396", "GSM2723397", "GSM2723398", "GSM2723399", "GSM2723400", "GSM2723401", "GSM2723402", "GSM2723403", "GSM2723404"], "sample_count": 257, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "FABP4 overexpressed in intratumoral hepatic stellate cells within hepatocellular carcinoma with metabolic risk factors (part 1)", "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:GSE149614", "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=GSE149614", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE149614", "version": null, "note": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4505944", "GSM4505945", "GSM4505946", "GSM4505947", "GSM4505948", "GSM4505949", "GSM4505950", "GSM4505951", "GSM4505952", "GSM4505953", "GSM4505954", "GSM4505955", "GSM4505956", "GSM4505957", "GSM4505958", "GSM4505959", "GSM4505960", "GSM4505961", "GSM4505962", "GSM4505963", "GSM4505964"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "A Single-Cell Atlas of the Multicellular Ecosystem of Primary and Metastatic Hepatocellular Carcinoma", "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:GSE69715", "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=GSE69715", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE69715", "version": null, "note": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1707730", "GSM1707731", "GSM1707732", "GSM1707733", "GSM1707734", "GSM1707735", "GSM1707736", "GSM1707737", "GSM1707738", "GSM1707739", "GSM1707740", "GSM1707741", "GSM1707742", "GSM1707743", "GSM1707744", "GSM1707745", "GSM1707746", "GSM1707747", "GSM1707748", "GSM1707749", "GSM1707750", "GSM1707751", "GSM1707752", "GSM1707753", "GSM1707754", "GSM1707755", "GSM1707756", "GSM1707757", "GSM1707758", "GSM1707759", "GSM1707760", "GSM1707761", "GSM1707762", "GSM1707763", "GSM1707764", "GSM1707765", "GSM1707766", "GSM1707767", "GSM1707768", "GSM1707769", "GSM1707770", "GSM1707771", "GSM1707772", "GSM1707773", "GSM1707774", "GSM1707775", "GSM1707776", "GSM1707777", "GSM1707778", "GSM1707779", "GSM1707780", "GSM1707781", "GSM1707782", "GSM1707783", "GSM1707784", "GSM1707785", "GSM1707786", "GSM1707787", "GSM1707788", "GSM1707789", "GSM1707790", "GSM1707791", "GSM1707792", "GSM1707793", "GSM1707794", "GSM1707795", "GSM1707796", "GSM1707797", "GSM1707798", "GSM1707799", "GSM1707800", "GSM1707801", "GSM1707802", "GSM1707803", "GSM1707804", "GSM1707805", "GSM1707806", "GSM1707807", "GSM1707808", "GSM1707809", "GSM1707810", "GSM1707811", "GSM1707812", "GSM1707813", "GSM1707814", "GSM1707815", "GSM1707816", "GSM1707817", "GSM1707818", "GSM1707819", "GSM1707820", "GSM1707821", "GSM1707822", "GSM1707823", "GSM1707824", "GSM1707825", "GSM1707826", "GSM1707827", "GSM1707828", "GSM1707829", "GSM1707830", "GSM1707831", "GSM1707832"], "sample_count": 103, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Infection with Hepatitis C Virus Depends on TACSTD2, a Regulator of Claudin-1 and Occludin Highly Downregulated in Hepatocellular Carcinoma [patient]", "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:GSE76427", "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=GSE76427", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76427", "version": null, "note": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2011285", "GSM2011286", "GSM2011287", "GSM2011288", "GSM2011289", "GSM2011290", "GSM2011291", "GSM2011292", "GSM2011293", "GSM2011294", "GSM2011295", "GSM2011296", "GSM2011297", "GSM2011298", "GSM2011299", "GSM2011300", "GSM2011301", "GSM2011302", "GSM2011303", "GSM2011304", "GSM2011305", "GSM2011306", "GSM2011307", "GSM2011308", "GSM2011309", "GSM2011310", "GSM2011311", "GSM2011312", "GSM2011313", "GSM2011314", "GSM2011315", "GSM2011316", "GSM2011317", "GSM2011318", "GSM2011319", "GSM2011320", "GSM2011321", "GSM2011322", "GSM2011323", "GSM2011324", "GSM2011325", "GSM2011326", "GSM2011327", "GSM2011328", "GSM2011329", "GSM2011330", "GSM2011331", "GSM2011332", "GSM2011333", "GSM2011334", "GSM2011335", "GSM2011336", "GSM2011337", "GSM2011338", "GSM2011339", "GSM2011340", "GSM2011341", "GSM2011342", "GSM2011343", "GSM2011344", "GSM2011345", "GSM2011346", "GSM2011347", "GSM2011348", "GSM2011349", "GSM2011350", "GSM2011351", "GSM2011352", "GSM2011353", "GSM2011354", "GSM2011355", "GSM2011356", "GSM2011357", "GSM2011358", "GSM2011359", "GSM2011360", "GSM2011361", "GSM2011362", "GSM2011363", "GSM2011364", "GSM2011365", "GSM2011366", "GSM2011367", "GSM2011368", "GSM2011369", "GSM2011370", "GSM2011371", "GSM2011372", "GSM2011373", "GSM2011374", "GSM2011375", "GSM2011376", "GSM2011377", "GSM2011378", "GSM2011379", "GSM2011380", "GSM2011381", "GSM2011382", "GSM2011383", "GSM2011384", "GSM2011385", "GSM2011386", "GSM2011387", "GSM2011388", "GSM2011389", "GSM2011390", "GSM2011391", "GSM2011392", "GSM2011393", "GSM2011394", "GSM2011395", "GSM2011396", "GSM2011397", "GSM2011398", "GSM2011399", "GSM2011400", "GSM2011401", "GSM2011402", "GSM2011403", "GSM2011404", "GSM2011405", "GSM2011406", "GSM2011407", "GSM2011408", "GSM2011409", "GSM2011410", "GSM2011411", "GSM2011412", "GSM2011413", "GSM2011414", "GSM2011415", "GSM2011416", "GSM2011417", "GSM2011418", "GSM2011419", "GSM2011420", "GSM2011421", "GSM2011422", "GSM2011423", "GSM2011424", "GSM2011425", "GSM2011426", "GSM2011427", "GSM2011428", "GSM2011429", "GSM2011430", "GSM2011431", "GSM2011432", "GSM2011433", "GSM2011434", "GSM2011435", "GSM2011436", "GSM2011437", "GSM2011438", "GSM2011439", "GSM2011440", "GSM2011441", "GSM2011442", "GSM2011443", "GSM2011444", "GSM2011445", "GSM2011446", "GSM2011447", "GSM2011448", "GSM2011449", "GSM2011450", "GSM2011451"], "sample_count": 167, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Microarray expression data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients", "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:GSE102079 not downloaded", "asset:data:geo:GSE102079 licence not read", "asset:data:geo:GSE149614 not downloaded", "asset:data:geo:GSE149614 licence not read", "asset:data:geo:GSE69715 not downloaded", "asset:data:geo:GSE69715 licence not read", "asset:data:geo:GSE76427 not downloaded", "asset:data:geo:GSE76427 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The prognostic model, composed of four genes, was constructed using LASSO and Cox regression algorithms, demonstrating good performance in predicting the three-year survival rate of HCC patients."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Principal Component Analysis"}}, {"id": "method-3", "family": "differential_expression", "specific": "deseq2", "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": 0.8, "band": "high", "quote": "DESeq2"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}], "targets": [], "gaps": []}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE149614", "GSE69715", "GSE102079", "GSE76427"], "resolved_accessions": ["GSE149614", "GSE69715", "GSE102079", "GSE76427"], "statements": ["All the original data were acquired from public databases such as The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO, RRID:SCR_005012). Further information is available from the corresponding author upon request."], "basis": "The paper names GSE149614, GSE69715, GSE102079, GSE76427 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:39227683", "data:geo:GSE102079"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102079"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:30:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13931, "completion_tokens": 2335, "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:39227683", "type": "paper", "label": "pmid:39227683"}, {"id": "source:pmid:39227683", "type": "manuscript", "label": "PMID 39227683 full text"}, {"id": "data:geo:GSE102079", "type": "dataset", "label": "GEO GSE102079"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39227683", "type": "paper", "label": "pmid:39227683"}, {"id": "source:pmid:39227683", "type": "manuscript", "label": "PMID 39227683 full text"}, {"id": "data:geo:GSE102079", "type": "dataset", "label": "GEO GSE102079"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39227683", "type": "extraction", "used": ["source:pmid:39227683"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102079", "type": "accession_resolution", "used": ["data:geo:GSE102079"], "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:39227683", "parent_hash": "sha256:dd0cb831aa39dd2607a0df83271bc5120f8615a39c82de52ec13cecaa5727269", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE102079 licence not read", "asset:data:geo:GSE102079 not downloaded", "asset:data:geo:GSE149614 licence not read", "asset:data:geo:GSE149614 not downloaded", "asset:data:geo:GSE69715 licence not read", "asset:data:geo:GSE69715 not downloaded", "asset:data:geo:GSE76427 licence not read", "asset:data:geo:GSE76427 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The prognostic model, composed of four genes, was constructed using LASSO and Cox regression algorithms, demonstrating good performance in predicting the three-year survival rate of HCC patients."], "order_basis": "analysis_only", "id": "assay:1"}]}