Bioinformatics analysis identifies immune-related gene signatures and subtypes in diabetic nephropathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36568106", "kind": "science-record", "revision": 3, "content_hash": "sha256:7a0c5e574498cfd5834867ef64646cf49aa1e9e7ad0679df9e7022818ceaba86", "created_at": "2026-11-01T19:01:07Z", "updated_at": "2026-11-01T22:08:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis identifies immune-related gene signatures and subtypes in diabetic nephropathy.", "doi": "10.3389/fendo.2022.1048139", "pmid": "36568106", "authors": ["Kunna Lu", "Li Wang", "Yan Fu", "Guanghong Li", "Xinhuan Zhang", "Mingfeng Cao"], "journal": "Frontiers in endocrinology", "year": 2022, "abstract": "Background: Systemic inflammation and immune response are involved in the pathogenesis of diabetic nephropathy (DN). However, the specific immune-associated signature during DN development is unclear. Our study aimed to reveal the roles of immune-related genes during DN progression.\nMethods: The GSE30529 and GSE30528 datasets were acquired from the Gene Expression Omnibus (GEO) database. Then, the intersection between differentially expressed genes (DEGs) and immune score-related genes (ISRGs) was screened. Subsequently, functional enrichment analyses were performed. The different immune phenotype-related subgroups were finally divided using unsupervised clustering. The core genes were identified by WGCNA and the protein-protein interaction (PPI) network. xCell algorithm was applied to assess the proportion of immune cell infiltration.\nResults: 92 immune score-related DEGs (ISRDEGs) were identified, and these genes were enriched in inflammation- and immune-associated pathways. Furthermore, two distinct immune-associated subgroups (C1 and C2) were identified, and the C1 subgroup exhibited activated immune pathways and a higher percentage of immune cells compared to the C2 subgroup. Two core genes (LCK and HCK) were identified and all up-regulated in DN, and the expressions were verified using GSE30122, GSE142025, and GSE104954 datasets. GSEA indicated the core genes were mainly enriched in immune-related pathways. Correlation analysis indicated LCK and HCK expressions were positively correlated with aDC, CD4+ Tem, CD8+T cells, CD8+ Tem, and mast cells.\nConclusions: We identified two immune-related genes and two immune-associated subgroups, which might help to design more precise tailored immunotherapy for DN patients.", "claims": [{"id": "claim-method", "statement": "WGCNA was used to establish potential modules associated with different subgroups of DN samples (29).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36568106", "locator": "sections[6] \"Weighted gene coexpression network analysis\" paragraph 2", "quote": "WGCNA was used to establish potential modules associated with different subgroups of DN samples (29)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36568106", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper identified LCK and HCK as two immune-related core genes that were up-regulated in diabetic nephropathy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36568106", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Two core genes (LCK and HCK) were identified and all up-regulated in DN, and the expressions were verified using GSE30122, GSE142025, and GSE104954 datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper identified LCK and HCK as two immune-related core genes that were up-regulated in diabetic nephropathy.", "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:36568106"], "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:GSE104954"], "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:GSE104954"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36568106", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2022.1048139", "sha256": "sha256:6f2e60f6626be02ed095a714f93ce16969956d4c74f1d7264891af3575570b13", "bytes": 31138, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2022.1048139", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9768367", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE104954", "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=GSE104954", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE104954", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2810894", "GSM2810895", "GSM2810896", "GSM2810897", "GSM2810898", "GSM2810899", "GSM2810900", "GSM2810901", "GSM2810902", "GSM2810903", "GSM2810904", "GSM2810905", "GSM2810906", "GSM2810907", "GSM2810908", "GSM2810909", "GSM2810910", "GSM2810911", "GSM2810912", "GSM2810913", "GSM2810914", "GSM2810915", "GSM2810916", "GSM2810917", "GSM2810918", "GSM2810919", "GSM2810920", "GSM2810921", "GSM2810922", "GSM2810923", "GSM2810924", "GSM2810925", "GSM2810926", "GSM2810927", "GSM2810928", "GSM2810929", "GSM2810930", "GSM2810931", "GSM2810932", "GSM2810933", "GSM2810934", "GSM2810935", "GSM2810936", "GSM2810937", "GSM2810938", "GSM2810939", "GSM2810940", "GSM2810941", "GSM2810942", "GSM2810943", "GSM2810944", "GSM2810945", "GSM2810946", "GSM2810947", "GSM2810948", "GSM2810949", "GSM2810950", "GSM2810951", "GSM2810952", "GSM2810953", "GSM2810954", "GSM2810955", "GSM2810956", "GSM2810957", "GSM2810958", "GSM2810959", "GSM2810960", "GSM2810961", "GSM2810962", "GSM2810963", "GSM2810964", "GSM2810965", "GSM2810966", "GSM2810967", "GSM2810968", "GSM2810969", "GSM2810970", "GSM2810971", "GSM2810972", "GSM2810973", "GSM2810974", "GSM2810975", "GSM2810976", "GSM2810977", "GSM2810978", "GSM2810979", "GSM2810980", "GSM2810981", "GSM2810982", "GSM2810983", "GSM2810984", "GSM2810985", "GSM2810986", "GSM2810987", "GSM2810988", "GSM2810989", "GSM2810990", "GSM2810991", "GSM2810992", "GSM2810993", "GSM2810994", "GSM2810995", "GSM2810996", "GSM2810997", "GSM2810998", "GSM2810999", "GSM2811000", "GSM2811001", "GSM2811002", "GSM2811003", "GSM2811004", "GSM2811005", "GSM2811006", "GSM2811007", "GSM2811008", "GSM2811009", "GSM2811010", "GSM2811011", "GSM2811012", "GSM2811013", "GSM2811014", "GSM2811015", "GSM2811016", "GSM2811017", "GSM2811018", "GSM2811019", "GSM2811020", "GSM2811021", "GSM2811022", "GSM2811023", "GSM2811024", "GSM2811025", "GSM2811026", "GSM2811027", "GSM2811028", "GSM2811029", "GSM2811030", "GSM2811031", "GSM2811032", "GSM2811033", "GSM2811034", "GSM2811035", "GSM2811036", "GSM2811037", "GSM2811038", "GSM2811039", "GSM2811040", "GSM2811041", "GSM2811042", "GSM2811043", "GSM2811044", "GSM2811045", "GSM2811046", "GSM2811047", "GSM2811048", "GSM2811049", "GSM2811050", "GSM2811051", "GSM2811052", "GSM2811053", "GSM2811054", "GSM2811055", "GSM2811056", "GSM2811057", "GSM2811058", "GSM2811059", "GSM2811060", "GSM2811061", "GSM2811062", "GSM2811063", "GSM2811064", "GSM2811065", "GSM2811066", "GSM2811067", "GSM2811068", "GSM2811069", "GSM2811070", "GSM2811071", "GSM2811072", "GSM2811073", "GSM2811074", "GSM2811075", "GSM2811076", "GSM2811077", "GSM2811078", "GSM2811079", "GSM2811080", "GSM2811081", "GSM2811082", "GSM2811083", "GSM2811084", "GSM2811085", "GSM2811086", "GSM2811087", "GSM2811088"], "sample_count": 195, "group_sizes": null, "group_sizes_basis": null, "platform": "22945;24120", "taxon": "Homo sapiens", "title": "Tubulointerstitial transcriptome from ERCB subjects with chronic kidney disease and living donor biopsies.", "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:GSE142025", "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=GSE142025", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE142025", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4217781", "GSM4217782", "GSM4217783", "GSM4217784", "GSM4217785", "GSM4217786", "GSM4217787", "GSM4217788", "GSM4217789", "GSM4217790", "GSM4217791", "GSM4217792", "GSM4217793", "GSM4217794", "GSM4217795", "GSM4217796", "GSM4217797", "GSM4217798", "GSM4217799", "GSM4217800", "GSM4217801", "GSM4217802", "GSM4217803", "GSM4217804", "GSM4217805", "GSM4217806", "GSM4217807", "GSM4217808", "GSM4217809", "GSM4217810", "GSM4217811", "GSM4217812", "GSM4217813", "GSM4217814", "GSM4217815", "GSM4217816"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Comparison of Kidney Transcriptomic Profiles of Early and Advanced Diabetic Nephropathy Reveals Potential New Mechanisms for Disease Progression", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE30122", "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=GSE30122", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30122", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM756992", "GSM756993", "GSM756994", "GSM756995", "GSM756996", "GSM756997", "GSM756998", "GSM756999", "GSM757000", "GSM757001", "GSM757002", "GSM757003", "GSM757004", "GSM757005", "GSM757006", "GSM757007", "GSM757008", "GSM757009", "GSM757010", "GSM757011", "GSM757012", "GSM757013", "GSM757014", "GSM757015", "GSM757016", "GSM757017", "GSM757018", "GSM757019", "GSM757020", "GSM757021", "GSM757022", "GSM757023", "GSM757024", "GSM757025", "GSM757026", "GSM757027", "GSM757028", "GSM757029", "GSM757030", "GSM757031", "GSM757032", "GSM757033", "GSM757034", "GSM757035", "GSM758485", "GSM758486", "GSM758487", "GSM758488", "GSM758489", "GSM758490", "GSM758491", "GSM758492", "GSM758493", "GSM758494", "GSM758495", "GSM758496", "GSM758497", "GSM758498", "GSM758499", "GSM758500", "GSM758501", "GSM758502", "GSM758503", "GSM758504", "GSM758505", "GSM758506", "GSM758507", "GSM758508", "GSM758509"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome Analysis of Human Diabetic Kidney Disease", "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:GSE30528", "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=GSE30528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30528", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM756992", "GSM756993", "GSM756994", "GSM756995", "GSM756996", "GSM756997", "GSM756998", "GSM756999", "GSM757000", "GSM757001", "GSM757002", "GSM757003", "GSM757004", "GSM757005", "GSM757006", "GSM757007", "GSM757008", "GSM757009", "GSM757010", "GSM757011", "GSM757012", "GSM757013"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Glomeruli vs. Control Glomeruli)", "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:GSE30529", "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=GSE30529", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30529", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM757014", "GSM757015", "GSM757016", "GSM757017", "GSM757018", "GSM757019", "GSM757020", "GSM757021", "GSM757022", "GSM757023", "GSM757024", "GSM757025", "GSM757026", "GSM757027", "GSM757028", "GSM757029", "GSM757030", "GSM757031", "GSM757032", "GSM757033", "GSM757034", "GSM757035"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Tubuli vs. Control Tubuli)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE104954 not downloaded", "asset:data:geo:GSE104954 licence not read", "asset:data:geo:GSE142025 not downloaded", "asset:data:geo:GSE142025 licence not read", "asset:data:geo:GSE30122 not downloaded", "asset:data:geo:GSE30122 licence not read", "asset:data:geo:GSE30528 not downloaded", "asset:data:geo:GSE30528 licence not read", "asset:data:geo:GSE30529 not downloaded", "asset:data:geo:GSE30529 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "Weighted gene coexpression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "WGCNA was used to establish potential modules associated with different subgroups of DN samples (29)."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE30529", "GSE30528", "GSE104954", "GSE142025", "GSE30122"], "resolved_accessions": ["GSE30529", "GSE30528", "GSE104954", "GSE142025", "GSE30122"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE30529, GSE30528, GSE104954, GSE142025, GSE30122 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:36568106", "data:geo:GSE104954"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE104954"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:21:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9101, "completion_tokens": 2098, "cached_tokens": 128}}, "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:36568106", "type": "paper", "label": "pmid:36568106"}, {"id": "source:pmid:36568106", "type": "manuscript", "label": "PMID 36568106 full text"}, {"id": "data:geo:GSE104954", "type": "dataset", "label": "GEO GSE104954"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36568106", "type": "paper", "label": "pmid:36568106"}, {"id": "source:pmid:36568106", "type": "manuscript", "label": "PMID 36568106 full text"}, {"id": "data:geo:GSE104954", "type": "dataset", "label": "GEO GSE104954"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36568106", "type": "extraction", "used": ["source:pmid:36568106"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE104954", "type": "accession_resolution", "used": ["data:geo:GSE104954"], "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:36568106", "parent_hash": "sha256:8814384ed906439f8dd22f84b0756dd783a15a262b4c0fb9363244ae5eb4d0da", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE104954 licence not read", "asset:data:geo:GSE104954 not downloaded", "asset:data:geo:GSE142025 licence not read", "asset:data:geo:GSE142025 not downloaded", "asset:data:geo:GSE30122 licence not read", "asset:data:geo:GSE30122 not downloaded", "asset:data:geo:GSE30528 licence not read", "asset:data:geo:GSE30528 not downloaded", "asset:data:geo:GSE30529 licence not read", "asset:data:geo:GSE30529 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}