← All .science files
pmid:31907669
Systems biology approaches toward autosomal dominant polycystic kidney disease (ADPKD).
Ilnaz Rahimmanesh · Razieh Fatehi
Clinical and translational medicine · 2020 doi:10.1186/s40169-019-0254-5
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 · 2 items
claims array · 2 items
[0] 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 · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 21 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 25 items
[0] array · 8 items
[1] array · 5 items
[2] array · 8 items
[3] array · 5 items
[4] array · 8 items
[5] array · 8 items
[6] array · 8 items
[7] array · 8 items
[8] array · 8 items
[9] array · 8 items
[10] array · 8 items
[11] array · 8 items
[12] array · 8 items
[13] array · 8 items
[14] array · 8 items
[15] array · 8 items
[16] array · 8 items
[17] array · 5 items
[18] array · 8 items
[19] array · 8 items
[20] array · 8 items
[21] array · 8 items
[22] array · 8 items
[23] array · 8 items
[24] array · 8 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 16 items
[0] array · 3 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
gaps array · 2 items
analysis object · 4 fields
methods array · 4 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 · 1 item
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 · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
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 · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 4 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 · 7 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] 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:31907669", "kind": "science-record", "revision": 5, "content_hash": "sha256:54453967e777786731605dbbd63a11527272caaa7adf87157663f02678ce1c89", "created_at": "2026-11-01T15:40:54Z", "updated_at": "2026-11-01T22:01:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Systems biology approaches toward autosomal dominant polycystic kidney disease (ADPKD).", "doi": "10.1186/s40169-019-0254-5", "pmid": "31907669", "authors": ["Ilnaz Rahimmanesh", "Razieh Fatehi"], "journal": "Clinical and translational medicine", "year": 2020, "abstract": "BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD), a common of monogenetic disorder caused by the polycystic kidney disease-1 (PKD1) or PKD2 genes deficiency. In this study, we have re-analyzed a microarray dataset to generate a holistic view of this disease.\nMETHODOLOGY: GSE7869, an expression profiling dataset was downloaded from the Gene Expression Omnibus (GEO) database. After quality control assessment, using GEO2R tool of GEO, genes with adjusted p-value ≤ 0.05 were determined as differentially expressed (DE). The expression profiles from ADPKD samples in different sizes were compared. Using CluePedia plugin of Cytoscape software, the protein-protein interaction (PPI) networks were constructed and analyzed by Cytoscape NetworkAnalyzer tool and MCODE application. Pathway enrichment analysis of clustered genes by MCODE with the high centrality parameters in PPI networks was performed using Cytoscape ClueGO plugin. Moreover, by Enrichr database, microRNAs (miRNAs) and transcription factors (TFs) targeted DE genes were identified.\nRESULTS: In this study to explore the molecular pathogenesis of kidney in ADPKD, mRNA expression profiles of cysts from patients in different sizes were re-analyzed. The comparisons were performed between normal with minimally cystic tissue (MCT) samples, MCTs with small cysts, and small cysts with large cysts. 512, 7024, and 655 DE genes were determined, respectively. The top central genes, e.g. END1, EGFR, and FOXO1 were identified with topology and clustering analysis. DE genes that were significantly enriched in PPI networks are critical genes and their roles in ADPKD remain to be assessed in future experimental studies beside miRNAs and TFs predicted. Furthermore, the functional analysis resulted in which most of them are expected to be associated with ADPKD pathogenesis, such as signal pathways that involved in cell growth, inflammation, and cell polarity.\nCONCLUSION: We have here explored systematic approaches for molecular mechanisms assay of ADPKD as a monogenic disease, which may also be used for other monogenetic diseases beside complex diseases to provide suitable therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Samples of normal tissues (n = 3), minimally cystic tissues (n = 5), small cysts (n = 5), and large cysts (n = 3) were compared based on during the time of disease progression, using Student’s t-test, respectively. Benjamini–Hochberg false discovery rate (FDR) was used for p-value correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31907669", "locator": "sections[3] \"Microarray data and DE genes screening\" paragraph 2", "quote": "Samples of normal tissues (n = 3), minimally cystic tissues (n = 5), small cysts (n = 5), and large cysts (n = 3) were compared based on during the time of disease progression, using Student’s t-test, respectively. Benjamini–Hochberg false discovery rate (FDR) was used for p-value correction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data analyzed during this study are included in article and its additional files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31907669", "locator": "sections[22] \"notes\" paragraph 1", "quote": "All data analyzed during this study are included in article and its additional files."}], "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:31907669"], "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:GSE7869"], "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:GSE7869"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31907669", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40169-019-0254-5", "sha256": "sha256:f94cb8bbe69b3fd389df15b6c7748b791c712f7338b9527e72f5d28f053d68b2", "bytes": 18889, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40169-019-0254-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6944722", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE7869", "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=GSE7869", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7869", "version": null, "note": "All data analyzed during this study are included in article and its additional files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data analyzed during this study are included in article and its additional files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM190858", "GSM190859", "GSM190860", "GSM190861", "GSM190862", "GSM190863", "GSM190864", "GSM190865", "GSM190866", "GSM190867", "GSM190868", "GSM190869", "GSM190870", "GSM190871", "GSM190872", "GSM190873", "GSM190874", "GSM190875", "GSM190876", "GSM190877", "GSM190878"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from renal cysts of autosomal dominant polycystic kidney disease (ADPKD) patients", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31907669:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:815bde657980debec3a4eeb9de15c372a342c52e1cdbb75358b0a8f788134dc6", "bytes": 2010, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab1", "version": null, "note": "Top clustered genes in the PPI networks. The seed genes with the highest density in PP networks are shown", "structure": {"pmcid": "PMC6944722", "section_index": 9, "section_title": "Protein–protein interaction networks were constructed", "row_count": 25, "column_count": 8}, "table": {"label": "Table 1", "caption": "Top clustered genes in the PPI networks. The seed genes with the highest density in PP networks are shown", "rows": [["GOID", "Betweenness centrality", "Closeness centrality", "Degree", "GOID", "Betweenness centrality", "Closeness centrality", "Degree"], ["Normal vs. MCT", "HSF1", "0.002468", "0.285681", "17"], ["EDN1", "0.412698", "0.313043", "3", "NRCAM", "0.001105", "0.25658", "13"], ["MCT vs. SC", "PRMT5", "0.000581", "0.296164", "17"], ["EGFR", "0.017832", "0.371711", "149", "POLR3C", "3.92E-05", "0.265655", "17"], ["RPL35", "5.85E-05", "0.30435847", "73", "SEMA3A", "3.9E-05", "0.28154", "16"], ["COPA", "0.00661", "0.299735", "54", "TAF9B", "0.00086", "0.274302", "15"], ["PMF1", "1.41E-05", "0.309089", "49", "PIAS4", "0.000677", "0.299916", "15"], ["ARF6", "0.006571", "0.317375", "45", "THRB", "0.000456", "0.312586", "13"], ["FBXW11", "0.002383", "0.324162", "44", "DCAF7", "0.000292", "0.276992", "12"], ["SMURF2", "0.003544", "0.323445", "40", "EIF1", "1.64E-05", "0.240752", "12"], ["WWTR1", "0.004166", "0.318269", "35", "GSN", "0.004329", "0.284374", "11"], ["CACNB2", "0.001283", "0.313691", "34", "OCLN", "0.001005", "0.269397", "11"], ["TBL1X", "0.001139", "0.317051", "33", "AES", "7.63E-05", "0.308475", "11"], ["CUL3", "0.001145", "0.302286", "28", "ATP6", "3.7E-07", "0.186567", "11"], ["RPP30", "0.000402", "0.250681", "28", "ALDOA", "0.001615", "0.264891", "4"], ["AP1M2", "5.86E-05", "0.281063", "26", "HSD17B8", "0.666667", "1", "3"], ["TGFB2", "0.002654", "0.314127", "25", "SC vs. LC"], ["PHAX", "0.000336", "0.294655", "23", "NCBP1", "0.153881", "0.26259", "17"], ["FABP4", "0.000212", "0.297939", "23", "KDELR2", "0.01875", "0.533333", "7"], ["SEC23A", "0.001501", "0.258339", "22", "FOXO1", "0.152968", "0.264493", "5"], ["CXCL9", "6.9E-05", "0.269514", "21", "EDN1", "0.121988", "0.302905", "7"], ["ND2", "5E-05", "0.215126", "21", "PSMA5", "0.066667", "0.769231", "7"], ["CTF1", "0.000322", "0.267398", "19", "ITGB5", "0.134354", "0.25", "5"], ["CITED2", "9.8E-05", "0.289845", "19", "PPIE", "0.105023", "0.216617", "7"]], "row_count": 25, "column_count": 8, "numeric_cells": 140, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31907669:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3bddb4e3abe868ecdd21eb762e7de80baaf1bfe0ce4805058acf868f5f05a327", "bytes": 762, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab2", "version": null, "note": "Transcription factor enrichment analysis", "structure": {"pmcid": "PMC6944722", "section_index": 11, "section_title": "miRNAs and TFs enriched with DE gene were determined", "row_count": 16, "column_count": 5}, "table": {"label": "Table 2", "caption": "Transcription factor enrichment analysis", "rows": [["Normal vs. MCT", "MCT vs. SC", "SC vs. LC"], ["HNF4A", "CLOCK", "ESR1", "BRD4", "VDR"], ["ESR1", "ZNF217", "TCF21", "NERF2", "AR"], ["RXR", "NUCKS1", "ESR2", "CEBPD", "PPARG"], ["", "RELA", "NR1H3", "TOP2B", "KDM5B"], ["", "WT1", "OLIG2", "SMARCA4", "TP53"], ["", "PAX3-FKHR", "SOX9", "STAT3", "MYB"], ["", "CEBPD", "FOXA1", "TP63", "KDM5A"], ["", "SMARCA4", "AR", "EBF1", "EKLF"], ["", "FOXA2", "KLF4", "PAX3-FKHR", "FOXA1"], ["", "PRDM5", "MYB", "SOX2", "CEBPB"], ["", "SOX2", "CTNNB1", "ZNF217", "PCGF2"], ["", "HNF4A", "KLF6", "NFE2L2", ""], ["", "NFE2L2", "P300", "NRF2", ""], ["", "NRF2", "VDR", "SMAD4", ""], ["", "SMAD4", "", "HNF4A", ""]], "row_count": 16, "column_count": 5, "numeric_cells": 6, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE7869 not downloaded", "asset:data:geo:GSE7869 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": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Pathway enrichment"}}, {"id": "method-3", "family": "network_analysis", "specific": "centrality", "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": "centrality"}}, {"id": "method-4", "family": null, "specific": null, "label": "Student’s t-test with Benjamini–Hochberg false discovery rate correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Samples of normal tissues (n = 3), minimally cystic tissues (n = 5), small cysts (n = 5), and large cysts (n = 3) were compared based on during the time of disease progression, using Student’s t-test, respectively. Benjamini–Hochberg false discovery rate (FDR) was used for p-value correction."}}], "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": ["GSE7869"], "resolved_accessions": ["GSE7869"], "statements": ["All data analyzed during this study are included in article and its additional files."], "basis": "The paper names GSE7869 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:31907669", "data:geo:GSE7869", "asset:table:pmid:31907669:1", "asset:table:pmid:31907669:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE7869"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 16016, "completion_tokens": 1054, "cached_tokens": 792}}, "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:31907669", "type": "paper", "label": "pmid:31907669"}, {"id": "source:pmid:31907669", "type": "manuscript", "label": "PMID 31907669 full text"}, {"id": "data:geo:GSE7869", "type": "dataset", "label": "GEO GSE7869"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31907669", "type": "paper", "label": "pmid:31907669"}, {"id": "source:pmid:31907669", "type": "manuscript", "label": "PMID 31907669 full text"}, {"id": "data:geo:GSE7869", "type": "dataset", "label": "GEO GSE7869"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31907669", "type": "extraction", "used": ["source:pmid:31907669"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE7869", "type": "accession_resolution", "used": ["data:geo:GSE7869"], "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:31907669", "parent_hash": "sha256:9735d170127fec87b6c5089b06458ad7b45fbdf763ddd5d0c4dc13dccbb39971", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE7869 licence not read", "asset:data:geo:GSE7869 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ciency. In this study, we have re-analyzed a microarray dataset to generate a holistic view of this"], "order_basis": "paper_text_order:254", "id": "assay:1"}, {"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": "consumes_earlier_output", "id": "assay:2"}]}