Identification of microRNA Signature and Key Genes Between Adenoma and Adenocarcinomas Using Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34511938", "kind": "science-record", "revision": 6, "content_hash": "sha256:c1fc3d249cc8d95a3b799f911dcf302c7663e5fc55e4e472f62096b2fe7cc5d7", "created_at": "2026-11-01T15:41:51Z", "updated_at": "2026-11-01T21:26:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of microRNA Signature and Key Genes Between Adenoma and Adenocarcinomas Using Bioinformatics Analysis.", "doi": "10.2147/OTT.S320469", "pmid": "34511938", "authors": ["Xinya Shi", "Guang Yu Gao", "Jiaofeng Shen"], "journal": "OncoTargets and therapy", "year": 2021, "abstract": "BACKGROUND: In worldwide, colorectal cancer (CRC) is very common and the mechanisms remain unclear. This study aims to identify between adenomas with epithelial dislocation (false invasion) and adenomas with early adenocarcinoma (true invasion).\nMETHODS: GSE41655 and GSE57965 datasets were obtained in the Gene Expression Omnibus (GEO) database. microRNA expression profiles and clinicopathological data from the TCGA (The Cancer Genome Atlas) database were downloaded to further validate the results in GEO. GEO software and the GEO2R calculation method were used to analyze two gene profiles. The co-expression of differentially expressed microRNAs (DEMs) and genes (DEGs) were identified and searched in the FunRich databases for pathway and ontology analysis. Cytoscape was utilized to construct the mRNA-microRNA network. Validation of gene expression levels was conducted by online databases and qRT-PCR and IHC experiments.\nRESULTS: In total, 6 DEMs and 34 DEGs are selected after calculating. KEGG results indicated that genes are enriched in certain tumor associated pathways. Four out of 6 microRNAs had a significant relationship with the overall survival (P < 0.05) and showed a good performance in predicting the survival risk of patients with colorectal carcinoma. Furthermore, expression levels of hsa-miR-455 and hsa-miR-125a were then verified by qRT-PCR which all target BCL2L12. IHC results showed that the expression level of BCL2L12 was higher in adenocarcinoma than in adenoma. Based on the selected gene, the top 10 small molecules were screened out as potential drugs.\nCONCLUSION: By using microarray and bioinformatics analyses, DEMs and DEGs were selected and a complete gene network was constructed. To our knowledge, BCL2L12 and related molecules including hsa-miR-455 and hsa-miR-125a were firstly identified as potential biomarkers in the progression from adenoma to adenocarcinoma.", "claims": [{"id": "claim-method", "statement": "GEO2R, an R-associated web application, was applied to filtrate DEMs between adenoma samples and adenocarcinoma samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34511938", "locator": "sections[4] \"DEMs Analysis\" paragraph 2", "quote": "GEO2R, an R-associated web application, was applied to filtrate DEMs between adenoma samples and adenocarcinoma samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34511938", "locator": "sections[22] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable 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:34511938"], "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:GSE41655"], "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:GSE41655"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34511938", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S320469", "sha256": "sha256:fc1cb4adf835484e08aa68e587a959de9143cafc58ede193e1253c4bb1529a5c", "bytes": 41291, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S320469", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8427077", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE41655", "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=GSE41655", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41655", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1021014", "GSM1021015", "GSM1021016", "GSM1021017", "GSM1021018", "GSM1021019", "GSM1021020", "GSM1021021", "GSM1021022", "GSM1021023", "GSM1021024", "GSM1021025", "GSM1021026", "GSM1021027", "GSM1021028", "GSM1021029", "GSM1021030", "GSM1021031", "GSM1021032", "GSM1021033", "GSM1021034", "GSM1021035", "GSM1021036", "GSM1021037", "GSM1021038", "GSM1021039", "GSM1021040", "GSM1021041", "GSM1021042", "GSM1021043", "GSM1021044", "GSM1021045", "GSM1021046", "GSM1021047", "GSM1021048", "GSM1021049", "GSM1021050", "GSM1021051", "GSM1021052", "GSM1021053", "GSM1021054", "GSM1021055", "GSM1021056", "GSM1021057", "GSM1021058", "GSM1021059", "GSM1021060", "GSM1021061", "GSM1021062", "GSM1021063", "GSM1021064", "GSM1021065", "GSM1021066", "GSM1021067", "GSM1021068", "GSM1021069", "GSM1021070", "GSM1021071", "GSM1021072", "GSM1021073", "GSM1021074", "GSM1021075", "GSM1021076", "GSM1021077", "GSM1021078", "GSM1021079", "GSM1021080", "GSM1021081", "GSM1021082", "GSM1021083", "GSM1021084", "GSM1021085", "GSM1021086", "GSM1021087", "GSM1021088", "GSM1021089", "GSM1021090", "GSM1021091", "GSM1021092", "GSM1021093", "GSM1021094", "GSM1021095", "GSM1021096", "GSM1021097", "GSM1021098", "GSM1021099", "GSM1021100", "GSM1021101", "GSM1021102", "GSM1021103", "GSM1021104", "GSM1021105", "GSM1021106", "GSM1021107", "GSM1021108", "GSM1021109", "GSM1021110", "GSM1021111", "GSM1021112", "GSM1021113", "GSM1021114", "GSM1021115", "GSM1021116", "GSM1021117", "GSM1021118", "GSM1021119", "GSM1021120"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "11487", "taxon": "Homo sapiens", "title": "MicroRNA expression profiling of colorectal normal mucosa, adenoma and adenocarcinoma tissues", "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:GSE57965", "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=GSE57965", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57965", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1398765", "GSM1398766", "GSM1398767", "GSM1398768", "GSM1398769", "GSM1398770", "GSM1398771", "GSM1398772", "GSM1398773", "GSM1398774", "GSM1398775", "GSM1398776", "GSM1398777", "GSM1398778", "GSM1398779", "GSM1398780", "GSM1398781", "GSM1398782", "GSM1398783", "GSM1398784", "GSM1563050", "GSM1563051", "GSM1563052"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "mRNA expression data from adenoma, gene modified, and colorectal cancer organoid.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34511938:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1facb413aa5950c4b500e0f187a5bfc2c248dcf14299787570a0f8e8ffde9547", "bytes": 714, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#t0001", "version": null, "note": "Clinicopathological Characteristics of the Whole Series", "structure": {"pmcid": "PMC8427077", "section_index": 9, "section_title": "Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR)", "row_count": 30, "column_count": 2}, "table": {"label": "Table 1", "caption": "Clinicopathological Characteristics of the Whole Series", "rows": [["Variable", "Number"], ["Patients", "40"], ["Sex"], ["Male", "28"], ["Female", "12"], ["Age"], ["Range", "30–79"], ["Median ± SD", "63.2±12.48"], ["Patients with colorectal adenoma", "20"], ["Age"], ["Range", "30–65"], ["Mean ± SD", "56.9±11.62"], ["Sex"], ["Female", "9"], ["Male", "11"], ["Patients with colorectal carcinoma", "20"], ["Age"], ["Range", "35–69"], ["TNM tumor stages"], ["T1", "4"], ["T2", "6"], ["T3", "2"], ["T4", "8"], ["TNM lymph node status"], ["N0", "12"], ["N1", "2"], ["N2", "6"], ["Metastases"], ["M0", "16"], ["M1", "4"]], "row_count": 30, "column_count": 2, "numeric_cells": 21, "header_rows": 1, "locator": "section[9]/table-wrap[1]#t0001"}}, {"id": "asset:table:pmid:34511938:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4614c11588297dc9b439bd4d6c9ec7bee967f2d16a94a4712c3ebd53cbfa1174", "bytes": 985, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#t0002", "version": null, "note": "KEGG Enrichment Analysis of Potential Target mRNAs", "structure": {"pmcid": "PMC8427077", "section_index": 14, "section_title": "Screening of Potential Transcription Factors and Enrichment Analysis", "row_count": 7, "column_count": 5}, "table": {"label": "Table 2", "caption": "KEGG Enrichment Analysis of Potential Target mRNAs", "rows": [["GOID", "GOTerm", "Ontology Source", "Nr. Genes", "Associated Genes Found"], ["KEGG:00603", "Glycosphingolipid biosynthesis", "KEGG_27.02.2019", "3", "[B3GALT5, GBGT1, ST3GAL1]"], ["KEGG:00830", "Retinol metabolism", "KEGG_27.02.2019", "7", "[ADH1A, ADH1C, ALDH1A1, CYP3A5, DHRS9, SDR16C5, UGT2B15]"], ["KEGG:04933", "AGE-RAGE signaling pathway in diabetic complications", "KEGG_27.02.2019", "4", "[AGER, AGT, COL1A2, HRAS]"], ["KEGG:04972", "Pancreatic secretion", "KEGG_27.02.2019", "11", "[CA2, CEL, CLCA1, CLCA4, CPA3, KCNMA1, PLA2G12B, PLA2G2A, RAB27B, SLC4A2, SLC4A4]"], ["KEGG:04750", "Inflammatory mediator regulation of TRP channels", "KEGG_27.02.2019", "4", "[PRKACB, PTGER2, PTGER4, TRPA1]"], ["KEGG:04924", "Renin secretion", "KEGG_27.02.2019", "7", "[AGT, CLCA1, CLCA4, KCNMA1, PRKACB, PTGER2, PTGER4]"]], "row_count": 7, "column_count": 5, "numeric_cells": 20, "header_rows": 1, "locator": "section[14]/table-wrap[1]#t0002"}}, {"id": "asset:table:pmid:34511938:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fcf0d239e5dbab761a87d1e76c59d55f4411f772a7cdeb54a5e77105a4ab82c8", "bytes": 346, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#t0003", "version": null, "note": "Expression of BCL2L12 Protein in Colorectal Adenoma and Carcinoma", "structure": {"pmcid": "PMC8427077", "section_index": 18, "section_title": "Verification of Potential Biomarker Expression by qRT-PCR and IHC", "row_count": 4, "column_count": 4}, "table": {"label": "Table 3", "caption": "Expression of BCL2L12 Protein in Colorectal Adenoma and Carcinoma", "rows": [["", "BCL2L12 Expression"], ["", "Case No.", "Low", "High"], ["Colorectal adenoma", "20", "18", "2"], ["Colorectal carcinoma", "20", "1", "19"]], "row_count": 4, "column_count": 4, "numeric_cells": 7, "header_rows": 2, "locator": "section[18]/table-wrap[1]#t0003"}}, {"id": "asset:table:pmid:34511938:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:65d0ee3d20bd06acdd33611d83698df756e71087f7bb74ae57b1508fde84fa93", "bytes": 1057, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#t0004", "version": null, "note": "Results of Connectivity Map Analysis", "structure": {"pmcid": "PMC8427077", "section_index": 19, "section_title": "Screening of Small Molecule Drugs", "row_count": 12, "column_count": 6}, "table": {"label": "Table 4", "caption": "Results of Connectivity Map Analysis", "rows": [["Rank", "Score", "Type", "ID", "Name", "Description"], ["1", "99.98", "cp", "BRD-K82746043", "Navitoclax", "BCL inhibitor"], ["2", "99.93", "cp", "BRD-A04352665", "Maraviroc", "CC chemokine receptor antagonist"], ["3", "99.93", "kd", "CGS001-23119", "HIC2", "BTB/POZ domain containing"], ["4", "99.86", "cp", "BRD-K26657438", "Imiquimod", "TLR agonist"], ["5", "99.79", "cp", "BRD-K01638814", "Rilmenidine", "Adrenergic receptor agonist"], ["6", "99.75", "kd", "CGS001-8771", "TNFRSF6B", "Tumour necrosis factor (TNF) receptor family"], ["7", "99.75", "cp", "BRD-K48923948", "BMS-641988", "Androgen receptor antagonist"], ["8", "99.68", "kd", "CGS001-6925", "TCF4", "Basic helix-loop-helix proteins"], ["9", "99.65", "kd", "CGS001-286530", "P2RY8", "GPCR/Class A: Purinergic receptors, P2Y"], ["10", "99.63", "cp", "BRD-A67373739", "AICA-ribonucleotide", "AMPK activator"], ["11", "99.61", "cp", "BRD-K16554956", "PTB1", "AMPK activator"]], "row_count": 12, "column_count": 6, "numeric_cells": 34, "header_rows": 1, "locator": "section[19]/table-wrap[1]#t0004"}}], "gaps": ["asset:data:geo:GSE41655 not downloaded", "asset:data:geo:GSE41655 licence not read", "asset:data:geo:GSE57965 not downloaded", "asset:data:geo:GSE57965 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan Meier"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R differential expression analysis using R software", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GEO2R, an R-associated web application, was applied to filtrate DEMs between adenoma samples and adenocarcinoma samples."}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE41655", "GSE57965"], "resolved_accessions": ["GSE41655", "GSE57965"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE41655, GSE57965 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": ["survival_km"], "assets": ["source:pmid:34511938", "data:geo:GSE41655", "asset:table:pmid:34511938:1", "asset:table:pmid:34511938:2", "asset:table:pmid:34511938:3", "asset:table:pmid:34511938:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE41655"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32034, "completion_tokens": 1352, "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:34511938", "type": "paper", "label": "pmid:34511938"}, {"id": "source:pmid:34511938", "type": "manuscript", "label": "PMID 34511938 full text"}, {"id": "data:geo:GSE41655", "type": "dataset", "label": "GEO GSE41655"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34511938", "type": "paper", "label": "pmid:34511938"}, {"id": "source:pmid:34511938", "type": "manuscript", "label": "PMID 34511938 full text"}, {"id": "data:geo:GSE41655", "type": "dataset", "label": "GEO GSE41655"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34511938", "type": "extraction", "used": ["source:pmid:34511938"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE41655", "type": "accession_resolution", "used": ["data:geo:GSE41655"], "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:34511938", "parent_hash": "sha256:25ffece180665081f460ebcde37c175c8050515e47d93be7990e0b89c7733601", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE41655 licence not read", "asset:data:geo:GSE41655 not downloaded", "asset:data:geo:GSE57965 licence not read", "asset:data:geo:GSE57965 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["onducted by online databases and qRT-PCR and IHC experiments. RESULTS: In total, 6 DEMs and 3", "erified by qRT-PCR which all target BCL2L12. IHC results showed that the expression level of"], "order_basis": "paper_text_order:988", "id": "assay:1"}, {"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": ["out as potential drugs. CONCLUSION: By using microarray and bioinformatics analyses, DEMs and DEGs w"], "order_basis": "paper_text_order:1688", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan Meier"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}