Integrated bioinformatic changes and analysis of retina with time in diabetic rats.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29785346", "kind": "science-record", "revision": 5, "content_hash": "sha256:0824864f261efcfeafbe425b4a1d22d2aeeebb5762b559cdcb5b5c21ef8f5871", "created_at": "2026-11-01T15:40:33Z", "updated_at": "2026-11-01T21:59:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatic changes and analysis of retina with time in diabetic rats.", "doi": "10.7717/peerj.4762", "pmid": "29785346", "authors": ["Zekai Cui", "Qiaolang Zeng", "Yonglong Guo", "Shiwei Liu", "Jiansu Chen"], "journal": "PeerJ", "year": 2018, "abstract": "Diabetic retinopathy (DR) is the most common chronic complication of diabetes. It can cause impaired vision and even blindness. However, the pathological mechanism of DR is still unknown. In the present study, we use bioinformatic analysis to reveal the pathological changes of early DR in a streptozotocin (STZ) induced diabetes rat model. The dataset GSE28831 was downloaded from the Gene Expression Omnibus (GEO) database. To clarify the pathological mechanism of early DR, genes which were up-regulated (UP group) or down-regulated (DOWN group) over time were identified. One hundred eighty six genes in the UP group and 85 genes in the DOWN group were defined. There were in total 28 Gene ontology (GO) terms with a P value lower than 0.05 in UP group, including astrocyte development, neutrophil chemotaxis, neutrophil aggregation, mesenchymal cell proliferation and so on. In the DOWN group, there were totally 14 GO terms with a P value lower than 0.05, including visual perception, lens development in camera-type eye, camera-type eye development, bicellular tight junction and so on. Signaling pathways were analyzed with all genes in the UP and DOWN groups, and leukocyte transendothelial migration and tight junction were selected. Protein-protein interaction (PPI) network was constructed and six hub genes Diras3, Actn1, Tssk6, Cnot6l, Tek and Fgf4 were selected with connection degree ≥5. S100a8, S100a9 and Tek may be potential targets for DR diagnosis and treatment. This study provides the basis for the diagnosis and treatment of DR in the future.", "claims": [{"id": "claim-method", "statement": "The dataset was analyzed with GEO2R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29785346", "locator": "sections[4] \"Analysis of DEGs over time\" paragraph 2", "quote": "The dataset was analyzed with GEO2R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data are provided in the Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29785346", "locator": "sections[15] \"Additional Information and Declarations\" paragraph 5", "quote": "The raw data are provided in the Supplemental Files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO2R on the GEO dataset GSE28831, the study identified genes with monotonically increasing or decreasing expression across days 7, 28, and 84, defining 186 UP genes and 85 DOWN genes, and selected six PPI hub genes: Diras3, Actn1, Tssk6, Cnot6l, Tek, and Fgf4.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29785346", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The dataset GSE28831 was downloaded from the Gene Expression Omnibus (GEO) database."}, {"asset": "source:pmid:29785346", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "One hundred eighty six genes in the UP group and 85 genes in the DOWN group were defined."}, {"asset": "source:pmid:29785346", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Protein–protein interaction (PPI) network was constructed and six hub genes Diras3, Actn1, Tssk6, Cnot6l, Tek and Fgf4 were selected with connection degree ≥5."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GEO2R on the GEO dataset GSE28831, the study identified genes with monotonically increasing or decreasing expression across days 7, 28, and 84, defining 186 UP genes and 85 DOWN genes, and selected six PPI hub genes: Diras3, Actn1, Tssk6, Cnot6l, Tek, and Fgf4.", "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:29785346"], "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:GSE28831"], "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:GSE28831"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29785346", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.4762", "sha256": "sha256:d04145f66c1198f0a5b7819213be1fdfdff9612aae47c26e5d12b370d74c94eb", "bytes": 22140, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.4762", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5960260", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28831", "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=GSE28831", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28831", "version": null, "note": "The raw data are provided in the Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data are provided in the Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM714108", "GSM714109", "GSM714110", "GSM714111", "GSM714112", "GSM714113", "GSM714114", "GSM714115", "GSM714116", "GSM714117", "GSM714118", "GSM714119", "GSM714120", "GSM714121", "GSM714122", "GSM714123", "GSM714124", "GSM714125", "GSM714126", "GSM714127", "GSM714128"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "7294", "taxon": "Rattus norvegicus", "title": "Changes in gene expression in the retina of diabetic Long Evans rats after one, four, and twelve weeks of diabetes", "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:29785346:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e44d55bc1523c2bfac8400f9352d6cdba4c2468b05b0bcfefa0198a08607cd50", "bytes": 187, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#table-1", "version": null, "note": "Gene ontology analysis of UP group.", "structure": {"pmcid": "PMC5960260", "section_index": 9, "section_title": "GO terms enrichment and signaling pathways analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Gene ontology analysis of UP group.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:29785346:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d79f8a0bb1038c396d1395711d579db7cf101c413acbf691816b3529e72b72cf", "bytes": 189, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#table-2", "version": null, "note": "Gene ontology analysis of DOWN group.", "structure": {"pmcid": "PMC5960260", "section_index": 9, "section_title": "GO terms enrichment and signaling pathways analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Gene ontology analysis of DOWN group.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[2]#table-2"}}, {"id": "asset:table:pmid:29785346:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5e15b10c59d58759505c579c7465b8b9000b9ac8d5899fe254856bf0ed5d9ea7", "bytes": 201, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[3]#table-3", "version": null, "note": "KEGG pathway analysis of UP group and DOWN group.", "structure": {"pmcid": "PMC5960260", "section_index": 9, "section_title": "GO terms enrichment and signaling pathways analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "KEGG pathway analysis of UP group and DOWN group.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[3]#table-3"}}], "gaps": ["asset:data:geo:GSE28831 not downloaded", "asset:data:geo:GSE28831 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": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The dataset was analyzed with GEO2R."}}], "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": ["GSE28831"], "resolved_accessions": ["GSE28831"], "statements": ["The raw data are provided in the Supplemental Files."], "basis": "The paper names GSE28831 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:29785346", "data:geo:GSE28831", "asset:table:pmid:29785346:1", "asset:table:pmid:29785346:2", "asset:table:pmid:29785346:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE28831"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:27Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 46243, "completion_tokens": 3145, "cached_tokens": 2072}}, "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:29785346", "type": "paper", "label": "pmid:29785346"}, {"id": "source:pmid:29785346", "type": "manuscript", "label": "PMID 29785346 full text"}, {"id": "data:geo:GSE28831", "type": "dataset", "label": "GEO GSE28831"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29785346", "type": "paper", "label": "pmid:29785346"}, {"id": "source:pmid:29785346", "type": "manuscript", "label": "PMID 29785346 full text"}, {"id": "data:geo:GSE28831", "type": "dataset", "label": "GEO GSE28831"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29785346", "type": "extraction", "used": ["source:pmid:29785346"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE28831", "type": "accession_resolution", "used": ["data:geo:GSE28831"], "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:29785346", "parent_hash": "sha256:8615d1a12cf1abc750da6538519a8cb3bb264ed10864cca8d10947361e0ba602", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE28831 licence not read", "asset:data:geo:GSE28831 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.834, "evidence": ["and analysis of retina with time in diabetic rats.", "R in a streptozotocin (STZ) induced diabetes rat model. The dataset GSE28831 was downloaded f"], "order_basis": "paper_text_order:33", "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"}]}