Proteomics dataset: The colon mucosa from inflammatory bowel disease patients, gastrointestinal asymptomic rheumatoid arthritis patients, and controls.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29085871", "kind": "science-record", "revision": 5, "content_hash": "sha256:a90ea5451717c58bf76db2a76b4381abf62b8f6483044c4797eeac27d856ff87", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T18:49:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomics dataset: The colon mucosa from inflammatory bowel disease patients, gastrointestinal asymptomic rheumatoid arthritis patients, and controls.", "doi": "10.1016/j.dib.2017.09.059", "pmid": "29085871", "authors": ["Tue Bjerg Bennike", "Thomas Gelsing Carlsen", "Torkell Ellingsen", "Ole Kristian Bonderup", "Henning Glerup", "Martin Bøgsted", "Gunna Christiansen", "Svend Birkelund", "Vibeke Andersen", "Allan Stensballe"], "journal": "Data in brief", "year": 2017, "abstract": "The datasets presented in this article are related to the research articles entitled \"Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies\" (Bennike et al., 2015 [1]), and \"Proteome Analysis of Rheumatoid Arthritis Gut Mucosa\" (Bennike et al., 2017 [2]). The colon mucosa represents the main interacting surface of the gut microbiota and the immune system. Studies have found an altered composition of the gut microbiota in rheumatoid arthritis patients (Zhang et al., 2015; Vaahtovuo et al., 2008; Hazenberg et al., 1992) [5], [6], [7] and inflammatory bowel disease patients (Morgan et al., 2012; Abraham and Medzhitov, 2011; Bennike, 2014) [8], [9], [10]. Therefore, we characterized the proteome of colon mucosa biopsies from 10 inflammatory bowel disease ulcerative colitis (UC) patients, 11 gastrointestinal healthy rheumatoid arthritis (RA) patients, and 10 controls. We conducted the sample preparation and liquid chromatography mass spectrometry (LC-MS/MS) analysis of all samples in one batch, enabling label-free comparison between all biopsies. The datasets are made publicly available to enable critical or extended analyses. The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.", "claims": [{"id": "claim-data-access", "statement": "The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29085871", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used label-free LC-MS/MS comparison across all biopsy samples, and the source data are available through PRIDE via ProteomeXchange under PXD001608 and PXD003082; no numerical statistical result is reported for this target.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29085871", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We conducted the sample preparation and liquid chromatography mass spectrometry (LC-MS/MS) analysis of all samples in one batch, enabling label-free comparison between all biopsies."}, {"asset": "source:pmid:29085871", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used label-free LC-MS/MS comparison across all biopsy samples, and the source data are available through PRIDE via ProteomeXchange under PXD001608 and PXD003082; no numerical statistical result is reported for this target.", "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:29085871"], "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:PXD001608"], "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:PXD001608"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29085871", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2017.09.059", "sha256": "sha256:0ce5a39782dda7c6842bc75f3def981cfeec2e2ea3ce42b6197feb6a2164078d", "bytes": 14245, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2017.09.059", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5650644", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001608", "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=PXD001608", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001608", "version": null, "note": "The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Human colon biopsies (healthy and Ulcerative Colitis) LC-MS/MS", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD003082", "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=PXD003082", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD003082", "version": null, "note": "The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A proteome analysis by LC-MS/MS of human colon mucosal biopsies from gastrointestinal healthy rheumatoid arthritis patients", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29085871:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:79e6d0f422f4cfedd5a75152f74539ab670248eb781acf1dfb145552d9e8e288", "bytes": 1693, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC5650644", "section_index": 1, "section_title": "p", "row_count": 14, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Characterization of the proteome of the colon mucosa of ulcerative colitis patients, gastrointestinal healthy rheumatoid arthritis patients, and controls."], ["Type of data", "Raw- mass spectrometry files and text/excel files"], ["How data was acquired", "Mass Spectrometry Liquid Chromatography"], ["Data was acquired using a high-resolution/high-accuracy Q Exactive plus (Thermo Scientific) mass spectrometer."], ["Data format", "Raw- and analyzed data."], ["Experimental factors", "Human colon mucosal biopsies from ulcerative colitis patients, gastrointestinal healthy rheumatoid arthritis patients, and controls."], ["Experimental features", "Biopsies were extracted by colonoscopy and immediately snap-frozen with liquid nitrogen. The biopsies were tryptic digested and analyzed by electrospray ionization liquid chromatography mass spectrometry."], ["Data source location", "The Laboratory for Medical Mass Spectrometry, Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7E, 9220 Aalborg East, Denmark"], ["Data accessibility", "The proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository, [13], [14], [15], [16] with dataset identifiers:"], ["PXD001608 – Ulcerative colitis patients, and controls."], ["PXD003082 – Gastrointestinal healthy rheumatoid arthritis patients."], ["Direct download links: http://www.ebi.ac.uk/pride/archive/projects/PXD001608"], ["http://www.ebi.ac.uk/pride/archive/projects/PXD003082"]], "row_count": 14, "column_count": 2, "numeric_cells": 6, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0015"}}, {"id": "asset:table:pmid:29085871:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:79e6d0f422f4cfedd5a75152f74539ab670248eb781acf1dfb145552d9e8e288", "bytes": 1693, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC5650644", "section_index": 2, "section_title": "p", "row_count": 14, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Characterization of the proteome of the colon mucosa of ulcerative colitis patients, gastrointestinal healthy rheumatoid arthritis patients, and controls."], ["Type of data", "Raw- mass spectrometry files and text/excel files"], ["How data was acquired", "Mass Spectrometry Liquid Chromatography"], ["Data was acquired using a high-resolution/high-accuracy Q Exactive plus (Thermo Scientific) mass spectrometer."], ["Data format", "Raw- and analyzed data."], ["Experimental factors", "Human colon mucosal biopsies from ulcerative colitis patients, gastrointestinal healthy rheumatoid arthritis patients, and controls."], ["Experimental features", "Biopsies were extracted by colonoscopy and immediately snap-frozen with liquid nitrogen. The biopsies were tryptic digested and analyzed by electrospray ionization liquid chromatography mass spectrometry."], ["Data source location", "The Laboratory for Medical Mass Spectrometry, Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7E, 9220 Aalborg East, Denmark"], ["Data accessibility", "The proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository, [13], [14], [15], [16] with dataset identifiers:"], ["PXD001608 – Ulcerative colitis patients, and controls."], ["PXD003082 – Gastrointestinal healthy rheumatoid arthritis patients."], ["Direct download links: http://www.ebi.ac.uk/pride/archive/projects/PXD001608"], ["http://www.ebi.ac.uk/pride/archive/projects/PXD003082"]], "row_count": 14, "column_count": 2, "numeric_cells": 6, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0015"}}, {"id": "asset:table:pmid:29085871:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ad7c5686dd3bc49a6247b95b8986856262239a1137f0990daed2667f6adf7917", "bytes": 3046, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t0005", "version": null, "note": "Raw-datafiles in PXD001608 and PXD003082. All samples were analyzed in technical triplicates, and all raw-files are named accordingly (e.g. Ctrl_10_3 is the third repeat of control 10). “Poor R” signifies a Pearson's correlation coefficient R<0.95 between the technical repeats, and additional data validation is recommended for studies including these datafiles. The number of identified proteins in each replicate is given, wo/w the MaxQuant match between runs feature which transfer MS/MS information between different LC-MS/MS analysis. RA: Rheumatoid arthritis, UC: ulcerative colitis, NA: Not available.", "structure": {"pmcid": "PMC5650644", "section_index": 3, "section_title": "Data", "row_count": 32, "column_count": 6}, "table": {"label": "Table 1", "caption": "Raw-datafiles in PXD001608 and PXD003082. All samples were analyzed in technical triplicates, and all raw-files are named accordingly (e.g. Ctrl_10_3 is the third repeat of control 10). “Poor R” signifies a Pearson's correlation coefficient R<0.95 between the technical repeats, and additional data validation is recommended for studies including these datafiles. The number of identified proteins in each replicate is given, wo/w the MaxQuant match between runs feature which transfer MS/MS information between different LC-MS/MS analysis. RA: Rheumatoid arthritis, UC: ulcerative colitis, NA: Not available.", "rows": [["Filename", "Sample", "#Proteins matching OFF", "#Proteins matching ON", "Dataset ID", "Comment"], ["Ctrl_1", "Control", "4362, 4279, 4241", "5967, 5903, 5897", "PXD001608", ""], ["Ctrl_2", "Control", "3613, 3607, 3595", "5657, 5664, 5723", "PXD001608", ""], ["Ctrl_3", "Control", "4203, 4203, 4188", "5936, 5952, 5939", "PXD001608", ""], ["Ctrl_4", "Control", "4245, 4268, 4191", "5863, 5865, 5849", "PXD001608", ""], ["Ctrl_5", "Control", "3961, 3881, 3903", "5694, 5683, 5632", "PXD001608", ""], ["Ctrl_6", "Control", "4290, 4281, 4242", "5966, 5959, 5932", "PXD001608", ""], ["Ctrl_7", "Control", "4080, 4099, 4097", "5856, 5822, 5817", "PXD001608", ""], ["Ctrl_8", "Control", "4269, 4325, 4336", "5968, 5986, 5966", "PXD001608", ""], ["Ctrl_9", "Control", "4560, 4549, 3974", "6103, 6126, 6103", "PXD001608", ""], ["Ctrl_10", "Control", "3974, 3993, 3972", "5781, 5817, 5779", "PXD001608", ""], ["UC_1", "UC", "4290, 4229, 4363", "5870, 5852, 5907", "PXD001608", ""], ["UC_2", "UC", "3328, 3285, 3328", "5148, 5101, 5139", "PXD001608", ""], ["UC_3", "UC", "4455, 4472, 4482", "6068, 6082, 6041", "PXD001608", ""], ["UC_4", "UC", "4236, 4005, NA", "5685, 5773, NA", "PXD001608", "UC_4_3 poor R"], ["UC_5", "UC", "3097, 3174, NA", "5051, 5017, NA", "PXD001608", "UC_5_3 poor R"], ["UC_6", "UC", "4458, 4424, 4482", "6118, 6108, 6115", "PXD001608", ""], ["UC_7", "UC", "3657, 3686, 3693", "5647, 5626, 5575", "PXD001608", ""], ["UC_8", "UC", "3356, 3288, 3303", "5237, 5207, 5164", "PXD001608", ""], ["UC_9", "UC", "4681, 4700, 4703", "6220, 6233, 6223", "PXD001608", ""], ["UC_10", "UC", "3762, 3688, 3674", "5587, 5557, 5562", "PXD001608", ""], ["RA_1", "RA", "3900, 3789, 3755", "5658, 5644, 5632", "PXD003082", ""], ["RA_2", "RA", "4347, 4141, 4285", "6023, 5997, 5973", "PXD003082", ""], ["RA_3", "RA", "4654, 4678, 4629", "6204, 6179, 6180", "PXD003082", ""], ["RA_4", "RA", "4298, 4287, 4267", "5933, 5925, 5899", "PXD003082", ""], ["RA_5", "RA", "3472, 3521, 3491", "5402, 5390, 5344", "PXD003082", ""], ["RA_6", "RA", "3545, 3485, 3526", "5735, 5742, 5728", "PXD003082", ""], ["RA_7", "RA", "4538, 4476, 4459", "6057, 6062, 6071", "PXD003082", ""], ["RA_8", "RA", "3619, 3439 NA", "5317, 5310, NA", "PXD003082", "RA_8_3 poor R"], ["RA_9", "RA", "3361, NA, 3427,", "5256, NA, 5187", "PXD003082", "RA_9_2 poor R"], ["RA_10", "RA", "4417, 4354, 4361", "5991, 6010, 6023", "PXD003082", ""], ["RA_11", "RA", "3094, 3055, 3051", "5005, 5050, 5006", "PXD003082", ""]], "row_count": 32, "column_count": 6, "numeric_cells": 128, "header_rows": 1, "locator": "section[3]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:29085871:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7c7f92c46bd92c21acbec1119a2a79d5f6957502f8169e3b82d1427cfa823a19", "bytes": 1153, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#t0010", "version": null, "note": "Additional submitted Search and FASTA files in PXD001608 and PXD003082. RA: Rheumatoid arthritis, UC: ulcerative colitis.", "structure": {"pmcid": "PMC5650644", "section_index": 3, "section_title": "Data", "row_count": 6, "column_count": 4}, "table": {"label": "Table 2", "caption": "Additional submitted Search and FASTA files in PXD001608 and PXD003082. RA: Rheumatoid arthritis, UC: ulcerative colitis.", "rows": [["Filename", "Dataset ID", "Content", "Description"], ["CombinedTxtFiles.zip", "PXD001608", "Zipped MaxQuant combined txt folder.", "Result of the label-free quantitative analysis of UC and controls in MaxQuant. The content of each file is described in “tables.pdf”."], ["131008_Swissprot_Human_Ref_ proteome.fasta", "PXD001608", "Protein FASTA database file.", "Protein database used for the UC and controls analysis."], ["MaxQuantOutput.zip", "PXD003082", "Zipped MaxQuant combined txt folder.", "Result of the label-free quantitative analysis of UC, RA, and controls in MaxQuant. The content of each file is described in “tables.pdf”."], ["UniprotHumanProteome P000005640Isoforms.fasta", "PXD003082", "Protein FASTA database file.", "Protein database used for the UC, RA, and controls analysis."], ["FASTA file parameters.txt", "PXD003082", "FASTA info.", "Information regarding the database."]], "row_count": 6, "column_count": 4, "numeric_cells": 7, "header_rows": 1, "locator": "section[3]/table-wrap[2]#t0010"}}], "gaps": ["asset:data:geo:PXD001608 not downloaded", "asset:data:geo:PXD001608 licence not read", "asset:data:geo:PXD003082 not downloaded", "asset:data:geo:PXD003082 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD001608", "PXD003082"], "resolved_accessions": ["PXD001608", "PXD003082"], "statements": ["The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples."], "basis": "The paper names PXD001608, PXD003082 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:29085871", "data:geo:PXD001608", "asset:table:pmid:29085871:1", "asset:table:pmid:29085871:2", "asset:table:pmid:29085871:3", "asset:table:pmid:29085871:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001608"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:37Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 34235, "completion_tokens": 3297, "cached_tokens": 2089}}, "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:29085871", "type": "paper", "label": "pmid:29085871"}, {"id": "source:pmid:29085871", "type": "manuscript", "label": "PMID 29085871 full text"}, {"id": "data:geo:PXD001608", "type": "dataset", "label": "GEO PXD001608"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29085871", "type": "paper", "label": "pmid:29085871"}, {"id": "source:pmid:29085871", "type": "manuscript", "label": "PMID 29085871 full text"}, {"id": "data:geo:PXD001608", "type": "dataset", "label": "GEO PXD001608"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29085871", "type": "extraction", "used": ["source:pmid:29085871"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001608", "type": "accession_resolution", "used": ["data:geo:PXD001608"], "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:29085871", "parent_hash": "sha256:fb2b66a78c04b9c53bf3339eb8f639573f085e8f745758385fd6d98b7a26402e", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:PXD001608 licence not read", "asset:data:geo:PXD001608 not downloaded", "asset:data:geo:PXD003082 licence not read", "asset:data:geo:PXD003082 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Proteomics dataset: The colon mucosa from inflammatory", "to enable critical or extended analyses. The proteomics data and search results, have been deposited", "gen followed by storage at minus 80 °C until proteomics sample preparation. All participants had giv", "Danish Data Protection Agency (2008-58-035). Proteomic sample preparation The biopsies were randomi"], "order_basis": "paper_text_order:0", "id": "assay:1"}]}