{"doi":"10.1002/pmic.202500007","title":"DICED (Database of Identified Cleavage Sites Endemic to Diseases States): A Searchable Web Interface for Terminomics/Degradomics","abstract":"Proteolysis is an irreversible posttranslational modification with immense biological impact. Owing to its high disease significance, there is growing interest in investigating proteolysis on the proteome scale, termed degradomics. We developed 'Database of Identified Cleavage sites Endemic to Disease states' (DICED; https://diced.lerner.ccf.org/), as a searchable knowledgebase to promote collaboration and knowledge sharing in degradomics. DICED was designed and constructed using Python, JavaScript, HTML, and PostgreSQL. Django (https://www.djangoproject.com) was chosen as the primary framework for its security features and support for agile development. DICED can be utilized on major web browsers and operating systems for easy access to high-throughput mass spectrometry-identified cleaved protein termini. The data was obtained using N-terminomics, comprising N-terminal protein labeling, labeled peptide enrichment, mass spectrometry and positional peptide annotation. The DICED database contains experimentally derived N-terminomics peptide datasets from tissues, diseases, or digests of tissue protein libraries using individual proteases and is searchable using UniProt ID, protein name, gene symbol or up to 100 peptide sequences. The tabular output format can be exported as a CSV file. Although DICED presently accesses data from a single laboratory, it is freely available as a Galaxy tool and the underlying database is scalable, permitting addition of new datasets and features.","journal":"PROTEOMICS","year":2025,"id":523346,"datarank":0.2578591809414005,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.016443494076285408,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.016443494076285408,"corpus_percentile":40.790593331786184,"corpus_rank":7655,"citation_count":4,"citer_count":2,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9376,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":20.8333,"fair_percentile":36.38031183124427,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":826247,"name":"Sumit Bhutada","orcid":"0000-0002-5274-5122","position":1,"is_corresponding":false},{"id":473741,"name":"Daniel R. Martin","orcid":"0000-0002-3517-3716","position":2,"is_corresponding":false},{"id":1396266,"name":"Joyce Guzowski","orcid":null,"position":3,"is_corresponding":false},{"id":11438,"name":"Daniel Blankenberg","orcid":"0000-0002-6833-9049","position":4,"is_corresponding":false},{"id":307984,"name":"Suneel Apte","orcid":"0000-0001-8441-1226","position":5,"is_corresponding":false},{"id":568353,"name":"Jayadev Joshi","orcid":"0000-0001-7589-5230","position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":null,"created_at":"2026-07-19T02:50:03.004175Z","pmid":"40351053","pmcid":"PMC12246766","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":22.2222,"fair_a":6.25,"fair_i":60.0,"fair_r":33.3333,"fair_zscore":-0.5389,"fair_rationale":{"fair_score":20.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":22.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","grounded":true,"rationale":"No persistent-identifier string (DOI, Handle, ARK, or repository accession) is given for the data. 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Bhutada S., Hoyle A., Piuzzi N. S., and Apte S. S., “Degradomics Defines Proteolysis Information Flow From Human Knee Osteoarthritis Cartilage to Matched Synovial Fluid and the Contributions of Secreted Proteases ADAMTS5, MMP13 and CMA1 to Articular Cartilage Breakdown,” Osteoarthritis and Cartilage 33, no. 1 (2025): 116–127, 10.1016/j.joca.2024.09.002.","grounded":true,"rationale":"The paper references source datasets with DOIs in the reference list, providing identifiers for resources the data derive from. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence or terms document is named for the data; the article's CC-BY licence applies to the paper, not the data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The data was obtained from N‐terminomics experiments using dimethyl, iTRAQ, or TMT labels that were analyzed on high‐resolution mass spectrometers and analyzed with a false discovery rate of 0.01 using Proteome Discoverer (for Orbitrap instrument data), or FragPipe and Peaks Online (for Bruker timsTOF Pro 2 data).","grounded":false,"rationale":"Specific instruments, platforms, and software are named. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is given to pin the data snapshot.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"We have made the DICED framework available as an open‐source project for local installation (GitHub project: https://github.com/jaidevjoshi83/DICEDWebApp.git ).","grounded":true,"rationale":"A machine-resolvable code-repository URL is provided. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"National Institutes of Health (AR078498 to S.A.; U24HG006620 to D.B.)","grounded":true,"rationale":"Specific grant numbers are attached to named funders. 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For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","why":"No persistent-identifier string (DOI, Handle, ARK, or repository accession) is given for the data. [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","why":"No repository is named; the data are held by the authors.","gain":16.67,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No licence or terms document is named for the data; the article's CC-BY licence applies to the paper, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","why":"No identifier for the dataset appears anywhere in the paper, neither in the reference list nor in body text. [majority verdict 'no' (4/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). 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For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:02:39.487185Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}