ArticleDatabase : the journal of biological databases and curation2013
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Article in Database : the journal of biological databases and curation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- Standardized Annotation of Quantitative Proteomics Datasets Using SDRF-Proteomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- The need for standardization and improved open (meta)data practices in metaproteomics.Microbiome · 2026Article
- Unlocking the Next Decade of Proteomics with Standardized, Structured Metadata.Journal of proteome research · 2026Review
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format.Journal of proteome research · 2025Review
- Enabling pan-repository reanalysis for big data science of public metabolomics data.Nature communications · 2025Article
- The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.Analytical chemistry · 2024Article
- NCI's Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data.Cancer research communications · 2024Article
- Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java.Journal of the American Society for Mass Spectrometry · 2024Article
- The IDSM mass spectrometry extension: searching mass spectra using SPARQL.Bioinformatics (Oxford, England) · 2024Article
- Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management.Journal of cheminformatics · 2024Article
- MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.Bioinformatics (Oxford, England) · 2023Article
- Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.Proteomics · 2023Article
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- Ontologies for increasing the FAIRness of plant research data.Frontiers in plant science · 2023Review
- A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics.Metabolites · 2022Review
- The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource.The Plant cell · 2021Article
- Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.Briefings in bioinformatics · 2021Article
- mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements.Journal of proteome research · 2021Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)-Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies. Database URL: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.