ArticleBioinformatics (Oxford, England)2015
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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
18 citing papers in PubMed.
- The PRIDE database at 20 years: 2025 update.Nucleic acids research · 2025Article
- The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.Nucleic acids research · 2022Article
- piNET: a versatile web platform for downstream analysis and visualization of proteomics data.Nucleic acids research · 2020Article
- The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.Nucleic acids research · 2020Article
- psims - A Declarative Writer for mzML and mzIdentML for Python.Molecular & cellular proteomics : MCP · 2019Article
- iProX: an integrated proteome resource.Nucleic acids research · 2019Article
- The PRIDE database and related tools and resources in 2019: improving support for quantification data.Nucleic acids research · 2019Article
- A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.Journal of visualized experiments : JoVE · 2018Article
- JAMI: a Java library for molecular interactions and data interoperability.BMC bioinformatics · 2018Article
- The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.Genome biology · 2018Article
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.Journal of proteome research · 2017Article
- Article
- Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.Cell systems · 2017Article
- The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.Molecular & cellular proteomics : MCP · 2017Article
- A Golden Age for Working with Public Proteomics Data.Trends in biochemical sciences · 2017Review
- Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.Journal of proteome research · 2016Article
- 2016 update of the PRIDE database and its related tools.Nucleic acids research · 2016Article
- PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.Molecular & cellular proteomics : MCP · 2016Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
unlabelledThe ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources. Finally, we present a set of algorithms and tools whose implementation illustrates the simplicity of developing applications using the library. AVAILABILITY AND IMPLEMENTATION: The software is freely available at https://github.com/PRIDE-Utilities/ms-data-core-api. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online CONTACT: juan@ebi.ac.uk.
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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.