ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

Perez‐Riverol, Yasset; Uszkoreit, Julian; Sánchez, Aniel; Ternent, Tobias; Toro, Noemí del; Hermjakob, Henning; Vizcaíno, Juan Antonio; Wang, Rui

doi:10.1093/bioinformatics/btv250

Cited by 34 publications

(31 citation statements)

References 10 publications

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“…Human-readable formats provide cross-platform compatibility and can live in-perpetuity independently from the source data and original instrument manufacturer. These formats continue to evolve and are supported by a diverse ecosystem of software tools and frameworks for bioinformatic analysis [47][48][49][50][51][52][53][54][55][56][57][58]. These advantages are tempered by the technical difficulties of establishing efficient schemes for random access to high-dimension data incorporated within XML-formatted files.…”

Section: Discussionmentioning

confidence: 99%

multiplierzv2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data

et al. 2017

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The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data. New features include support for a wider range of native mass spectrometry file types, interfaces to additional database search engines, compatibility with new reporting formats, and high-level tools to perform post-search proteomic analyses. A GUI desktop environment, mzDesktop, provides access to multiplierz functionality through a user friendly interface. multiplierz is available for download from: https://github.com/BlaisProteomics/multiplierz; and mzDesktop is available for download from: https://sourceforge.net/projects/multiplierz/.

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Section: Discussionmentioning

confidence: 99%

multiplierzv2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data

et al. 2017

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“…In all cases, when users select a concrete term, all the associated details will be presented in the "Term Details" table in the GUI, including its identifier, annotations and synonyms. The OLS Client is part of PRIDE-Utilities [8] and OLS Dialog is part of the PRIDE Inspector Toolsuite [9] a set of Java components that can be reuse in proteomics Java applications.…”

Section: Doi: 101002/pmic201700244mentioning

confidence: 99%

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

et al. 2017

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The availability of user‐friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open‐source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog.

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“…In fact, proteogenomics data encoded in the PSI standard formats mzIdentML and mzTab can be converted into proBAM and proBed, although it should be noted that the representation for proteogenomics data in mzIdentML has only been formalized recently [33]. In this context, first of all, the open-source Java library ms-data-core-api, created to handle different proteomics file formats using the same interface, can be used to write proBed [34]. A Java command line tool, PGConverter (https://github.com/PRIDE-Toolsuite/PGConverter), is also able to convert from mzIdentML and mzTab to proBed and bigBed.…”

Section: Overview Of the Probam And Probed Formatsmentioning

confidence: 99%

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Menschaert

Xioajing

Jones

et al. 2017

Preprint

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SummaryOn behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI), we are here introducing two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations from the well-defined, widely used file formats SAM/BAM and BED respectively, and both have been extended to meet specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several very popular genome browsers, can be used to manipulate and visualize these formats already out-of-the-box. We also highlight that a number of specific additional software tools, properly supporting the proteomics information available in these formats, are now available providing functionalities such as file generation, file conversion, and data analysis. All the related documentation to the formats, including the detailed file format specifications, and example files are accessible at http://www.psidev.info/probam and http://www.psidev.info/probed.

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ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

Cited by 34 publications

References 10 publications

multiplierzv2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data

multiplierzv2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

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