ArticleGenome biology2018
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed.
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.GigaScience · 2020Article
- The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.Nucleic acids research · 2020Article
- Long non-coding RNA profiling in LPS-induced intestinal inflammation model: New insight into pathogenesis.Innate immunity · 2019Article
- PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms.Molecular & cellular proteomics : MCP · 2019Article
- Proteomics Standards Initiative Extended FASTA Format.Journal of proteome research · 2019Article
- PDV: an integrative proteomics data viewer.Bioinformatics (Oxford, England) · 2019Article
- Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets.Molecular & cellular proteomics : MCP · 2019Article
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.Journal of proteome research · 2017Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here 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 of the well-defined, widely used file formats SAM/BAM and BED, respectively, and both have been extended to meet the specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several widely used genome browsers, can already be used to manipulate and visualize these formats "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, including the detailed file format specifications and example files, are accessible at http://www.psidev.info/probam and at http://www.psidev.info/probed .
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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.