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

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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.
Keywords
PROTEOGENOMIC CHARACTERIZATION, CANCER, REPRESENTATION, BROWSER, UPDATE, DRAFT

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Chicago
Menschaert, Gerben, Xiaojing Wang, Andrew R Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W Deutsch, Tobias Ternent, and Juan Antonio Vizcaíno. 2018. “The proBAM and proBed Standard Formats : Enabling a Seamless Integration of Genomics and Proteomics Data.” Genome Biology 19.
APA
Menschaert, G., Wang, X., Jones, A. R., Ghali, F., Fenyö, D., Olexiouk, V., Zhang, B., et al. (2018). The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data. GENOME BIOLOGY, 19.
Vancouver
1.
Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, et al. The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data. GENOME BIOLOGY. 2018;19.
MLA
Menschaert, Gerben, Xiaojing Wang, Andrew R Jones, et al. “The proBAM and proBed Standard Formats : Enabling a Seamless Integration of Genomics and Proteomics Data.” GENOME BIOLOGY 19 (2018): n. pag. Print.
@article{8547340,
  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 {\textacutedbl}out-of-the-box.{\textacutedbl} 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.},
  articleno    = {12},
  author       = {Menschaert, Gerben and Wang, Xiaojing and Jones, Andrew R and Ghali, Fawaz and Feny{\"o}, David and Olexiouk, Volodimir and Zhang, Bing and Deutsch, Eric W and Ternent, Tobias and Vizca{\'i}no, Juan Antonio},
  issn         = {1474-760X},
  journal      = {GENOME BIOLOGY},
  language     = {eng},
  pages        = {8},
  title        = {The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data},
  url          = {http://dx.doi.org/10.1186/s13059-017-1377-x},
  volume       = {19},
  year         = {2018},
}

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