Title |
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
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Published in |
Genome Biology, January 2018
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DOI | 10.1186/s13059-017-1377-x |
Pubmed ID | |
Authors |
Gerben Menschaert, Xiaojing Wang, Andrew R. Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W. Deutsch, Tobias Ternent, Juan Antonio Vizcaíno |
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 . |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 7 | 25% |
United Kingdom | 7 | 25% |
France | 2 | 7% |
Portugal | 1 | 4% |
Norway | 1 | 4% |
Germany | 1 | 4% |
Belgium | 1 | 4% |
Spain | 1 | 4% |
Russia | 1 | 4% |
Other | 0 | 0% |
Unknown | 6 | 21% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 15 | 54% |
Scientists | 12 | 43% |
Science communicators (journalists, bloggers, editors) | 1 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 55 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 13 | 24% |
Researcher | 12 | 22% |
Student > Master | 8 | 15% |
Other | 5 | 9% |
Student > Bachelor | 3 | 5% |
Other | 9 | 16% |
Unknown | 5 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 24 | 44% |
Agricultural and Biological Sciences | 13 | 24% |
Computer Science | 2 | 4% |
Medicine and Dentistry | 2 | 4% |
Business, Management and Accounting | 1 | 2% |
Other | 5 | 9% |
Unknown | 8 | 15% |