1.) Original submission (after steering group review):
The attached documents are a new submission of the Recommendation Document for the file format "proBAM".
"The format represents output from proteogenomic studies, mapping the MS-based proteomics PSM information to the genome." (see also Cover Letter attached)
Background: The proBAM format builds upon the structure of the original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf) by extending it with other mandatory fields to accommodate unique features on MS-based proteomics peptide-spectrum matches (PSMs) information. Relation to other formats: Similar to the situation with mzIdentML/mzQuantML and mzTab, the proBAM and proBED formats represent analogous information with a different level of detail, leading to different use cases. Both well-established and heavily used genomics counterparts (BAM and BED) whereupon these proteogenomics formats are built, already exist for multiple years as separate entities and it it advisable to keep this situation aligned (also for maintenance issues).
After having passed a 30-day review of the PSI steering group with minor changes, the proposed document version 1.0.0 DRAFT now goes through 60-days public comments and external review phase (end: 31st May 2017).
The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.
Attached are the proBAM submission cover letter and the specification document in Word and PDF format. Example files and existing tools are linked here.
Please add comments to this page or send them directly to martin.eisenacher: at : rub.de for example regarding the following criteria of the specification:
- That it is well formed – that is, it is presented in accordance with the templates and is clearly written.
- That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format.
- That the examples are in accordance with the specification.
This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal.
If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI.