The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso
2012 GigaScience  
Attached please find our revised manuscript and response to the reviewer's comments. As we discussed, I approached Jonathan Eisen about writing a commentary on our paper, and specifically on the "ome-ome" idea and the proliferation of "omics terms" in the biomedical literature. He mentioned that he is interested in principle, so we have left our discussion of this in the text. If it's OK with you, I'd like to send him this draft of the manuscript. At that point I'll confirm his interest in
more » ... ng a commentary, and he can use this draft to base his commentary on. We have pasted the full text of the reviewers' comment below, and provided our responses in red. Thank you again for considering our manuscript for publication in GigaScience. Sincerely, J. Gregory Caporaso Reviewer: Frederick Matsen Minor essential revision: I have one real suggestion, which is to separate the description of the format from its implementation in Python. The history of formats that are defined wholly or partially by a reference implementation is not pretty. The description on seems complete to me, and I think that link should be given in this manuscript as the specification. Similarly, I'm a bit surprised by the decision to tie the BIOM format version to the version number of the biom-format software. If the goal is to parsers in lots of languages, won't they at some point be at different versions? I think that versioning the spec is the appropriate thing to do here. We see the reviewer's point about decoupling the version of the biom-format package and the version of the specification, and will act on that suggestion. We have updated the text describing this point in the paper. If it acceptable to the reviewer and the editor, we would like to synchronize the change to the software and specification with the publication of the paper. At that time, we will create a 1.0.0 version of the BIOM specification, which will be under independent versioning from the biom-format project. The reason we would like to wait until the publication of the paper is that we are already planning a 1.0.0 release of the biom-format project at that time, and, given that several software development groups either have or are in the process of integrating the BIOM format into their tools, we feel that doing a release now and an additional release in the near future will be disruptive of that process (and could thus hinder the adoption of BIOM). We thank the reviewer for this very valuable suggestion. Discretionary revisions: Abstract:(1) "JSON-derived": I would prefer "JSON-based" rather than "JSONderived" as the latter makes it sound like you are extending JSON in some way. Modified as requested. (2) "bioinformatics bottleneck": I would prefer something more precise like "the file format incompatibility problem". We have opted to keep this terminology for consistency with the cited references in this section.
doi:10.1186/2047-217x-1-7 pmid:23587224 pmcid:PMC3626512 fatcat:mvod5riw6zhfbmutpxpnodtgva