Re: [CDAO-discuss] [Nexml-discuss] BIOM format

[Arlin S. <ar...@um...>]

I haven't heard of any such interaction.  Note that this JSON file  
format aims to support something broader than just an OTU X character  
matrix.

Arlin

On Feb 20, 2012, at 3:40 PM, Vision, Todd J wrote:

> I think there's an opportunity here to find common cause with other  
> active developers interested in interoperability of comparative  
> observational data.   Has there been any interaction with the BIOM  
> group already?
>
> Todd
>
> ********
>
> Date: Mon, 20 Feb 2012 12:00:51 -0700
> From: Greg Caporaso <gre...@gm...>
> To: dev...@li...
>
> GSC developers,
>
> Attached please find a proposal for recognition of the Biological
> Observation Matrix (BIOM, pronounced 'biome') format as a GSC Core
> Project. A brief description of the motivation for this file format is
> below (this is also presented as the abstract in the attached PDF).
> You can find additional details on the BIOM format at:
>
> http://www.qiime.org/svn_documentation/documentation/biom_format.html
>
> I look forward to feedback on this proposal from the GSC community,
> and would be very interested in joining a call at some point soon to
> discuss the next steps in moving this toward GSC recognition.
>
> Thanks!
>
> Greg Caporaso, on behalf of the Biological Observation Matrix (BIOM)
> project team
>
>
> Project Abstract:
> A central data type in 'comparative -omics' analyses (e.g.,
> metagenomes, comparative genomics, marker-gene-based community
> surveys, and metabolomics) is a sample by observation matrix. In
> marker gene surveys, this would contain counts of OTUs on a per-sample
> basis; in metagenome analyses, this might contain counts of
> orthologous groups of genes, taxa, or enzymatic activity on a
> per-metagenome basis; in comparative genomics, this would contain
> counts of genes or orthologous groups on a per-genome basis. Many
> tools have been developed to analyze this data, but are generally
> focused on a specific type of study (e.g., QIIME for marker gene
> analysis; MG-RAST for metagenome analysis; VAMPS for taxonomic
> analysis). Many of the techniques, however, generalize across data
> types (e.g., rarefaction analysis/collector curves are generally
> applicable to all of these data types). A standard format for the
> sample by observation matrix will support interoperability of these
> tools, and facilitate development of future analysis tools.
> Additionally the incorporation of sample and observation metadata in
> this file allows for convenient sharing and archiving of these data
> within a single file.
>
> The BIOM file format has been developed with input from the QIIME,
> MG-RAST, and VAMPS development groups. BIOM format is based on JSON, a
> human?readable, open standard for data exchange. In addition to
> consolidating data and metadata in a single standard file format, BIOM
> supports sparse and dense matrix representations to efficiently store
> these data on disk. Sparse representations of QIIME OTU tables in BIOM
> format, for example, can be more than 3X smaller than the same data
> represented in tab-delimited text.
>
> To support the use of this file format a new open-source software
> package will be available at http://biom-format.sourceforge.net. This
> will include a format validator, and new Python objects to support
> working with this data. This software package will additionally serve
> as a repository where other developers can submit implementations of
> these objects in other languages. Full format and API documentation
> (for the Python objects) will be available to coincide with submission
> of an article describing the BIOM format (target submission date of
> late Feb 2012). Draft documentation is currently available at
> http://biom-format.org.
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft  
> developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,  
> MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> Nexml-discuss mailing list
> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss

-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org