Difference between revisions of "NeXML to ISAtab Mapping v0.1"

From Phyloinformatics
Jump to: navigation, search
(Created page with "File:NeXML_to_ISA_v0.1.jpg")
 
Line 1: Line 1:
 
[[File:NeXML_to_ISA_v0.1.jpg]]
 
[[File:NeXML_to_ISA_v0.1.jpg]]
 +
 +
 +
The diagram above shows the logical mapping of NeXML elements to ISAtab files.
 +
 +
'''NeXML Baiscs''
 +
[NeXML nexml.org] is an XML specification for phylogenetic data.  It is designed to be richly annotatable.
 +
 +
'''ISAtab Basics'''
 +
[ISAtab http://isatab.sourceforge.net/format.html] is a tab delimited file format underpinning the [ISAtools isa-tools.org] software suite.  It breaks microbiology studies into three logical units:
 +
:Investigations, representing the overall inquiry. 
 +
:Studies, representing a biological sample, usually a physical specimin, and
 +
:Assays, representing analysis of the sample via a variety of methods.
 +
 +
I'll refer to these as I, S, and A files below, respectively.
 +
 +
We are adapting this paradigm, built around wet lab experements, to 'in silico' experements such as the creation of phylogenetic trees from character state matrices.  We have the support of the ISAtools team in doing this, as a successful mapping will open their software up to much of computational biology more broadly.
 +
 +
 +
 +
 +
:In general, information directly within <<nexml>> the element and its <<meta>> children will be mapped to the appropriate field of the

Revision as of 11:14, 13 June 2012

NeXML to ISA v0.1.jpg


The diagram above shows the logical mapping of NeXML elements to ISAtab files.

'NeXML Baiscs [NeXML nexml.org] is an XML specification for phylogenetic data. It is designed to be richly annotatable.

ISAtab Basics [ISAtab http://isatab.sourceforge.net/format.html] is a tab delimited file format underpinning the [ISAtools isa-tools.org] software suite. It breaks microbiology studies into three logical units:

Investigations, representing the overall inquiry.
Studies, representing a biological sample, usually a physical specimin, and
Assays, representing analysis of the sample via a variety of methods.

I'll refer to these as I, S, and A files below, respectively.

We are adapting this paradigm, built around wet lab experements, to 'in silico' experements such as the creation of phylogenetic trees from character state matrices. We have the support of the ISAtools team in doing this, as a successful mapping will open their software up to much of computational biology more broadly.



In general, information directly within <<nexml>> the element and its <<meta>> children will be mapped to the appropriate field of the