Merge pull request #76 from LuisFF/master

bruker example for the reference spectra of 2-ketobutyric acid
nmrML example of a reference spectra recorded with a Bruker spectrometer
remove the white space in the folder name
nmrML example of a reference spectra recorded with a Bruker spectrometer, now located in the examples folder.
Merge branch 'master' of https://github.com/LuisFF/nmrML
A first rough draft of an NMR-ML Specification document. This version with comments and in very drafty stage. All text blocs from the original mzML Doc that can stay as they are are highlighted in yellow,  the rest has been aligned for nmrML mainly by adding text form the D2.4 deliverable.
Merge pull request #77 from LuisFF/master

nmrML example for bmse000325 NMR experiment
pynmrML
Updated nmrML.py
Modifications to spec doc
Added xerces xsd validation errors as comments. Added further comments based on a meeting with our nmr expert.
Update README.md

update covering the new example
update in the nmrML example file. Generated with the Java converter.
minor additions in comment fields
some additions as bulleted ideas
This is an experimental CV version that uses BFO 2.0 as top level ontology instead of BiotopLight.

I still like to expresses my doubts on a potential switch to BFO, as
* BFO is a Top level ontology and does not provide an intuitive bio upper level, making the semantic gap between the re-binned classes quite large at times. The only way to circumvent this is the import of an intermediate bio layer from e.g. OBI and others.
* BFO classes are not intuitive to our users ( e.g. dependent continuant, or the distinctions fiat object to object to object aggregate). The geek factor is too high and the gap to the PSI CV design principles will be enlarged even more.
* BFO and OBI complex setup, e.g. reliance on external scripts and dependency on further artefacts like IAO, OBI to be usable.
* The geek factor of BFO together with IAO and OBI is quite high and this is exactly what CVs don't need. These are Description logics focused and lack ergonomy to serve as communication channel. The overhead of constructs, that we are not requiring for our scope, is quite high.

Please all look at this version and compare to the nmrCV under (btl2) in terms of intelligibility to a biologist.

Here the single changes I made while re-binning under BFO2.0:
BFO 2.0 (Graz version) is  imported from http://www.ifomis.org/bfo/ (outdated?)
Some required re-binning ...
btl2:information object subclasses were moved under bfo:generically dependent continuant
or import IAO to close gap (is there a version for BFO2.0?)?
software moved from btl2:plan to bfo:realizable entity. (Obi or IAO needed to close gap?)
data transformation moved from btl2:plan execution to bfo:process
chemical compound and instrument were put under bfo:object aggregate (do we expect that our users will be able to distinguish these form objects and fiat objects ?)

all namespace references and an orphan btl2 relation (is bearer of) were deleted from this file.
some rewordings, formattings and additions
Improve pynmrML readme
Reorganize
Add var2nmrML bin