nmrML/nmrML — pull request #92 by proccaserra (2014-01-21 17:04:52+00:00)
Title: Using CHEBI for chemical entities instead of asserting them directly under the NMRML-CV namespace

Dear All,

Before accepting the request, check my forked repo.
I have created an import file holding (most) chemical entities currently used in NMRCV (the missing ones have been submitted and I am waiting for CHEBI to issue to identifiers). I believe it would ensure consistency with regard to the reporting of metabolite identifications.
I have also moved a number of classes to make them children of 'material entity' and created defined classes for 'buffer', 'solvent' and so on (with respective role classes), set the role at the level of the 'molecular entity' and let the classifier do its job. This has to the potential to prevent issuing several NMRCV identifiers for the same entity (something that may have already happened: see Chloroform-d and Chloroform-d1 classes

Note: all axioms set on the imported classes are saved in NMR-CV.owl, so updates from CHEBI should be simply a matter of upgrading the ontofox files.

The next action, if the proposed changes are accepted', would be to deprecate the asserted classes under 'acquisition nucleus' and the likes.

Cheers

Philippe