Messenger RNA not listed as a material entity

[luciansmith]

When validating SBML files from biomodels, we get the following warning whenever a species is annotated as messenger RNA:

• The value of the 'sboTerm' attribute on a <species> is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity"). Reference: L2V4 Section 5 SBO term 'SBO:0000278' on the <species> is not in the appropriate branch.

It's possible that this is a validation problem, but I do think that messenger RNA is indeed a material entity (as well as being a 'functional entity'), and should be cross-added to that branch (like 'gene' is).

[shoepfl]

Hi,

today I encountered the same issue as I had several warnings that the SBO terms of my species were not in the appropriate branch. One of them was also the mRNA but in my oppinion also microRNAs should be included there.

What was the reasoning why it has been changed to material entity only in L2V4? In my oppinion microRNAs, mRNAs etc. would make it more precise.