#120 Term request: biomass

[Anonymous]

Hi all,

I am working on the encoding of (dynamic) FBA models in SBML. An important part of such models is a 'biomass' species. It would be very helpful to be able to annotate this species with the a term.
Currently there is only a term 'biomass production'
https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000629
to annotate the biomass reaction in FBA models, but no term to annotate the actual biomass in the model.

The best
Matthias

[Varun Kothamachu]

Dear Matthias,

Thank you for the term request.

Why not use one of the terms under material entity (SBO:0000240) or functional entity (SBO:0000241) nodes for this ?

Varun

[Nicolas Rodriguez]

Which term(s) in particular would you advice Matthias to use ?

[Varun Kothamachu]

Dear Matthias,

Following our email conversation, we will be creating a new term for biomass under SBO:0000241. Kindly comment on the definition for the term that we are considering.

biomass - A composite representation of material entities required for organismal growth. It includes macromolecular content (eg. cellular protein fraction), metabolic constitution of each fraction (eg. amino acids), and atomic composition (eg. nitrogen atoms).

Varun

[Varun Kothamachu]

Dear Matthias,

Thank you for your feedback via email. The term for biomass is now online and can be referred to using the id SBO:0000649.

I will now close this ticket. Thank you for your support.

Best,
Varun