including PO terms into TO: e.g. shoot fresh weight

[teatree1212]

I am getting confused by the way you handle certain traits like fresh and dry weight as always being associated with a plant part, but when it comes to ontologies like phosphorus content (TO:0001024), you are less strict: I also found it as leaf (TO:0001025) as well as seed (TO:0002666) and shoot (TO:0020114) phosphorus content. I would prefer having the a fresh and dry weight trait not associated to any plant part, as you seem to have the choice with some element content. Thanks, Annemarie

[cmungall]

Do you want the generic term for query purposes, or for annotation? What are the scenarios where you would not know which plant part was weighed?

[teatree1212]

In many experiments people use either the whole plant's aboveground/ root/ or leave fresh or dry weight. So on our side it would be helpful to associate a PO term with a TO term, such as . so that it is easier to generate tissue specific traits rather than only finding the trait tied to one single plant part/ tissue (in the above example, phosphorus content is a standalone trait, yes, but there are leaf, seed and shoot phosphorus content traits as well. But there is no "shoot" phosphorus content trait. If we just created our own trait using and < phosphorus content> ourselves from PO and TO, that would be quick and easy. However, we would then not be consistent with the TO ids, in comparison with the leaf, seed and shoot TO terms.

[cmungall]

You can post-compose your own trait descriptions using combinations of ontology terms, but you can only do this if the data model you are using is rigorous and well-aligned with the ontology model. If you are interested in going this route you can point your developers at the emerging PXF standard (http://phenopackets.org)

However, it is often simpler to pre-compose the term in TO. This can be done a few ways

• Add a ticket for each term here
• Get a term instantly using a web-based templating system. We are using http://to.termgenie.org for this

I will consult with @cooperl09 and @jaiswalp on the best route for you

[cooperl09]

Hi Annemarie, I agree that things are not yet completely consistent in the current TO, these are legacy issues we are working to resolve. I understand the argument for the "generic" fresh weight or dry weight terms. In fact the phosphorus content (TO:0001024) is associated with the PO term plant structure (PO:0009011), which encompasses any part of the plant, or a whole plant. The more specific phosphorus content terms are child terms.
For the fresh and dry weight terms we could reasonably add a corresponding upper level term, but you will probably want to use the more specific child term such as whole plant fresh weight (TO:0000442), root fresh weight (TO:0000578) or shoot fresh weight (TO:0000571).