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Planteome / plant-trait-ontology

Explore the Plant Trait Ontology on the Planteome site.
http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab
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metal concentrations in plant parts #456

Open ramonawalls opened 4 years ago

ramonawalls commented 4 years ago

As part of an environmental health project I am working on, @kaiiam and I are creating new terms for the concentration of different metals in plant parts such as fruits or leaves. We feel that TO would be a better long term home for these traits than ENVO.

We want these to correspond to a set of ENVO concentration terms we are creating, but TO has terms for content rather than concentration. These terms are not yet logically defined, however. Would you be open to defining them based on PATO_0000033 (concentration of) using the design pattern:

concentration of X in Y is equivalent to 'concentration of' and 'inheres in' some (X and 'part of' some Y) as used at https://github.com/EnvironmentOntology/envo/blob/master/src/envo/patterns/chemical_concentration.yaml?

This should also lead to TO_0000465 (mineral and ion content) being a subclass of PATO concentration of.

If this is acceptable, I am happy to create the terms and do a pull request.

cooperl09 commented 4 years ago

The TO currently has a number of concentration terms as well as content ones. Which metals are you interested in? Example: TO:0006049 iron concentration TO:0006052 copper concentration TO:0006053 zinc concentration

kaiiam commented 4 years ago

Hey @cooperl09 Kai Blumberg here ENVO editor, thanks for the quick response! I've been preparing for the creation of such terms by making csvs formatted for use within the TO composition DOSDP. We're still waiting for some data from some our our collaborators but once I have the complete set I can share it with you.

Let us know if you'd be interested in adding it to the DOSDP. I'd be happy to make a pull request as well. Perhaps you'll want to review it prior?

Here is a small preview of what we have:

defined_class defined_class_label entity entity_label plant_part plant_part_label
TO:0000xxx vascular leaf elemental beryllium content CHEBI:33784 elemental beryllium PO:0009025 vascular leaf
    CHEBI:33628 elemental aluminium PO:0009025 vascular leaf
    CHEBI:35171 elemental vanadium PO:0009025 vascular leaf

...