Connecting Plant Ontologies


#1

Earlier today @dornawcox, @sudokita, @ziamehrabi, @julietnpn , @celineaubert , @malaporte, and Elizabeth met to discuss the idea of connecting various plant ontologies that we use or developed.

We’d like to welcome others on this forum to share the ontologies they’ve used or created. Individually we have created plant ontologies for distinct applications. Moving forward we would like to organize a meeting or online gathering where we present our ontologies to each other. From there we would like to discuss about the opportunities and implications for connecting some or all of these ontologies.

The plant ontologies discussed today include:
Crop Ontology: http://www.cropontology.org/
Agronomy Ontology: https://github.com/AgriculturalSemantics/agro
Planteome (Plant and Plant Trait ontologies): http://planteome.org/
For an easy exploration of the ontologies, you can use this website: https://www.ebi.ac.uk/ols/index
The ontology that underlies the Software for Agricultural Ecosystems (SAgE Plant Database): https://sage-pdb.herokuapp.com/
Cover Crop Decision Support Tool (no website/github yet)

Let us know if you’re interested in this topic!

– Juliet


#2

@mstenta @gbathree fodder for biddy goat and moar!


#4

Can someone provide some background on this subject (ie, what the problem is, what the goal is, what success looks like, etc) to a software engineer with no previous ag experience?


#5

Utilizing common vocabularies generally allow us to model data in compatible ways across tools. My potato should ideally be compatible with your potato.

Problem: concepts are not consistent across tools, models, databases etc.
Goal/succes: achieve conceptual consistency and therefore interop.

Crop and agronomy ontologies offer things like: controlled vocabularies to represent crops and their characteristics (e.g., Banana example; agronomic concepts and what they entail; categories and classification structures etc. Lots of nouns, so to speak.

Such ontologies enable domain specific modeling and the underlying infrastructure for conceptually interoperable tools.

Apologies for rambling- about to board a plane and typing on my phone. But I’m really excited to begin the ontology discussions. I’d been tracking planteome for a while and so am keen for this collab to get off the ground. Might write more later. Does any of this address your question?


#6

It looks like the listed projects have some overlap but have different goals. Broadly, the goal of these projects seems to be the creation of a standard, machine-readable language for the myriad characteristics of every organism. A document type definition for biological traits.

Am I close?


#7

Yes, these projects have different goals.

In the case of my project (SAgE), the ontology is still fluctuating because the way people conceptualize and use plant information within the communities I’m working with (grassroots sustainable agriculture communities) vary so much. My goal is not to create a standard, but to figure out away to aggregate knowledge within a community and share that information across the community. Creating an ontology is a way to grapple with the complexity of this problem, but not the end goal. Were I not trying to develop information systems to address this problem, the communities I work with may never consider creating an ontology. I’m not sure how much the ontology will be used in their day-to-day design practice - there is a good chance that my participants will keep on thinking about plants the way that they always have been. An ontology is, however, helpful for organizing, storing, and sharing this information so my participants can reference it for their own uses, and so the information can be utilized by other information systems.

Could my ontology for non-professional/amateur/enthusiast sustainable agriculture practitioners be useful in other contexts? Could one of the other ontologies support mine and the over arching goals of my research? I think this is what we’re trying to figure out here. At least its what I’d like to figure out. :slight_smile:


#8

Also check out the United Nation’s AgroPortal via AIMS: http://aims.fao.org/agroportal; also the OWL ontology Agrontology.


#9

I wonder if we should have this topic be part of the GOAT web series? Any volunteers to present and host?