In addition to the three main “core” datasets above, there is another equally important dataset describing all kinds of properties, especially the ones that vary within a crop/livestock/microorganism: the basis for why we treat them as cultivars (and breeds and strains) in the first place. To find and to structure these kinds of data for all the worlds domesticated organisms is an overwhelming task, and will be a main objective of the foundations activity.
Sources
Sources we currently use:
- Crop Ontology: https://cropontology.org/
- Bioversity: https://www.bioversityinternational.org/e-library/publications/detail/descripteurs-de-passeport-multi-cultures-faobioversity-v21/
- CropTrust’s Genesys: Descriptor lists (genesys-pgr.org)
- The Czech genebank: https://grinczech.vurv.cz/gringlobal/search.aspx
Tell us about other sources we should check!
Method
We don’t know yet how detailed we need to build the trait system for it to serve the purpose of the Culton checklist. The most important info concerning cultivation, storage and use (sowing temperature, soil type preference, light/darkness for germination, harvesting method, storage method, etc) is obviously needed. But there are so many datapoints one might measure that it can be quite overwhelming. Many of the systems we look at are developed for research and breeding purposes, so it will be necessary to extract the most important traits.
The structural goal is to make one single list of traits (with persistent UUID’s) and then a way for the system to use only the relevant traits for each organism or group of organisms when describing those. For example the traits describing fruit color or potato diseases isn’t relevant for carrots, but root shape, root color and carrot diseases are. There is no point in a system that sort of expects irrelevant data.
There are obviously some traits that are relevant for all organisms, like origin, habitat, etc. Those can be stored in the main symbio-table where all crop/livestock/microorganism entries are stored.
The “symbio-dependent” traits however, is better stored in separate tables so that these can be built without this expectance of irrelevant data, and the tables thus be smaller and more easily maintained. The data in those tables will be the actual cultivar discriptor data, for example fruit color, maturation time, storability etc for apples.
Our method will initially look like this:
- create the first version of the core traits to be stored directly in the crops/livestock/microorganisms table (the symbio table as we call it technically)
- populate that list with available data for the crops/livestock/microorganisms whe have identified
- start building separate trait lists for the main crops/livestock/microorganisms based on a comparison of the descriptor-systems we have found, and keep the reference to those within the tables
- for all traits we thus incorporate into the system, the total list of traits will grow, each given their unique ID (UUID)
- when the system is made public, we will be able to invite the users to contribute data and actually handle those data in a structured way, since the framework is ready
Data
Our first beta version of the checklist service will run from beta.culton.org. Here at culton.org development datasets, mostly in spreadsheet format, are intended for internal discussion among logged in participants of the project. If such data has been posted, there is a link to it below here:
Last Updated on 2023-09-02 by Karl Aakerro