various drought related traits not in TO

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From Brigitte Courtois, CIRAD France. brigitte.courtois@cirad.fr

Dear Richard, Dear Pankaj,

As mentioned by Manuel, we are presently synthetizing all the rice drought QTLs from the literature with the available information, in the framework of a GCP project. This does not duplicate Gramene database in the sense that we are focusing moslty on drought QTLs and we have collected, from the original published papers, many more information than included in Gramene, allowing to run searches on hydrological condsitions of the trial, type of experimental conditions (stressed or not), etc., this with the idea of running meta-QTL analyses (also planned in the framework of the same project). Then, Farkhanda Khowaja, a post-doc in Adam Price's lab in University of Aberdeen, that had done a similar work on the QTLs detected in the Azucenax Bala population provided us with her own data. We started harmonizing the two data sets. For such harmonization, we realized fast that we needed to use a trait ontology. We chose to use Gramene one but discovered, with some surprise, that many of our traits were not included in the TO list or that we disagreed with the definition (that sometimes did not fit with the M&M of the QTL paper or did not apply so well to rice). Attached is the present version developed by Farkhanda and myself. The link with Gramene TO is mentioned when we found one. We do not pretend that it is exempt of mistakes and that better definitions cannot be developed but we feel that it may be a contribution to the discussion on trait ontology that you are going to have in your June meeting. Woudl it be possible to include the traits of our list without TO into Gramene's own ontology and to give them a TO?

Of course, we intend to put the QTLs themselves into our database and made it available to everyone.We still have some checking to be done before putting it in the public domain but to have it done before the end of 2007.

All the best Brigitte

Reported by: jaiswalp

Original Ticket: "obo/plant-trait-ontology-to-requests/11":https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/11

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drought QTL traits mapped/missing in TO

Original comment by: jaiswalp

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Logged In: YES user_id=561361 Originator: YES

Dear Brigitte,

This seems a very exciting project to me. I will look into your list of traits and see what's the best way to get them in. Just a quick look at some of the traits that have in the definition "..in a drought stressed plot versus a control plot". I think in TO we want to have the trait names and their definitions represented in a more generic way, so that a person using the TO can use the terms independent of what environment/treatemnt was used to evaluate them. e.g. [not from your list] if we have TO for leaf color then anyone using it, whether someone has done it using a normal environment or using a drought like condition the same trait can be used. However the environment/treatment is important to the very experiment that was carried out for the study. My suggestion is that the environment be listed as a separate entity in your database or in any otherdb. Gramene is working on it too to get this implemented.

Another such reason you will notice in Gramene that a person searching for drought resistance won't get a lot of QTL results. This is so because the real parameter trait that was measured was not drought tolerance but something like e.g. root length under drought like environment to assess the overall tolerance for drought. SO if a person goes to environment list and select drought then they will get a long list of QTL but when in TO they get only those that are actually recorded for a given parameter.

Another possibility is that all such QTL that were assessed for drought tolerance but assayed using a different parameter (an underlying trait e.g. root length), then we can chose to annotate this QTL to two TO terms, drought tolerance as well as to root length. This will leverage the use of TO and will give a full list of QTL for drought tolerance.

In any case it should not be difficult to get the traits from your list into the TO. I will let you know when I am done.

Pankaj

Original comment by: jaiswalp

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• summary: various dorught related traits not in TO --> various drought related traits not in TO

Original comment by: jaiswalp

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• priority: 8 --> 5

Original comment by: cooperl09