Hi Pankaj
I've added a new worksheet to the attached which details the unique
traits/rows in the main file and with an initial definition of the trait
(parent and possible child relationships). It's a fairly complex jobs,
as there are traits at multiple levels in the TO hierarchy and defining
all their parent/child relationships is not trivial. I welcome your
suggestions!
Thanks, Emma
-----Original Message-----
From: Pankaj Jaiswal (OSU) [mailto:[email protected]]
Sent: Tuesday, 10 May 2011 10:29 AM
To: Mace, Emma
Cc: Youens-Clark, Ken; Ware, Doreen
Subject: Re: Uploading QTL information to Gramene
Emma,
See my inserts below. Many of my comments are based on my expertise in
rice and not necessarily in Sorghum. That's why we need sorghum experts
like you and your colleagues to help us define it. Often times I see in
the list provide by you that the actual trait is written in brackets. I
also see teh use of stages. Please elaborate on them as well.
Do let me know and I am more than happy to work with your group on
enriching the TO and getting the data successfully integrated in
Gramene.
Pankaj
On 5/9/2011 4:57 PM, Mace, Emma wrote:
> > Hi Pankaj
> > In the attached file there are 4 definitions of the traits.
> >
> > Column I: trait category
> > Column J: Trait sub-category
> > Column K: trait (shortened description) Column L: Trait (longer
> > description, as it appeared in the original publication).
> >
Thanks for pointing the columns. Yes I have about 220 unique rows, with
some duplicates still hanging around.
>>> >>>
>>> >>> 1. Trait symbol to use from Gramene's Trait Ontology I have
attempted
> >
>>> >>> to search on the trait name following the link to the Trait Ontology
>>> >>> search function, however with the exception of seed weight, I have
>>> >>> been unable to find the appropriate symbol to use. As you can see
>>> >>> from
>> >>
Many are still there and it all depends on how one names their trait and
defines the parameters to be evaluated. e.g. many of the leaf traits are
listed as children
http://gramene.org/db/ontology/search?id=TO:0002637
seed yield
http://gramene.org/db/ontology/search?id=TO:0000589
another example from your list of traits
Maturity (# days from planting to 50% anthesis)
is the same as
Maturity (Number of days from planting until 50% of plants
flower)
many of them are similar as well and equivalent to
http://gramene.org/db/ontology/search?id=TO:0000344
Maturity (days to anthesis)
Maturity (days to maturity)
Maturity (DTF average)
Maturity (DTF of first flowering tiller)
Maturity (Duration of Vegetative stage)
Maturity (flowering dates)
Maturity (flowering time)
Maturity (photoperiod sensitivity)
For many biotic resistance terms like the following I would like to get
the definitions so that I can judiciously add them to TO if they do not
exist already. provide causal agent/pest/pathogen name, any official
disease name etc.
Mean stem thickness
Midge resistance (antibiosis)
Midge resistance (antixenosis)
Milo disease (causative fungus: Periconia circinata)
Molds after harvest (1-5)
Molds during germination (%)
Rust resistance
Shoot fly resistance (glossiness)
Shoot fly resistance (mean deadheart % on 28 DAE)
Shoot fly resistance (mean eggs after 21 days post sdlg emergence)
Shoot fly resistance (mean eggs after 28 days post sdlg emergence)
Shoot fly resistance (seedling vigour)
Shoot fly resistance (trichome density on lower leaf surface)
Shoot fly resistance (trichome density on upper leaf surface)
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/43