Explore the Plant Trait Ontology on the Planteome site.
Home Page: http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab
License: Creative Commons Attribution 4.0 International
This is the repository for the Plant Trait Ontology.
The current release version of the TO can be accessed through the official PURLs:
Or via http://planteome.org/
All releases can be found here: https://github.com/Planteome/plant-trait-ontology/releases
(no defs)
these look like process terms and are in or should be found in GO
perhaps they should be obsoleted and consider tags made to new terms such as “nitrogen recycling rate”?
see also the *uptake terms and children of
[TO:0000349](http://purl.obolibrary.org/obo/TO_0000349) physiological process related trait
Reported by: cmungall
Original Ticket: obo/plant-trait-ontology-to-requests/25
the ratio of the number of stomata in a given area divided by the total number of stomata and other epidermal cells in that same area.
Reported by: dosza
Original Ticket: obo/plant-trait-ontology-to-requests/47
Diameter of rosette at maturity of main axis.
Reported by: dosza
Original Ticket: obo/plant-trait-ontology-to-requests/45
> from a user
6. We would like to add the trait “enhanced nutrient utilization”. The proposed definition for this trait is “enhanced efficiency in using available nutrients to generate yield, as compared to plants with lower nutrient utilization efficiency of the same crop”.
Pankaj: working on it
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/10
>from a user:
We would like to alter the definition of the trait “drought tolerance” [(TO:0000276](http://purl.obolibrary.org/obo/%28TO_0000276)). The current definition is “Becoming tolerant to drought like conditions of minimal or no water content in environment or high salt stress due to flash flooding in coastal areas”. We think
that too specific and would propose deleting the ending to read “Becoming tolerant to drought-like conditions of minimal or no water content in the environment.”
Pankaj:
updated definition: Becoming tolerant to drought like conditions of minimal or no water content in the growth environment.
Comment: Often the plants exhibiting high salt tolerance also exhibit drought tolerance.
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/5
I would like to request two terms related to “anatomy and morphology related trait”
root anatomy and morphology related trait [TO:0000043](http://purl.obolibrary.org/obo/TO_0000043)
-[i] root curvature
shoot anatomy and morphology related trait [TO:0000077](http://purl.obolibrary.org/obo/TO_0000077)
-[i] coleoptile curvature
reference: PMID 15598797
Please advise, thank you.
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/2
first_name:“Raymond”
last_name:“DiDonato”
organization: “BIOBASE Corporation”
address:“100 Cummings Center Ste. 107A”
city:“Beverly”
state:“MA”
suggested_term: “diterpenoid phytoalexin content”
is a child of (instance of): TO:0000290
definition:“Diterpenoid phytoalexins are polycyclic diterpenes involved in pathogen response.”
Takahashi A, Agrawal GK, Yamazaki M, Onosato K, Miyao A, Kawasaki T, Shimamoto K, Hirochika H.
Rice Pti1a Negatively Regulates RAR1-Dependent Defense Responses.
Plant Cell. 2007 Sep 21
PMID: 17890377
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/15
Hi Pankaj,
I am resubmitting this because I was not logged in and therefore would not receive updates/change e-mails.
Please uploaded TO suggestions (text-file).
Best regards,
Ray
Reported by: rdidonat
Original Ticket: obo/plant-trait-ontology-to-requests/22
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
from a user:
We would like to change the definition of the trait “insect resistance” [(TO:0000261](http://purl.obolibrary.org/obo/%28TO_0000261)). The current definition is “represents the damage done by the insects to the crop. The damage is a direct measure of resistance to the particular insect variety. The test evaluation is valid if insect population is uniformly distributed at a high level across the screening box or the field”. We think this is too specific and propose the following alternative “resistant to specific insect species such that insect damage and hence agronomic yield is not significantly reduced when compared to susceptible plants of the same crop.”
In addition, we would like to have the insect resistance trait subsumed by the following 2 trait categories:
“European Corn Borer (ECB) Resistance” (“resistant to such that insect damage and hence agronomic yield is not reduced when compared to susceptible plants of the same crop”) agent: Ostrinia nubialis
“Rootworm Resistance” (“resistant to Diabrotica spp. (rootworms) such that insect damage and hence agronomic yield is not reduced when compared to susceptible plants of the same crop”)
-—————————
Pankaj: Working on it. Its a good suggestion.
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/8
Please review the following terms and their relationship
TO:0000371 (yield trait)
*-i- TO: new (fruit number)
** -i- TO: new (filled fruit number)
TO:0002639 (shoot branching)
*-i- TO:new (apical axillary branch number)
*** -i- TO:new (apical axillary primary branch number)
*** -i- TO:new (apical axillary secondary branch number)
*** -i- TO:new (apical axillary tertiary branch number)
TO:0000190 (seed coat color)
-i- TO:new (seed coat spots)
TO:0000184 (seed anatomy and morphology trait)
-i- TO:new (seed texture)
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/29
Have you considered adding the traits in the USDA Plant Variety Protection Office forms http://www.ams.usda.gov/AMSv1.0/ams.fetchTemplateData.do?template=TemplateJ&navID=PVPOForms&page=PVPOForms&description=PVPO%20Forms, or noting in the existing traits where they correspond? Other countries also have similar forms, traits tested may be slightly different. An example is uploaded.
Reported by: splewis
Original Ticket: obo/plant-trait-ontology-to-requests/34
Hi Pankaj,
I've completed the spreadsheet for the 27 new Trait Ontology terms that the T-CAP participants would like to add to the ontology. Brian Steffenson, a pathologist at Univ. of Minnesota approved all of the pathology terms and Tom Blake, a malt barley breeder approved the remaining. For all, I got the sources from 2-3 places and paraphrased.
Thanks for all of your suggestions. I did eliminate the Winter Hardiness trait and used the Cold Tolerance trait as it suits our phenotype as well. I left a note about phenolics to you, i.e. these vary so staying generic is ok. I also used the Ontology term spike exsertion, as it existed in the Ontology, was distinct from panicle exsertion but had no definition. I provided one if you wish to use it.
Can you please let me know when these are added and I can update the databases supporting the T-CAP data to reflect the more granular TO terms.
Cheers,
Victoria
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/41
From a user:
> 3. We would like to add a series of traits related to herbicide tolerance (definitions in parentheses):
“herbicide tolerance” (“tolerance to label field application rates of herbicide, with little or no phenotypic effect and no effect on agronomic yield”), subsumed by the following 3 trait subcategories;
“glyphosate tolerance” (“tolerance to label field application rates of glyphosate, with little or no phenotypic effect and no effect agronomic yield”);
“glufosinate tolerance (”tolerance to label field application rates of glufosinate, with little or no phenotypic effect and no effect on agronomic yield");
“acetolactate synthase (ALS) inhibitor tolerance (”tolerance to label field application rates of herbicides of the acetolactate synthase inhibitor class, with little or no phenotypic effect and no effect on agronomic yield").
Pankaj:
Do you thing a generic definition like thsi would work:
—An assay to determine the tolerance to the applied XXX-herbicide of a plant or a group of plants (population).
Do you really want to add ..with little or no phenotypic effect and no effect on agronomic yield.
There is already a phenotype (…tolerance ) so we cant say little or no.
Thsi is okay to say : The herbicide application may not affect the agronomic yield.
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/7
I am using the plant_trait cross product definitions to find missing is_a links in TO
http://www.berkeleybop.org/ontologies\#plant\trait\xp
http://obofoundry.org/cgi-bin/detail.cgi?plant\trait\xp
I have a question re nutrients. In ChEBI, carbon is_a macronutrient. Does reflect an anti-plant bias or are there links missing from TO? For example, TO does not have carbon sensitivity under macronutrient sensitivity.
We are working with ChEBI on their treatment of roles, so feedback from PO would be useful here
“carbon sensitivity” [[TO:0000001](http://purl.obolibrary.org/obo/[TO_0000001)] is_a “macronutrient sensitivity” [[TO:0000176](http://purl.obolibrary.org/obo/[TO_0000176)] because of rule: genus_differentia : “macronutrient sensitivity” [[TO:0000176](http://purl.obolibrary.org/obo/[TO_0000176)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “macronutrient” [[CHEBI:33937](http://purl.obolibrary.org/obo/[CHEBI_33937)] , and it is the case that “carbon sensitivity” [[TO:0000001](http://purl.obolibrary.org/obo/[TO_0000001)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “carbon sensitivity” [[TO:0000001](http://purl.obolibrary.org/obo/[TO_0000001)] towards “macronutrient” [[CHEBI:33937](http://purl.obolibrary.org/obo/[CHEBI_33937)]“hydrogen sensitivity” [[TO:0000012](http://purl.obolibrary.org/obo/[TO_0000012)] is_a “macronutrient sensitivity” [[TO:0000176](http://purl.obolibrary.org/obo/[TO_0000176)] because of rule: genus_differentia : “macronutrient sensitivity” [[TO:0000176](http://purl.obolibrary.org/obo/[TO_0000176)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “macronutrient” [[CHEBI:33937](http://purl.obolibrary.org/obo/[CHEBI_33937)] , and it is the case that “hydrogen sensitivity” [[TO:0000012](http://purl.obolibrary.org/obo/[TO_0000012)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “hydrogen sensitivity” [[TO:0000012](http://purl.obolibrary.org/obo/[TO_0000012)] towards “macronutrient” [[CHEBI:33937](http://purl.obolibrary.org/obo/[CHEBI_33937)]“oxygen sensitivity” [[TO:0000015](http://purl.obolibrary.org/obo/[TO_0000015)] is_a “macronutrient sensitivity” [[TO:0000176](http://purl.obolibrary.org/obo/[TO_0000176)] because of rule: genus_differentia : “macronutrient sensitivity” [[TO:0000176](http://purl.obolibrary.org/obo/[TO_0000176)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “macronutrient” [[CHEBI:33937](http://purl.obolibrary.org/obo/[CHEBI_33937)] , and it is the case that “oxygen sensitivity” [[TO:0000015](http://purl.obolibrary.org/obo/[TO_0000015)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “oxygen sensitivity” [[TO:0000015](http://purl.obolibrary.org/obo/[TO_0000015)] towards “macronutrient” [[CHEBI:33937](http://purl.obolibrary.org/obo/[CHEBI_33937)]“cobalt sensitivity” [[TO:0000016](http://purl.obolibrary.org/obo/[TO_0000016)] is_a “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] because of rule: genus_differentia : “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)] , and it is the case that “cobalt sensitivity” [[TO:0000016](http://purl.obolibrary.org/obo/[TO_0000016)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “cobalt sensitivity” [[TO:0000016](http://purl.obolibrary.org/obo/[TO_0000016)] towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)]“selenium sensitivity” [[TO:0000032](http://purl.obolibrary.org/obo/[TO_0000032)] is_a “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] because of rule: genus_differentia : “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)] , and it is the case that “selenium sensitivity” [[TO:0000032](http://purl.obolibrary.org/obo/[TO_0000032)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “selenium sensitivity” [[TO:0000032](http://purl.obolibrary.org/obo/[TO_0000032)] towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)]“iodine sensitivity” [[TO:0000033](http://purl.obolibrary.org/obo/[TO_0000033)] is_a “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] because of rule: genus_differentia : “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)] , and it is the case that “iodine sensitivity” [[TO:0000033](http://purl.obolibrary.org/obo/[TO_0000033)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “iodine sensitivity” [[TO:0000033](http://purl.obolibrary.org/obo/[TO_0000033)] towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)]“chromium sensitivity” [[TO:0000034](http://purl.obolibrary.org/obo/[TO_0000034)] is_a “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] because of rule: genus_differentia : “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)] , and it is the case that “chromium sensitivity” [[TO:0000034](http://purl.obolibrary.org/obo/[TO_0000034)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “chromium sensitivity” [[TO:0000034](http://purl.obolibrary.org/obo/[TO_0000034)] towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)]“fluorine sensitivity” [[TO:0000038](http://purl.obolibrary.org/obo/[TO_0000038)] is_a “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] because of rule: genus_differentia : “micronutrient sensitivity” [[TO:0000080](http://purl.obolibrary.org/obo/[TO_0000080)] is defined as a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] that towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)] , and it is the case that “fluorine sensitivity” [[TO:0000038](http://purl.obolibrary.org/obo/[TO_0000038)] is_a “sensitive toward” [[PATO:0000516](http://purl.obolibrary.org/obo/[PATO_0000516)] and “fluorine sensitivity” [[TO:0000038](http://purl.obolibrary.org/obo/[TO_0000038)] towards “micronutrient” [[CHEBI:27027](http://purl.obolibrary.org/obo/[CHEBI_27027)]
Reported by: cmungall
Original Ticket: obo/plant-trait-ontology-to-requests/12
TO:0000664 (fungal blight disease resistance)
-i- TO:new (Sorghum leaf blight resistance)
-i- TO:new (chickpea ascochyta blight resistance)
-i- TO:new (chickpea colleotrichum blight resistance)
-i- TO:new (chickpea fusarium wild resistance)
-i- TO:new (chickpea botrytis grey mold resistance)
TO:0000439 (fungal disease resistance)
-i- TO:new (sorghum downy mildew resistance)
-i- TO:new (sorghum rust resistance)
TO:0000023 (fungal infection related grain discoloration)
-i- TO:new (sorghum grain mold)
TO:0000261 (insect damage resistance)
-i- TO:new (sorghum shoot fly resistance)
-i- TO:new (chickpea pod borer)
TO:0000454 (stem borer resistance)
-i- TO:new (sorghum stem borer resistance)
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/30
Please find attached a list of plant trait terms I suggest to be added in the Plant Trait ontology.
In the file please find the term and definition.
Reported by: alexandraviel
Original Ticket: obo/plant-trait-ontology-to-requests/49
From Brigitte Courtois, CIRAD France.
[email protected]
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
Please find attached a list of plant trait terms I suggest to be added in the Plant Trait ontology.
In the file please find the term and corresponding definition.
Reported by: alexandraviel
Original Ticket: obo/plant-trait-ontology-to-requests/50
Area of total upper leaf surface of vegetation.
Reported by: dosza
Original Ticket: obo/plant-trait-ontology-to-requests/46
Hi Pankaj,
I am curating a gene, rice SPK, which affects starch accumulation in the endosperm of immature seed (2 weeks after flowering). The authors analyzed the protein contents in immature seed, they grind the immature seeds without the lemma and palea to get the crude protein extract. I am wondering if we should have a term “endosperm storage proteins” to represent this crude protein extract.
protein composition related trait [(TO:0000490](http://purl.obolibrary.org/obo/%28TO_0000490))
-[i] endosperm storage proteins (TO:new)
-[p] endosperm storage protein-1 [content(TO:0000107](http://purl.obolibrary.org/obo/content%28TO_0000107))
-[p] endosperm storage protein-2 [content(TO:0000109](http://purl.obolibrary.org/obo/content%28TO_0000109))
Reference:
Gramene reference [ID:6603](http://purl.obolibrary.org/obo/ID_6603)
[PMID:11910009](http://purl.obolibrary.org/obo/PMID_11910009)
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/3
term name: jasmonic acid content
synonym(s): JA content, jasmonate content
definition: none
Reference/citation PMID: 17031029
suggested parent(s): growth hormone content [TO:000476](http://purl.obolibrary.org/obo/TO_000476)
Reported by: rdidonat
Original Ticket: obo/plant-trait-ontology-to-requests/13
Request new term for following rice insertional mutants phenotype:
Spiral leaf
Culm diameter (Thin culm and thick culm)
Culm senescence
Neck leaf
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/28
Hi Pankaj,
Please find attached the document of TO suggestion and do needful
Regards,
Arul
Reported by: bioinarul
Original Ticket: obo/plant-trait-ontology-to-requests/24
first_name:“Raymond”
middle_initial:""
last_name:“DiDonato”
organization:“BIOBASE Corporation”
address:“100 Cummings Center Ste. 107A”
city:“Beverly”
state:“MA”
postal_code:""
country:“USA”
telephone:""
fax:""
email_address:“[email protected]”
submission_type:“New Term”
submission_type_other:""
suggested_term:“gibberellic acid acid content”
associated_ontology:“TO: Trait Ontology”
plant_type:""
plant_type_other:""
parent_term1:""
relationship_to_parent1:“is a child of (instance of)”
[parent1_go_po_id:“TO:0000476](http://purl.obolibrary.org/obo/parent1_go_po_id:”TO_0000476)"
parent_term2:""
relationship_to_parent2:""
parent2_go_po_id:""
definition:“content of gibberellic acid within the plant”
synonym:“GA content”
reference_category:“Published”
reference_curator:""
reference_source:“PubMed”
reference_details:“1: Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y,
Matsuoka M, Yamaguchi J.
slender rice, a constitutive gibberellin response mutant, is caused by a null
mutation of the SLR1 gene, an ortholog of the height-regulating gene
GAI/RGA/RHT/D8.
Plant Cell. 2001 [May;13(5):999](http://purl.obolibrary.org/obo/May;13%285%29_999)-1010.
PMID: 11340177 [PubMed – indexed for MEDLINE]”
comments:""
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/19
The trait "seed number" TO:0000445 is currently a child of "yield trait" TO:0000371. Seed number is also a fruit quality trait in many crops including citrus, watermelon, other cucurbits, grapes, etc. See references "QTL analysis of yield and fruit quality in Citrus" http://www.springerlink.com/index/WJ897QCH50NM2CKD.pdf and "Evaluation of 22 populations achieved from controlled crossing between some
seeded x seedless grapevine cultivars" http://www.sciencedirect.com/science?\_ob=MImg&\_imagekey=B6TC3-4TJTTPP-3-1&\_cdi=5159&\_user=612300&\_pii=S0304423808003476&\_orig=search&\_coverDate=02%2F17%2F2009&\_sk=998809995&view=c&wchp=dGLbVtb-zSkzS&md5=605c891f62a7191f4299438a16099f4c&ie=/sdarticle.pdf. Could you please add "fruit quality trait" TO:0002728 as a parent of "seed number" TO:0000445?
Reported by: splewis
Original Ticket: obo/plant-trait-ontology-to-requests/35
Definition: The Zeaxanthin content in a plant or plant part
is_a: TO:0000301
Reported by: askarthikeyan
Original Ticket: obo/plant-trait-ontology-to-requests/37
Hi Pankaj,
Please find attached a tab-delimited list of new TO suggestions.
Reported by: rdidonat
Original Ticket: obo/plant-trait-ontology-to-requests/21
Ontology submission from Gramene
“Rice sheath blight (at least the one we’ve been studying) isn’t bacterial but fungal, caused by Rhizoctonia solani. So unless there are bacterial sheath blights, it should be under Fungal disease resistance instead of Bacterial ditto.
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/14
Create new ontology terms for the following:
glume length; glume width; glume pubescence density; glume pubescence length; glume waxiness; leaf pubescence density; leaf pubescence length
Reported by: *anonymous
Original Ticket: obo/plant-trait-ontology-to-requests/33
New TO term request from GCP:
[Term]
id: GCP_324.0000031
name: in vitro organic matter digestibility:
def: " This value predicts the amount of organic matter from the stover that would eventually be digested by animals. Value derived from chemical and in vitro analysis with rumen microbial inoculum of dried and ground stover, usually using Near Infrared Reflectance Spectrophotometry (NIRS) after appropriate calibration.calibration. Measured as %" [ICRISAT: Vincent Vadez; ILRI : Michael Bl|mmel; ICRIS: 022]
is_a: GCP_324.0000030 ! stover related traits
[Term]
id: GCP_324.0000036
name: metabolised energy
def: " The value takes into account energy losses occurring in the animal in faeces, urine and CH4 and estimates how much energy (in calories or joules) a given unit of ground stover is actually available for meat and milk production . Value derived from chemical and in vitro analysis of dried and ground stover.Units: Kcal/kg." [ICRISAT: Vincent Vadez; ILRI : Michael Bl|mmel;ICRIS:026]
is_a: GCP_324.0000030 ! stover related traits
[Term]
id: GCP_324.0000016
name: Nitrogen content :
def: " This is actually a value of % nitrogen concentration in the stover sample used for predicting crude protein (CP) content of stover by multiplication with a factor of 6.25 (CP = N x 6.25). This concentration is one of the criteria to assess the quality of fodder. Value derived from the analyis of stover using Near Infrared Reflectance Spectrophotometry (NIRS)." [ICRIS AT: Vincent Vadez; ILRI : Michael Bl|mmel;ICRIS:024]
is_a: GCP_324.0000030 ! stover related traits
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/32
Please add a trait for two-spotted spider mite or red spider mite (Tetranychus urticae) damage resistance http://en.wikipedia.org/wiki/Tetranychus\_urticae. This could be added under TO:0000054 “animal damage resistance” or under one or more intermediates “arachnid damage resistance”, “mite damage resistance”, etc. See references “Twospotted Spider Mite (Acari: Tetranychidae) Infestations on Soybeans: Effect on Composition and Growth of Susceptible and Resistant Cultivars” http://www.ingentaconnect.com/content/esa/jee/1986/00000079/00000004/art00007 and “Red spider mite tolerance in cucumber” http://www.springerlink.com/index/KN602R61738V7V76.pdf.
Reported by: splewis
Original Ticket: obo/plant-trait-ontology-to-requests/36
first_name:“Raymond”
middle_initial:""
last_name:“DiDonato”
organization:“BIOBASE Corporation”
address:“100 Cummings Center Ste. 107A”
city:“Beverly”
state:“MA”
postal_code:""
country:“USA”
telephone:""
fax:""
email_address:“[email protected]”
submission_type:“New Term”
submission_type_other:""
suggested_term:“amino acid content”
associated_ontology:“TO: Trait Ontology”
plant_type:""
plant_type_other:""
parent_term1:""
relationship_to_parent1:“is a child of (instance of)”
[parent1_go_po_id:“TO:0000281](http://purl.obolibrary.org/obo/parent1_go_po_id:”TO_0000281)"
parent_term2:""
relationship_to_parent2:""
parent2_go_po_id:""
definition:“None”
synonym:""
reference_category:“Published”
reference_curator:""
reference_source:“PubMed”
reference_details:“1: Wakasa K, Hasegawa H, Nemoto H, Matsuda F, Miyazawa H, Tozawa Y, Morino K,
Komatsu A, Yamada T, Terakawa T, Miyagawa H.
High-level tryptophan accumulation in seeds of transgenic rice and its limited
effects on agronomic traits and seed metabolite profile.
J Exp Bot. [2006;57(12):3069](http://purl.obolibrary.org/obo/2006;57%2812%29_3069)-78. Epub 2006 Aug 14.
PMID: 16908506 [PubMed – indexed for MEDLINE]”
comments:""
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/17
Definition is currently "The grain yield, measured in kilograms per hectare at 14 percent moisture." Generalize definition: amount of grain measured in weight per unit of area, at a given grain moisture"
Reported by: splewis
Original Ticket: obo/plant-trait-ontology-to-requests/39
TO:0000608 (sodium content)
-i- TO:new (shoot sodium content)
TO:0000609 (potassium content)
-i- TO:new (shoot potassium content)
TO:0000590 (grain weight)
-i- TO:new (grain weight to panicle weight ratio)
TO:0000014 (panicle weight)
-i- TO:new (grain weight to panicle weight ratio)
TO:0000373 (inflorescence anatomy and morphology trait)
-i- TO:new (panicle compactness and shape)
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/31
"Ethanol yield from biomass (predicted)" and measured in "L/Mg DM"
any suggested update for the methane yield terminology?
>
> For ethanol yield, my own opinion is that liters per megagram of dry biomass would make more sense. This is consistent with the volume/mass unit used by DOE; it's also consistent with the common measure of fuel ethanol (volume, not mass) and common measure of biomass. I'd call it biomass, not silage.
>
> That being said, ethanol yield in liters per megagram would depend on both the ethanol conversion process and the composition (not just the quantity) of the biomass. And in most cases (at least for breeding), it probably would be predicted ethanol yield instead of ethanol yield that is directly measured from a pretreatment and fermentation process.
>
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/44
first_name:“Raymond”
middle_initial:""
last_name:“DiDonato”
organization:“BIOBASE Corporation”
address:“100 Cummings Center Ste. 107A”
city:“Beverly”
state:“MA”
postal_code:""
country:“USA”
telephone:""
fax:""
email_address:“[email protected]”
submission_type:“New Term”
submission_type_other:""
suggested_term:“auxin content”
associated_ontology:“TO: Trait Ontology”
plant_type:""
plant_type_other:""
parent_term1:""
relationship_to_parent1:“is a child of (instance of)”
parent1_go_po_id:“TO: 0000476”
parent_term2:""
relationship_to_parent2:""
parent2_go_po_id:""
definition:“None”
synonym:""
reference_category:“Published”
reference_curator:""
reference_source:“PubMed”
reference_details:“1: Wakasa K, Hasegawa H, Nemoto H, Matsuda F, Miyazawa H, Tozawa Y, Morino K,
Komatsu A, Yamada T, Terakawa T, Miyagawa H.
High-level tryptophan accumulation in seeds of transgenic rice and its limited
effects on agronomic traits and seed metabolite profile.
J Exp Bot. [2006;57(12):3069](http://purl.obolibrary.org/obo/2006;57%2812%29_3069)-78. Epub 2006 Aug 14.
PMID: 16908506 [PubMed – indexed for MEDLINE]”
comments:""
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/16
Measure of the fresh weight of leaf.
Reported by: dosza
Original Ticket: obo/plant-trait-ontology-to-requests/48
Forom a user:
> 1. The trait “disease resistance trait” [(TO:0000112](http://purl.obolibrary.org/obo/%28TO_0000112)) has as synonyms “disease tolerance” and “disease susceptibility”. The latter is clearly in error (susceptibility is the opposite of resistance), and we propose it be deleted as a synonym. In addition, we would ask to add as a synonym “disease control”.
Pankaj: Ideally the trait term be called ‘response to disease’ and then attached to it are evaluation/phenotype scales namely’
susceptibile and tolerant. Because the trait can be scored for any of the above two values or an intermediated forms like moderately susceptibile, moderately tolerant etc.
Since there was is mechanism in teh TO so far to add the scored values we thought of adding the synonyms so that users are able to find the terms easily and their associations. Clearly more work is required. I will look into it.
I will add the synonym “disease control”.
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/6
Shuly,
Can we add a real seearch box on the index page of
plantontology.org
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/1
is_a: TO:0000301
Reported by: askarthikeyan
Original Ticket: obo/plant-trait-ontology-to-requests/38
Hi Pankaj,
Please find attached the document of TO suggestion and do needful
Regards,
Arul
TO Term Suggested Parent Definition Reference PMID Contributor
Iron content TO:0000465 The total iron ion content measured in a plant or a plant part. 17559517 Arul Prakasam
Zinc content TO:0000465 The total zinc ion content measured in a plant or a plant part. 17559517 Arul Prakasam
Manganese content TO:0000465 The total manganese ion content measured in a plant or a plant part. 17559517 Arul Prakasam
Copper content TO:0000465 The total copper ion content measured in a plant or a plant part. 17559517 Arul Prakasam
Nitrogen content TO:0000465 The total nitrogen content measured in a plant or a plant part. 17559517 Arul Prakasam
Nitrate content Nitrogen content The total nitrate content measured in a plant or a plant part. 17559517 Arul Prakasam
Stomatal process related trait TO:0000349 Trait associated with stomatal opening/closure/conductance/resistance process 12509525 Arul Prakasam
Stomatal opening Stomatal process related trait A process of opening of stomatal pores 12509526 Arul Prakasam
Sensitivity to nitrate TO:0000011 Sensitivity to the nitrate content in the growth medium 16415212 Arul Prakasam
Mineral and ion transport trait TO:0000349 “Trait associated with directed movement of minerals and ions into, out of, within or between cells.” 16415212 Arul Prakasam
Nitrate transport Mineral and ion transport trait “Trait associated with directed movement of nitrate into, out of, within or between cells.” 16415212 Arul Prakasam
Nitrate uptake nitrate transport The total nitrate ion uptake measured in a plant or a plant part 16415212 Arul Prakasam
Starch mobilization TO:0002658 Trait associated with directed movement of starch 15333754 Arul Prakasam
Phosphate content TO:0001024 The total phosphate content measured in a plant or a plant part. 18263782 Arul Prakasam
Adventitious rootless TO:0000198 Absence of adventitious roots in the plant 15960615 Arul Prakasam
Adventitious root length TO:0000227 Average maximum length of adventitious root of a plant in a study 18317796 Arul Prakasam
CW-cytoplasmic male sterility TO:0000580 Abnormal pollen germination 18308761 Arul Prakasam
Indole-3-acetic acid (IAA) content TO:0002672 Measures the IAA content in a plant or plant part. 17220367 Arul Prakasam
Root cortical cell length TO:0000043 Length of the root cortical cell 18317796 Arul Prakasam
Plant cell length TO:0002684 Length of the plant cell 18317796 Arul Prakasam
Vascular bundle development trait TO:0006015 Traits associated with observing effects on the development of vascular bundle 12506001 Arul Prakasam
Gynoecium development trait TO:0006022 Traits associated with observing effects on the development of the gynoecium 12506001 Arul Prakasam
Ovary development trait Gynoecium development trait Traits associated with observing effects on the development of the ovary 12506001 Arul Prakasam
Phosphorus toxicity TO:0000102 Accumulation of phosphate level in a plant or a plant part at toxic level 18263782 Arul Prakasam
Leaf chlorosis TO:0000419 Leaf surface area affected by abiotic stresses like insecticides and cold temperature as evidenced by chlorotic tissue 18263782 Arul Prakasam
Shoot phosphorus content TO:0001024 Amount of phosphorus in the shoot 18263782 Arul Prakasam
chlorophyll fluorescence quenching TO:0000283 The process to maintain the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules 15952067 Arul Prakasam
photochemical quenching chlorophyll fluorescence quenching 15952067 Arul Prakasam
non photochemical quenching chlorophyll fluorescence quenching 15952067 Arul Prakasam
neoxanthin content TO:0000301 The neoxanthin content in a plant or plant part 15952067 Arul Prakasam
violaxanthin content TO:0000301 The violaxanthin content in a plant or plant part 15952067 Arul Prakasam
Reported by: bioinarul
Original Ticket: obo/plant-trait-ontology-to-requests/27
chebi says glyphosate is_a acid
Reported by: *anonymous
Original Ticket: obo/plant-trait-ontology-to-requests/26
first_name:“Raymond”
middle_initial:“J”
last_name:“DiDonato”
organization:“BIOBASE Corporation”
address:“100 Cummings Center Ste. 107A”
city:“Beverly”
state:“MA”
postal_code:""
country:“USA”
telephone:""
fax:""
email_address:“[email protected]”
submission_type:“New Term”
submission_type_other:""
suggested_term:“brassinosteroid sensitivity”
associated_ontology:“TO: Trait Ontology”
plant_type:""
plant_type_other:""
parent_term1:""
relationship_to_parent1:“is a child of (instance of)”
[parent1_go_po_id:“TO:0000401](http://purl.obolibrary.org/obo/parent1_go_po_id:”TO_0000401)"
parent_term2:""
relationship_to_parent2:""
parent2_go_po_id:""
definition:“response with respect to application of brassinosteroid”
synonym:“BR sensitivity, brassinosteroid response, BR response”
reference_category:“Published”
reference_curator:""
reference_source:“PubMed”
reference_details:"1: Bai MY, Zhang LY, Gampala SS, Zhu SW, Song WY, Chong K, Wang ZY.
Functions of OsBZR1 and 14-3-3 proteins in brassinosteroid signaling in rice.
Proc Natl Acad Sci U S A. 2007 Aug [21;104(34):13839](http://purl.obolibrary.org/obo/21;104%2834%29_13839)-44. Epub 2007 Aug 15.
PMID: 17699623 [PubMed – in process]
"
comments:""
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/20
first_name:“Raymond”
middle_initial:""
last_name:“DiDonato”
organization:“BIOBASE Corporation”
address:“100 Cummings Center Ste. 107A”
city:“Beverly”
state:“MA”
postal_code:""
country:“USA”
telephone:""
fax:""
email_address:“[email protected]”
submission_type:“New Term”
submission_type_other:""
suggested_term:“tryptophan content”
associated_ontology:“TO: Trait Ontology”
plant_type:""
plant_type_other:""
parent_term1:""
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/18
> From a user
5. We would like to change the definition of the trait “nematode damage resistance” [(TO:0000384](http://purl.obolibrary.org/obo/%28TO_0000384)). The current definition is “crop damage done by nematode infection”, but this does not capture the trait, which is resistance to this damage. We would propose changing this to “resistant to nematodes such that nematode damage and hence agronomic yield is not reduced when compared to susceptible plants of the same crop”.
-————-
Pankaj: working on it. Good suggestion.
Reported by: jaiswalp
Original Ticket: obo/plant-trait-ontology-to-requests/9
Hi Pankaj,
I am confused by starch content [(TO:0000696](http://purl.obolibrary.org/obo/%28TO_0000696)) and starch yield [(TO:0000697](http://purl.obolibrary.org/obo/%28TO_0000697)), both have relationship to seed quality [(TO:0000162](http://purl.obolibrary.org/obo/%28TO_0000162)). Since there are no definition associated with each term, I can’t decide which one is better to describe the phenotype of “defect in starch accumulation”, should I use both?
p.s. starch granules were not formed in the Spk mutant.
Reported by: cwtung
Original Ticket: obo/plant-trait-ontology-to-requests/4
A record of our submission on 2008-01-09
Reported by: dsenalik
Original Ticket: obo/plant-trait-ontology-to-requests/23
Hello,
Working through different crops, some plant traits are missing in the plant trait ontology. Is it possible to add these new terms?
I send the excel file I have with the new terms listed.
Please let me know if you need additional information or if there is another way to proceed to request new traits.
Kind regards
alexandra
Reported by: alexandraviel
Original Ticket: obo/plant-trait-ontology-to-requests/40
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