FW: Compositae vocabulary

Mon Aug 14 14:16:49 EDT 2006

Hi Kent,

1. Thanks for the list of terms. After brief look, I noticed that most 
terms are attributes of plant parts (i.e., entities or terms in the 
Plant Structure Ontology, abbreviated as PSO). However, PSO doesn’t 
include attributes or experimental conditions. Attribute (and value) 
terms are part of the Phenotype and Attribute ontology, PATO (URL: 
http://obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_value). This 
ontology is generic and is meant to be sufficient for phenotype 
description across kingdoms. It is currently maintained by curators from 
M. Ashburner’s group, contact person is George Gkoutos, 
e-mail:g.gkoutos at imperial.ac.uk.

2. There are some Compositeae terms on your list that we don’t have in 
PSO yet, I’ll pass the list to the curator at Gramene (Pankaj Jaiswal). 
After August 31, someone from their group will coordinate the Plant 
Ontology project.

3. Also, POC ontology developers will discuss terms that I marked with 
red font in the attached document on our August phone conference.

4. A couple of terms on your list are already in the PSO (phyllary, 
PO:0009045, and leaf margin, PO:0020128).

5. Terms that include stages based on days after germination, flowering 
or similar, are intentionally excluded from PO. Best you can do is to 
replace them with terms (stages) in PO based on morphological features 
of the organ/plant at a particular time point depicted by counting days.

6. Regarding phenotype descriptions, TAIR, Gramene and MaizeGDB use PSO 
terms and free text description for describing mutant phenotypes. At 
TAIR, we have had a pilot project to test the description of phenotypes 
using several ontologies (PO, GO, PATO and perhaps some others). Also, 
NASC has already started using PATO (although it is not on their web 
site yet either). I can perhaps get some example from them too.

Here is an example from TAIR pilot project, an early attempt to use PATO 
terms (although they were not entered with term IDs, as some terms are 
not yet added in PATO.
Note, this is not yet displayed on TAIR web site, and is just a first 
trial. Also, please note that this is a description from published 
literature.

AN EXAMPLE of a description of mutant phenotype at TAIR, using Entity, 
Attribute and Value model (EAV):

grmplasm CS6130, allele abi3-4, locus AT3G24650, pub ref ID 5348,

Description: Abscisic acid resistant, strong allele, reduced sensitivity 
to ABA inhibition of germination, germination of seeds only slightly 
inhibited by 1mM ABA; normal plant growth; seeds fail to degrade 
chlorophyll during maturation keeping seeds green until mature.

Controlled vocabulary description:
Seed coat (PO:0009088) entity: color (attribute):green (value)
Seed maturation stage (PO:0007632): altered
Acquisition of desiccation tolerance (GO:0048700): reduced

Hope this helps. I'll get back to you after discussing this issue with 
the POC ontology group.

Best regards,

Katica

KENT BRADFORD wrote:
> Katica:
> 
> Thank you for your reply. I miss messages myself these days due to spam
> filters. 
> 
> I have worked on our character lists today, and have developed a draft
> of how we might enter our data under your PO terms. The attached
> spreadsheet has a page with all of the phenotypic characters we have (or
> expect to have) data for, and the second sheet is a rough effort by me
> to slot those characters under your existing terms, or indicate where it
> appears that new terms may be needed. Some terms can also be cross
> listed under other terms, and I have not tried to do that as yet. Am I
> on the right track with this? Thanks for your assistance.
> 
> Kent Bradford
> 
> -----Original Message-----
> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] 
> Sent: Friday, August 11, 2006 4:08 PM
> To: po-dev at plantontology.org; KENT BRADFORD
> Subject: Re: FW: Compositae vocabulary
> 
> Dear Kent,
> 
> I apologize for inexcusable delay in responding to your messages to 
> po at plantontology.org. All your emails got caught in our spam filter. We 
> will certainly try to do our best to prevent this from happening again.
> 
> As Leszek already mentioned, it would help if you could send us the list
> 
> of the characteristics/characters that you have recorded. This would
> help 
> us understand the scope of the request. We would work together with you
> on 
> incorporating botanical terms specific for Compositae in the PSO. If an 
> extensive changes need to be done to PO to accommodate all updates, it 
> would probably take several rounds of dialogs, and may involve 
> taxonomists-experts for the Compositae family.
> 
> A good way to start is to learn more about phenotypic data that you have
> 
> and to review few examples of phenotype description, and also a list of 
> controlled vocabulary terms that you would like to see in the PO.
> 
> Best regards,
> 
> Katica Ilic, POC Project Coordinator
> 
> 
> On Fri, 11 Aug 2006, KENT BRADFORD wrote:
> 
>> I am trying the email that was published in Jaiswal et al (2005) in an
>> attempt to make contact regarding the questions below.
>> Kent Bradford
>>
>> _____________________________________________
>> From: KENT BRADFORD
>> Sent: Tuesday, August 01, 2006 2:10 PM
>> To: 'po at plantontology.org'
>> Subject: RE: Compositae vocabulary
>>
>> I am trying again to obtain a response from the plant ontology group.
>> Kent Bradford
>>
>> _____________________________________________
>> From: KENT BRADFORD
>> Sent: Monday, May 01, 2006 2:13 PM
>> To: 'po at plantontology.org'
>> Subject: RE: Compositae vocabulary
>>
>> I did not get any response to the message below. Is this address
> listed
>> on the Plant Ontology website viable?
>> Kent Bradford
>>
>> _____________________________________________
>> From: KENT BRADFORD
>> Sent: Tuesday, April 18, 2006 2:33 PM
>> To: 'po at plantontology.org'
>> Subject: Compositae vocabulary
>>
>> To Whom It May Concern:
>> I am a Co-PI on the Compositae Genome Project that has been developing
>> EST and mapping resources for the Compositae, primarily lettuce and
>> sunflower but now expanding into 15 additional species
>> (http://cgpdb.ucdavis.edu). As part of this project, we have also
>> collected extensive phenotypic data on several hundred accessions in
> the
>> Compositae. We are in the process of developing a database to compile
>> and store this data and make it accessible via our website. In
>> describing our phenotypic data, we would like to be compatible with
> your
>> controlled vocabularies in choosing our terms. However, you note on
> your
>> website that these vocabularies are not yet available for the
>> Compositae, and we have many types of data that I do not see in the
>> current descriptions, (e.g., specific leaf shapes, rosettes, presence
> of
>> trichomes, inflorescence branching patterns, etc.). I would appreciate
>> your advice on how we should proceed in a way that will remain
>> consistent the goals of the plant ontology project to allow broad and
>> consistent searching on controlled vocabularies. Is anyone working on
> a
>> list of terms for the Compositae that we could work from? I can send a
>> list of the characteristics that we have recorded if it would help.
>>
>> Sincerely,
>> Kent Bradford
>>
>> Kent J. Bradford
>> Professor
>> Department of Plant Sciences
>> Mail Stop 5
>> One Shields Ave.
>> University of California
>> Davis, CA 95616-8780
>> Phone: 1-530-752-6087
>> Fax: 1-530-754-7222
>> Email: kjbradford at ucdavis.edu
>>
>>
>>
>>
> 

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