Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

suggestions requested for plant trait ontology

Pankaj Jaiswal pj37 at cornell.edu
Tue Aug 21 08:56:38 PDT 2001


Dated: 08-21-2001

Dear GO users/Developers,

At gramene database I am trying to curate the trait ontologies for the monocot
plants (mainly rice)  follwoing the similar
DAG structure being in use for the GO. 

I will appreciate your feedback/suggestions on what way should the traits be
represented in Plant trait ontology.
Your feedback will be useful in creating certain structure on how to curate the
traits 
and how good the terms/relationships can maintain the architecture so as to
suffice for different organism (and still remain flexible). 
Otherwise this will simply go on to flood the database with terms. 
A word of caution, please do not bother yourself by looking at the GO-id in my
terms, this was generated by the 
GO-editor. We will change it to "TO" for trait ontology. 

Right now we have two different options for the structures. 

OPTION-1

If you follow the terms as follows, then it represents that there is a disease
infecting an organism
(in this case Oryza sativa), and the assessment for the level of infection can
be measured on a scale of 0-9,
i.e. different scales of resistance (0) to susceptibilty (9). Each scale has its
own definition 
(or set of identifiers/way of evaluation) which makes it unique from the similar
term for scale 
(scale can also be different) for a different disease. 

eg. %leaf blast ; GO:1100046 ; synonym:Bl
     %highly resistant ; GO:0300387 ; scale:1

     %panicle blast ; GO:1100047 ; ICIS:1119 ; synonym:PB
      %highly resistant ; GO:0300393 ; scale:0

the terms "highly resistant" are the same (vocabulary wise), however their
definitions make them unique by assigning 
them a unique GO/TO id. (Don't worry i am not using "GO", instead it will be
"TO" for trait ontology).
    



         %fungal diseases ; GO:0300337
          %bakanae disease ; GO:1100071 ; synonym:Bak
          %blast disease ; GO:1100045 ; ICIS:1104
           %leaf blast ; GO:1100046 ; synonym:Bl
            %highly resistant ; GO:0300387 ; scale:1
            %highly susceptible ; GO:0300385 ; scale:8
            %intermediate susceptible ; GO:0300391 ; scale:5
            %moderate resistant ; GO:0300389 ; scale:3
            %moderate susceptible ; GO:0300388 ; scale:4
            %resistant ; GO:0300390 ; scale:2
            %susceptible ; GO:0300386 ; scale:7
            %towards susceptible ; GO:0300392 ; scale:6
            %very highly resistant ; GO:0300383 ; scale:0
            %very highly susceptible ; GO:0300384 ; scale:9
           %panicle blast ; GO:1100047 ; ICIS:1119 ; synonym:PB
            %highly resistant ; GO:0300393 ; scale:0
            %higly susceptible ; GO:0300398 ; scale:9
            %intermediate susceptible ; GO:0300396 ; scale:5
            %moderate resistant ; GO:0300395 ; scale:3
            %resistant ; GO:0300394 ; scale:1
            %susceptible ; GO:0300397 ; scale:7


the definitions for option-1 are as follows..

term: highly resistant
goid: GO:0300387
definition: small brown specks of pin-point size or lager brown specks with out
sporulating center. rapid observation does not reveal lesions, but careful
scrutiny of each row reveals few lesions. diseased leaf area less than
0.3percent
definition_reference: GR:pj37
definition_reference: IRRI:SES

term: highly resistant
goid: GO:0300393
definition: no visible lesions observed or lesions on a very few pedicels.
severely infected panicles- no incidence
definition_reference: IRRI:SES
definition_reference: GR:pj37

term: highly susceptible
goid: GO:0300385
definition: Exrtensive curling and browing of upper and middle leaves, plants
are either dead or stunted. diseased leaf area 51-75 percent
definition_reference: IRRI:SES
definition_reference: GR:pj37

term: higly susceptible
goid: GO:0300398
definition: lesions completely around panicles base or uppermost internode or
panicle axis near the base with less than 30% of filled grains. Severely
infected panicles more than 50 percent
definition_reference: IRRI:SES
definition_reference: GR:pj37

term: intermediate susceptible
goid: GO:0300396
definition: lesions partly around the base (node) or the uppermost internode or
the lower part of panicle axis near the base. Severely infected panicles 11-25
percent
definition_reference: IRRI:SES
definition_reference: GR:pj37

these are a few examples, I am not presenting all the definitions here.



OPTION-2


The other option is as follows where the blast disease has two child instances
for (1) leaf blast and (2) panicle blast.  
All the related children of these two (as shown in the previous structure) does
not exist as the new terms, 
where as all those evaluation scales with their respective terms can be
represented in the definitions of the two terms
(1) leaf blast and (2) panicle blast 


the DAG
         %fungal diseases ; GO:0300337
          %bakanae disease ; GO:1100071 ; synonym:Bak
          %blast disease ; GO:1100045 ; ICIS:1104
           %leaf blast ; GO:1100046 ; synonym:Bl

the rest of the terms and their individual definitions goes into the definition
for 
the "leaf blast" as mentioned later........

         scale- term
          0-  very highly resistant
          1-  highly resistant
          2-  resistant
          3-  moderate resistant
          4-  moderate susceptible
          5-  intermediate susceptible
          6-  towards susceptible
          7-  susceptible
          8-  highly susceptible            
          9-  very highly susceptible
and 
           %panicle blast ; GO:1100047; synonym:PB

the rest of the terms and their individual definitions goes into the definition
for 
the "panicle blast" as mentioned later........

         scale- term
          0-  highly resistant
          1-  resistant
          3-  moderate resistant
          5-  intermediate susceptible
          7-  susceptible
          9-  higly susceptible


the definition sin option-2 are as follwos

term: leaf blast
goid:1100045
definition: causal agent: Magnaporthe grisea (Pyricularia oryzae - 
the imperfect/anamorphic stage name). Use this scale only for the nursery.
Actual estimation of blast affected leaf area is recommended for field 
assessment of blast disease together with predominant lesion type. 
Entries with scores 4-9 may also have lesions of scale 1 or 2. 
The scale value of 4 is to be given when lesions develop only on 
collar (joint of leaf sheath and leaf blade), 
causing the leaf blade to drop off. scale 5,7 and 9 are 
considered typical susceptible lesions.  
monitored at growth stage 2-3 (field or green house)
scale-0: very highly resistant
no lesions observed. diseased leaf area zero percent
scale-1: highly resistant
small brown specks of pin-point size or lager brown specks with out sporulating
center. rapid observation does not reveal lesions, but careful scrutiny of each
row reveals few lesions. diseased leaf area less than 0.3percent
scale-2: resistant
small circular-slightly elongated necrotic grey spots about 1-2 mm in diameter,
with a distinct brown margin. Lesions are mostly found on lower leaves. Rapid
observation detects a few lesions. Diseased leaf area 0.3-0.9 percent
scale-3: moderate resistant
lesion types same as in resistant variety (scale2), except a significant number
of lesions are on the upper leaves also. Several lesions are randomly scattered
within a plot. diseased leaf area 1-2 percent
scale-4: moderate susceptible
several to many lower leaves become necrotic and few dead leaves. tips of
several upper leaves show brown color and begin to fold. diseased leaf area 4-10
percent 
scale-6: towards susceptible
lower leaves uniformly exhibit brown color and several dead leaves. Tip necrosis
of upper leaves is predominant. diseased leaf are 11-25 percent
scale-7: susceptible
Tips of most most upper leaves start curling, middle and lower leaves turn
brown. several plants or tillers are stunted or dead. diseased leaf area 26-50
percent
scale-8: highly susceptible
Exrtensive curling and browing of upper and middle leaves, plants are either
dead or stunted. diseased leaf area 51-75 percent
scale-9: very highly susceptible
Majority of plants are severly stnted, brown and dead. Only a few to several
plants have green leaves with heavy infection. Diseased leaf area more than 75
percent


term: panicle blast
goid:1100047
definition: Causal agent: Magnaporthe grisea (Pyricularia oryzae). 
Symptoms are dark necrotic lesions covering partially or completely 
around the panicle base (node) or the uppermost internode or the lower part.
monitored at growth stage:8-9
scale-0: highly resistant
no visible lesions observed or lesions on a very few pedicels. severely infected
panicles- no incidence
scale-1: resistant
lesions on several pedicels or secondary brabches. Severely infected panicles
less than 5 percent
scale-3: moderate resistant
esions on afew primary branches or the middle part of panicle axis. Severely
infected panicles 5-10 percent
scale-5: intermediate susceptible
lesions partly around the base (node) or the uppermost internode or the lower
part of panicle axis near the base. Severely infected panicles 11-25 percent
scale-7: susceptible
lesion completely around panicle base or uppermost internode (also found on
lower part of internode which is covered by leaf sheath) or panicle axis near
the base with more than 30% of filled grains. Severely infected panicles 26-50
percent.
scale-9: higly susceptible
lesions completely around panicles base or uppermost internode or panicle axis
near the base with less than 30% of filled grains. Severely infected panicles
more than 50 percent


Suggestions for a different approach as compared to the above two structures is
most welcome.  

Regards

Pankaj






**************************************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   http://ars-genome.cornell.edu/rice
**************************************************************


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list