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suggestions requested for plant trait ontology

Vincent, Leszek Leszek at Missouri.edu
Tue Aug 28 14:49:12 PDT 2001


Dear colleagues

I also prefer option 2 (original below) because it represents
discontinuities in information & biology more clearly - I think. This is
difficult to express in a few words. However, I think Chris Mungall's
comments (08/21) in which he suggests 3 subgraphs is probably even better
because discontinuities are even more distinct. I also suspect implementing
W3C PICs standards would be easier with this 3 subgraph structure (?). The
idea of being able to perform boolean searches etc. is an excellent
prospect.

- Leszek
============================
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein at cshl.org]
> Sent: Saturday, August 25, 2001 3:07 PM
> To: gramene at brie.cshl.org
> Cc: gofriends at geneontology.org; monocot-cv at cgnet.com; pj37 at cornell.edu
> Subject: Re: suggestions requested for plant trait ontology
> 
> 
> I also strongly support option 2.  However, I think a mini-ontology
> for scores would be useful.  The type of ontology I'm thinking of
> would describe whether the score is boolean, discrete or continuously
> varying, and what its range is.  There's been quite some work with
> abstract scoring systems as part of the W3C PICs project.
> 
> Lincoln
> 
> Michael Ashburner (Genetics) writes:
>  > 
>  > Pankaj
>  > 
>  > I do not like option 1 at all (over and above the fact 
> that each term
>  > must be lexically unique, it suffers from mixing chalk 
> (the diseases)
>  > and cheese (the scoring system).  It is a very good principle that
>  > within a DAG all terms should belong to the same "semantic family"
>  > - if I may create a phrase.  So, option 2 it should be.  I 
> thought of
>  > creating a separate "score" DAG but think that would be 
> too cumbersome -
>  > especially as the scores are disease specific.
>  > 
>  > 
>  > Michael
> 
> -- 
> ==============================================================
> ==========
> Lincoln D. Stein                           Cold Spring Harbor 
> Laboratory
> lstein at cshl.org			                  Cold 
> Spring Harbor, NY
> 
> NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
> PLEASE WRITE FOR DETAILS.
> ==============================================================
> ==========
> 
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



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