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first proposed new GO terms from Wormbase

Pankaj Jaiswal pj37 at cornell.edu
Wed Aug 1 08:36:55 PDT 2001


Dear Eric and Midori,

Ever since i have started curating the CV/Os for monocot plants, by literally
extending the frame wprk of GO to traits and nantomy and morphology, I started
looking at the mails sent from GO. here is what i have found:

1
I beleive the GO consortium, is for curating the more generic level of terms
that can gather the wide acceptance of a term by other model organisms. This is
true to an extent but recently I have seen so many inputs that carry sensu
suffixes. This is not good. lets say for example "cell wall". upto that level or
if you go a bit lower in node then "inner membrane" and "outer membrane" (as
part of cell wall is fine. but sensu things should not come up in terms. there
may be opinions, so as to say for cell wall where chemical composition is
different that makes things look different in different organism. But this
should be pointed out in the definition or in the comments, and definitely not
as a new term. otherwise defeats the whole purpose of having a CV/O or glossary
of terms. I would always prefer this type of structure, plus a possibility of
creating a new term by putting together a bunch of already existing terms (as
was discussed in the afternoon session of GO users meeting at Bar Harbor),
rather than creating someting, which is already there but adding a "sensu". I am
suggesting to put a more generic term, with a definition covering all the
aspects and not just for any one particular organism. e.g in any dictionary a
trem may have one generic and several supportive definition, and not several
terms for same thing with each having their own definitions, Check eg.
"structural protein" in GO.

2
CV/O means a very restricted vocabulary to create a term , but definitely not a
"sentence", which is not a term, eg. "extracellular matrix structural protein
conferring tensile strength"  and "age-dependent yeast cell size increase".  GO
consortium /the contributors will have to work on how to limit/restrict.

3
ref. from Eric
>     The main reason for having "fertility" is to try to create a
> term that is as good as possible an antonym to the defect seen in
> worms with Sterile phenotypes in RNAi.  To do this better (i.e.,
> make it an actual function-like term) maybe I should instead propose
> "establishment and maintenance of fertility".

fertilily is a trait, which could be associated to genetic defects/localized
defects / secondary effects due to biochemical changes/processes. certainly it
is not a biological process/function on its own entirity. Its a bunch of factors
that lead to this trait. therefore trait should not be confused with Biological
process/mol function. Secondly this term is a very generic one and should be
treated as such and giving it a generic definition. It occurs in almost every
organism in some way or the other and not only in worms. 

for "establishment and maintenance of fertility", i have in my CVOs for plants
(under traits)

fertility
 male sterility
  male sterility types
   cytoplasmic male sterility
   genetically engineered (PS:a generic name and can have other parents)
   geneic male sterility
   nuclear type
  male sterility measure
  sterility maintenance (PS:has multiple parents)
  fertility restoration (PS:has multiple parents)

These are all generic terms and if one wishes to then they can be taken to an
even lower node to suffice for the respective requirements, but again with an
emphasis on trying to be more generic.


Maybe I am misinterpreting, but will certainly appreciate your feedback.

Regards

Pankaj


> 
> Midori,
> 
>     Thanks for your comments.  As you can tell, I really have
> *started* working on this, so lots of things aren't obvious; I
> really appreciate having somebody like yourself  go over this and
> point out corrections.
> 
>     The definitions in some cases were taken from textbooks, in some
> cases were paraphrased from textbooks, and in some cases were just
> made up on the spot.  I didn't know that references were needed, and
> am also not sure what to do about a definition that was inspired by
> a textbook but didn't in fact follow the textbook verbatim.  If it's
> OK to cite two sources I can cite the dictionary and also cite
> WB:EMS.
> 
>     Mainly I did the definitions in order to try to be a good
> "citizen" of GO.  I hope that if somebody else can come up with
> better ones, somebody will.
> 
>     The main reason for having "fertility" is to try to create a
> term that is as good as possible an antonym to the defect seen in
> worms with Sterile phenotypes in RNAi.  To do this better (i.e.,
> make it an actual function-like term) maybe I should instead propose
> "establishment and maintenance of fertility".
> 
>     I think I understand the restriction on species-specific parent
> terms.  After I have more comments from your end I can mull
> over what to do about that.
> 
> --Erich Schwarz
> 
> --
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-- 

**************************************************************
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
**************************************************************


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