Botany meeting: Abstracts

Mon Mar 29 19:32:18 EST 2004

Hi Felipe,

I tried sending you the world document of my comments on abstracts
thorugh the Explorer, but it failed for (to me) unknown reasons, so here
is the txt attachement (unfortunately you can't see the red lines of what I
added), and instead of the PDF of Sue's review in NRG (that I thought
might be helpful to you), here is the URL:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Search&DB=PubMed.

I hope this helps. As for my suggestions, take what you like and leave out
what you don't. Italicized  were (those are now in brackets), just my
comments, they don't belong to the body of the abstract.

I'll try to send you the proper doc file with my comments again later.

Cheers,

Katica
P.S. I am going to take a look at your updated anatomy ontology right now.

On Mon, 29 Mar 2004, Felipe Zapata wrote:

> Hello,
>
> I am sending the abstracts for the 2 presentations we (Peter, Toby and
> I) are planning to give at Botany 2004 (Botanical Society of
> America/American Society of Plant Taxonomists/American Fern
> Society/American Bryological and Lichenological Society). Toby or Peter
> would give the first talk and I would give the second one.
>
> Please send us your comments.
>
> Thanks,
>
> Felipe
>
> Overview of the Plant Ontology Consortium: goals and general structure.
> Kellogg etc.
>
> As genomic data accumulate, databases have been established to
> coordinate and disseminate information about specific plant species,
> primarily Arabidopsis (The Arabidopsis Information Resource, TAIR),
> rice (OryzaBase and Gramene), and maize (Maize Genome Database,
> MaizeGDGB), although others exist for other species as well.  One goal
> of these databases is to provide an index of genes, such that a user
> could, for example, find all genes known to affect fruit morphology, or
> all genes known to be expressed in young roots.  However, the databases
> have developed largely independently of each other, so that
> descriptions of phenotypes are not uniform.  Searching TAIR with the
> word "fruit" will produce no results, because all fruit-related genes
> are connected to the word "silique," and in Gramene a similar search
> would have to be conducted using the word "caryopsis."  The Plant
> Ontology Consortium (POC) is a collaborative effort that will provide a
> standard vocabulary to be applied across multiple plant databases, such
> that one could search each one using the same descriptor.  The POC
> (www.plantontology.org) currently involves several plant databases and
> workers in plant systematics, development and genomics.  Our first
> efforts are to unite terminology for Arabidopsis and the cereals; in
> subsequent years we will expand the descriptors as necessary to include
> tomato and legumes, and we will develop ontologies for describing plant
> growth and developmental stages.  The goal is to provide a set of
> "bins" into which genes and associated phenotypes can be placed.  The
> Plant Ontology is not designed to recapitulate or replace the entire
> rich vocabulary of plant taxonomy. It will also not provide a full set
> of morphological descriptors, although those it uses will be familiar. 
> Rather it will provide a framework for connecting genotypic data with
> phenotypes in a way that permits comparisons across databases and among
> plants.
> The project is supported by National Science Foundation grant No.
> 0321666 to the Plant Ontology Consortium.
>
> Developing the Plant Ontology: examples and computational tools
> F. Zapata, et al.
>
> The Plant Ontology follows an existing structure and set of rules
> already developed for the Gene Ontology.  It includes a set of terms
> related according to a Directed Acyclic Graph (DAG), in which parent
> terms can have multiple children (like a conventional hierarchy), but
> child terms can also have multiple parents (unlike a strict hierarchy
> or classification).  For example, the gynoecium (a parent term) is
> composed of carpel, ovary, style and stigma (all of them child terms).
> A carpel is also a particular kind of modified leaf, a megasporophyll.
> Hence, carpel, a child term, has multiple parents: gynoecium and
> megasporophyll.  The resulting structure is quite flexible and can
> accommodate plant morphological data that are not strictly hierarchical
> in nature. For instance, some wholes cannot be defined exhaustively by
> their parts; not all embryos have cotyledons, and the only thing common
> to all embryos would be a mass of four cells.  We use the computer
> program DAG Edit, an application that creates and maintains the files
> in a standard format for describing and modifying DAGs (DAG-edit
> format).  Individual members of the consortium are assigned particular
> sets of terms (nodes) in the hierarchy.  The hierarchy is not intended
> to be exhaustive even for the organisms currently under focus, but care
> is taken not to label nodes in such a way that subsequent inclusion of
> plants with very different morphologies will necessitate a
> restructuring of the hierachy. As portions of the ontology are drafted
> they are submitted to the CVS (control version system) repository,
> where all versions of the working files and documents are stored. There
> they can be viewed, compared with older versions, discussed and edited
> simultaneously by all members of the group.
> The project is supported by National Science Foundation grant No.
> 0321666 to the Plant Ontology Consortium.
>
>
>
> ~~~~~~
> Felipe Zapata
> University of Missouri St. Louis
> Department of Biology
> 8001 Natural Bridge Rd.
> St. Louis, MO 63121
> 314 516-6200

--------------------------------------------------------------------------
Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------

-------------- next part --------------
(Note: I don't have any suggestion in this one)

I. Abstract: Overview of the Plant Ontology Consortium: goals and general structure.

Kellogg etc.

As genomic data accumulate, databases have been established to

coordinate and disseminate information about specific plant species,

primarily Arabidopsis (The Arabidopsis Information Resource, TAIR),

rice (OryzaBase and Gramene), and maize (Maize Genome Database,

MaizeGDGB), although others exist for other species as well.  One goal

of these databases is to provide an index of genes, such that a user

could, for example, find all genes known to affect fruit morphology,

or all genes known to be expressed in young roots.  However, the

databases have developed largely independently of each other, so that

descriptions of phenotypes are not uniform.  Searching TAIR with the

word "fruit" will produce no results, because all fruit-related genes

are connected to the word "silique," and in Gramene a similar search

would have to be conducted using the word "caryopsis."  The Plant

Ontology Consortium (POC) is a collaborative effort that will provide

a standard vocabulary to be applied across multiple plant databases,

such that one could search each one using the same descriptor.  The

POC (www.plantontology.org) currently involves several plant databases

and workers in plant systematics, development and genomics.  Our first

efforts are to unite terminology for Arabidopsis and the cereals; in

subsequent years we will expand the descriptors as necessary to

include tomato and legumes, and we will develop ontologies for

describing plant growth and developmental stages.  The goal is to

provide a set of "bins" into which genes and associated phenotypes can

be placed.  The Plant Ontology is not designed to recapitulate or

replace the entire rich vocabulary of plant taxonomy. It will also not

provide a full set of morphological descriptors, although those it

uses will be familiar.  Rather it will provide a framework for

connecting genotypic data with phenotypes in a way that permits

comparisons across databases and among plants.

The project is supported by National Science Foundation grant No.

0321666 to the Plant Ontology Consortium.

II Abstract: Developing the Plant Ontologies: examples and computational tools

F. Zapata, et al.

(Note: Perhaps you may want to add an introductory sentence here on POC.)

The Plant Ontology follows an existing structure and set of rules

already developed by  the Gene Ontology Consortium (http://www.geneontology.org/). 

It includes a set of terms arranged in a structure called Directed Acyclic Graph (DAG), in which parent

terms can have multiple children (like a conventional hierarchy), but

child terms can also have multiple parents (unlike a simple hierarchy

or classification). Also, children are not allowed to be their own ancestors; hence cycles are forbidden. 

For example, the gynoecium (a parent term) is

composed of carpel, ovary, style and stigma (all of them child terms). 

A carpel is also a particular kind of modified leaf, a megasporophyll. 

Hence, carpel, a child term, has multiple parents: gynoecium and

megasporophyll.  The resulting structure is quite flexible and can

accommodate plant morphological data that are not strictly

hierarchical in nature. For instance, some wholes cannot be defined

exhaustively by their parts; not all embryos have cotyledons, and the

only thing common to all embryos would be a mass of four cells.  We

use the ontology editing tool, DAG Edit (available from SourceForge.net), for creating  and

editing plant ontology files in a standard flat file format. Individual members of the POC consortium are

assigned particular sets of terms (nodes) in the hierarchy.  The

hierarchy is not intended to be exhaustive even for the organisms

currently under focus, but care is taken not to label nodes in such a

way that subsequent inclusion of plants with very different

morphologies will necessitate a restructuring of the hierarchy. 

As portions of the ontology are drafted they are submitted to the CVS

(control version system) repository, where all versions of the working

files and documents are stored. There they can be viewed, compared

with older versions, discussed and edited simultaneously by all

members of the group.

(This last part is a bit too technical, to me at least, considering the audience. It would be just fine if it's shorter. I would rather like to see an info on where to find and download the plant ontologies, i.e., availability of PO.)

The project is supported by National Science Foundation grant No.

0321666 to the Plant Ontology Consortium.

(Note: You may also want to mention different relationship types, instance_of, a, part_of and develops_from, and perhaps synonyms too.)