Difference between revisions of "Wood anatomy ontology meeting, 2012 at NYBG, agenda"

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* Elisabeth Wheeler*  [http://cnr.ncsu.edu/fb/about/faculty/wheeler.php North Carolina State University], paleobotany and wood anatomy; curator of the [http://insidewood.lib.ncsu.edu/welcome Inside Wood database]
 
* Elisabeth Wheeler*  [http://cnr.ncsu.edu/fb/about/faculty/wheeler.php North Carolina State University], paleobotany and wood anatomy; curator of the [http://insidewood.lib.ncsu.edu/welcome Inside Wood database]
  
* Rachel Spicer  [http://www.conncoll.edu/academics/web_profiles/spicer.html Connecticut College], wood anatomy, development, and physiology  
+
* Rachel Spicer* [http://www.conncoll.edu/academics/web_profiles/spicer.html Connecticut College], wood anatomy, development, and physiology  
  
 
* Meg (Margeret) Staton*  [http://www.fagaceae.org/ Fagaceae Genomics Web], curator; bioinformatics
 
* Meg (Margeret) Staton*  [http://www.fagaceae.org/ Fagaceae Genomics Web], curator; bioinformatics

Revision as of 07:50, 20 January 2012

This page is under construction.

Tentative dates: 5-7 February, 2012 (Sunday through Tuesday)

Location: Lewis B. and Dorothy Cullman Conference Room, Pfizer Laboratory, New York Botanical Garden

This page has a Tiny Url: http://tinyurl.com/7dyv4f9


Attendees

From the Plant Ontology Consortium:

  • Dennis Stevenson, Vice President for Laboratory Research, New York Botanical Garden
  • Ramona Walls, Post-doctoral researcher and Plant Ontology curator, New York Botanical Garden
  • Maria Alejandra Gandolfo, Cornell University
  • Laurel Cooper, PO Project Coordinator and Curator, Oregon State University

Co-organizers:

Invited attendees:

(*confirmed)

Meeting Goals

1. Develop ontology terms and definitions for wood structure, as part of the Plant Anatomical Entity branch of the Plant Ontology.

2. Develop ontology terms and definitions the time course of development of wood, as part of the Plant Structure Development Stage branch of the Plant Ontology.

3. Develop ontology terms and definitions, as well as ontology structure, for wood qualities and phenotypes, as an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO, formerly the Phenotype and Trait Ontology).

By the end of the meeting, we will have list of terms for these three areas (anatomy, development stages, qualities), plus proposed definitions, and a good idea of how the terms will fit into the PO.

Agenda, Day 1

9:00AM-12:00PM Introduction to Bio-ontologies - Public Session

This session will be open to people outside the meeting participants, and will be advertised to the wider scientific community.

If you are interested in attending this session, please contact Ramona Walls by February 1, 2012.

Link to the meeting announcment.

9AM-9:15AM Welcome and Introductions (Dennis Stevenson)

9:15AM-11:00AM Introduction to Bio-ontologies (Barry Smith)

Barry Smith, an ontology expert and consultant to the PO, will provide an introduction to ontologies for the life sciences.

1. What is an ontology and what is it for?

2. Ontology success stories in the life sciences

3. The bio-ontologies landscape

  • Open Biomedical Ontologies (OBO) Foundry
  • National Center for Biomedical Ontology (NCBO) and its Bioportal
  • Ontologies and the Semantic Web

4. How to build your first ontology

-with illustrations from the Plant Ontology

  • definitions and cross-products
  • relations
  • types and instances
  • use of OBO-Edit and Protege

11:00AM-11:15AM Coffee break

11:15AM-12:00PM Introduction to the Plant Ontology (Ramona Walls)

1. What is the Plant Ontology and what is it for?

2. How the Plant Ontology is structured: anatomy and development stages

  • The two main branches of the PO are plant anatomical entity and plant structure development stage

3. Plant Ontology relations and definitions

Relations:

  • Types and subtypes: is_a, the fundamental relation in the PO
  • Parts: part_of and has_part; what they means for anatomical entities (things) versus development stages (processes); when to use has_part instead of part_of
  • Development and derivation: the develops_from and derives_by_manipulation_from relations
  • Specifying spatial relations: adjacent_to, part_of, and other relations
  • Links between anatomical entities and development stages: the participates_in and has_participant relations

Definitions:

  • Definitions for humans and computers
  • Genus-differentia definitions - importance of reading up the tree for properties of a term
  • Logical definitions and relations

4. Neighboring ontologies of the PO: Traits (TO) and Phenotypes (PATO)

  • Domains of Trait Ontology (TO), and Phenotypic Quality Ontology (PATO), versus the PO
  • How do they differ? How are they similar? How do they interact?
  • The difference between an entity and a phenotype
  • What is a trait? What is a quality?

5. Different types of plant data made available through the Plant Ontology

  • Linking genomic and phenomic data to PO terms
  • Example: mapping maize tissue samples to PO terms
  • How annotation files are created and maintained; responsibilities of the PO versus contributing databases.

12:00PM-1:00PM Lunch break

1:00PM-2:00PM Overview of the goals for the meeting

Setting goals

The following goals were established prior to this meeting:

1. Develop ontology terms and definitions for wood structure, as part of the Plant Anatomical Entity branch of the Plant Ontology.

2. Develop ontology terms and definitions the time course of development of wood, as part of the Plant Structure Development Stage branch of the Plant Ontology.

3. Develop ontology terms and definitions, as well as ontology structure, for wood qualities and phenotypes, as an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO, formerly the Phenotype and Trait Ontology). What they are and how we expect to meet them.

What are users ontology needs?

-In addition to working on the terms used to describe wood, we can review the needs for other anatomy terms for woody plants that may not be in PO (e.g., reproductive structures in gymnosperms).

-If necessary, we can also make suggestions for developmental processes in the Gene Ontology.

Achieving our goals

  • strategy for creating new or revising existing PO terms

2:30PM-6:00PM Work on goal 1 - Anatomical Entities

Goal 1. Develop ontology terms and definitions for wood structure, as part of the Plant Anatomical Entity branch of the Plant Ontology.

review existing terms and definitions

develop list of terms that are missing

work on definitions of new terms

Agenda, Day 2

9:00AM-12:00PM Work on goal 2 - Development stages

2. Develop ontology terms and definitions for the time course of development of wood, as part of the Plant Structure Development Stage branch of the Plant Ontology.

-If necessary, we can also make suggestions for developmental processes in the Gene Ontology.

12:00PM-1:00PM Lunch

Lunch time tutorial on how to use OBO Edit, for interested participants.

1:00PM-2:00PM Continue work on goal 2

3:00PM-6:00PM Work on goal 3 - Qualities and Phenotypes

3. Develop ontology terms and definitions, as well as ontology structure, for wood qualities and phenotypes, as an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO, formerly the Phenotype and Trait Ontology).

Background

Unlike goals 1 and 2, this goal goes beyond the current domain of the PO.

Ontological descriptions of plant qualities and phenotypes

The E-Q statement.

What is a cross-product?

Work on list of terms needed

Existing glossaries as sources of terms

IAWA glossaries

Others

User needs

How will quality/phenotype terms be used?

Creating a separate "Wood Quality Ontology" versus describing phenotypes on the fly using cross products.

6:00-8:30 Working dinner and evening session at NYBG

Developing and Incorporating new annotations for woody plants- Laurel Cooper Linking to TreeGenes and other databases.

Agenda, Day 3

Note change in schedule. We will finish at noon on Tuesday, to allow participants to return home on Tuesday.

9:00AM-10:00AM Review ontology structure from days 1 and 2

Review of any unfinished items from goals 1-3.

10:00AM-12:00PM Break-out groups

Create a woody anatomy slim?

2. Wood anatomy term development

Action items

What still needs to be done?

Who will do what?