Difference between revisions of "Wood anatomy ontology meeting, 2012 at NYBG, agenda"
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=Agenda, Day 2= | =Agenda, Day 2= | ||
− | ==Work on goal 2== | + | ==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. | 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. | ||
Revision as of 14:00, 21 December 2011
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
- Barry Smith, University at Buffalo Ontology site, Department of Philosophy site
- Laurel Cooper, PO Project Coordinator and Curator, Oregon State University (tentative)
Co-organizers:
- Andrew Groover: Plant Biology, Geneticist, USDA Forest Service, Institute of Forest Genetics
- Jill Wegrzyn of the TreeGenes Database at UCDavis, Bioinformatics
Invited attendees:
(*confirmed)
- Frederic Lens* Netherlands Centre for Biodiversity Naturalis, wood anatomy
- Barb Lachenbruch* College of Forestry, Oregon State University, wood science and anatomy
- Elisabeth Wheeler North Carolina State University, paleobotany and wood anatomy; curator of the Inside Wood database
- Rachel Spicer Connecticut College, wood anatomy, development, and physiology
- John Carlson School of Forest Resources, Pennsylvania State University, genomics of hardwood trees
- Meg (Margeret) Staton* Fagaceae Genomics Web, curator; bioinformatics
Meeting Goals
1. Develop ontology terms and definitions for wood structure, as part of the Plant Anatomical Entity branch of the Plant Ontology.
-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).
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.
-If necessary, we can also make suggestions for developmental processes in the Gene 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
Introductions (D. Stevenson and whole group)
Introduction to Bio-ontologies (B. Smith)
Barry Smith, an ontology expert and consultant to the PO, will provide an introduction to ontologies for the life sciences.
This presentation will be open to people outside the meeting participants, and will be advertised to the wider bio-ontologies community.
Topics:
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
Introduction to relevant ontologies (R. Walls)
PO, TO, and PATO
Brief overview of the three relevant ontologies.
- Domains of each ontology
- How do they differ? How are they similar? How do they interact?
- More details on TO and PATO be given when we start work on goal 3
Plant Ontology
How the PO is organized
- the two main branches of the PO: PAO and PDSO
- what is a PO term?
- term attributes: id, synonyms, definition, comment
- PO association data
Relations in the PO
- is_a
- part_of
- has_part
- develops_from
- derives_from
- adjacent_to
- participates_in
- has_participant
Definitions in the PO
- genus-differentia definitions - importance of reading up the tree for properties of a term
- logical definitions and relations
- definitions for humans and computers
Trait Ontology (TO) and Phenotypic Quality Ontology (PATO)
- What is a trait? What is a quality?
- The difference between an entity and a phenotype
- The E-Q statement
Overview of the goals for the meeting (R. Walls and whole group)
What they are and how we expect to meet them.
What are users ontology needs?
Work on goal 1
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
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.
Work on goal 3
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 phenotype son the fly using cross products.
Agenda, Day 3
Review ontology structure from days 1 and 2
Incorporating new annotations for woody plants
Linking to TreeGenes and other databases.
Create a woody anatomy slim?
Action items
What still needs to be done?
Who will do what?