Wood anatomy ontology meeting, 2012 at NYBG, agenda
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Dates: Three days, during the first two weeks of February, 2012, TBD
Location: Pfizer Lab Conference Room, New York Botanical Garden
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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)
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.
-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
Introduction to Ontologies
Introductions
Overview of the goals for the meeting
What they are.
How we expect to meet them.
Introduction to Bio-ontologies
Barry Smith, an ontology expert and consultant to the PO, will provide an introduction to ontologies for the life sciences.
Introduction to relevant ontologies
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
Trait Ontology
Phenotypic Quality Ontology
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
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.
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?