Difference between revisions of "Wood anatomy ontology meeting, 2012 at NYBG, agenda"
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This session will be open to people outside the meeting participants, and will be advertised to the wider scientific community. | This session will be open to people outside the meeting participants, and will be advertised to the wider scientific community. | ||
− | ===Introduction to Bio-ontologies ( | + | ===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. | '''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?==== | ====1. What is an ontology and what is it for?==== | ||
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* use of OBO-Edit and Protege | * use of OBO-Edit and Protege | ||
− | ===Introduction to the Plant Ontology ( | + | ===Introduction to the Plant Ontology (Ramona Walls)=== |
====1. What the Plant Ontology is for | ====1. What the Plant Ontology is for | ||
====2. Organization of the Plant Ontology ==== | ====2. Organization of the Plant Ontology ==== | ||
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*adjacent_to | *adjacent_to | ||
*participates_in and has_participant: links between anatomical entities and development stages | *participates_in and has_participant: links between anatomical entities and development stages | ||
− | ====4. Plant | + | ====4. Plant Ontology definitions==== |
*genus-differentia definitions - importance of reading up the tree for properties of a term | *genus-differentia definitions - importance of reading up the tree for properties of a term | ||
*logical definitions and relations | *logical definitions and relations |
Revision as of 12:53, 3 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
- 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
- Meg (Margeret) Staton* Fagaceae Genomics Web, curator; bioinformatics
- John Carlson School of Forest Resources, Pennsylvania State University, genomics of hardwood trees- not able to attend
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
9AM-9:30AM Introductions (D. Stevenson and whole group)
9:30AM-12:30PM 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.
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
Introduction to the Plant Ontology (Ramona Walls)
====1. What the Plant Ontology is for
2. Organization of the Plant Ontology
- the two main branches of the PO: plant anatomical entity and plant structure development stage
3. Plant Ontology relations
- is_a: the most basic relation, type-subtype
- part_of: what it means for anatomical entities versus development stages
- has_part: why use this instead of part_of
- develops_from
- derives_by_manipulation_from: used for in vitro plant structures
- adjacent_to
- participates_in and has_participant: links between anatomical entities and development stages
4. Plant Ontology definitions
- genus-differentia definitions - importance of reading up the tree for properties of a term
- logical definitions and relations
- definitions for humans and computers
5. Neighboring ontologies of Traits (TO) and Phenotypes (PATO)
Trait Ontology (TO), and Phenotypic Quality Ontology (PATO)
- Domains of each ontology
- How do they differ? How are they similar? How do they interact?
- What is a trait? What is a quality?
- The difference between an entity and a phenotype
6. Different types of plant data made available through the Plant Ontology
- linking data to PO terms
- example: mapping maize tissue samples to PO terms
- responsibilities of the PO versus contributing databases: how annotation files are created and maintained
12:30PM-1:30PM Lunch
1:30PM-2:30PM 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-5:30PM 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 phenotype son the fly using cross products.
Agenda, Day 3
9:00AM-12:00PM Review ontology structure from days 1 and 2
We can use this time to complete work on any remaining items from goals 1-3.
12:00PM-1:00PM Lunch
1:00PM-5:00PM* Break-out groups
1. Incorporating new annotations for woody plants
Linking to TreeGenes and other databases.
Create a woody anatomy slim?
2. Wood anatomy term development
Action items
What still needs to be done?
Who will do what?
(*exact end time TBD, depending on participants travel schedules)