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 the Plant Ontology, Trait Ontology and Phenotypic Quality Ontology

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?