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 and how we expect to meet them.

What are users ontology needs?

Introduction to Bio-ontologies

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

This presentation will focus on bio-ontologies: what exists, where the PO fits into what exists, and how to build an ontology like this, with examples from the PO.

This presentation will be open to people outside the meeting participants, and will be advertised to the wider bio-ontologies community.

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 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?