Plant Ontology Webinar- May 2011 release

This page is under construction....

Time and Date:

Proposed dates: Monday May 23rd or Tuesday May 24th (preferred)

Time: Possibly at the regular POC Conference call time 10am PDT?

Preparing a doodle poll to send out

Goals:

To demonstrate the new plant anatomy terms that have been added to accommodate mosses and give reviewers a brief tutorial on how to use PO.

-To facilitate the review process

People to invite- potential reviewers:

• Stefan Rensing and Daniel Lang of the Physcomitrella group, University of Freiburg, Germany;

Cosmoss Moss Ontology, along with their associates Manuel Hiss and Peter Szovenyi

• Brent Mishler, UC Berkeley, USA, Brent Mishler (bmishler at berkeley.edu)

• Bill Buck (NYBG) William Buck (bbuck at nybg.org)

• Barbara Crandall-Stotler, Department of Plant Biology Southern Illinois University Bryophytes at SIU, home (crandall at plant.siu.edu)

• Bernard Goffinet, University of Connecticut Goffinet Lab (bernard.goffinet at uconn.edu)

• Scott Schuette (Southern Illinois University) Bryophytes at SIU, Schuette (swschuette at gmail.com)

(will present talk on Physco bioinformatics at our symposium at the IBC)

1. Philosophy behind the organization of the ontology

Ontology structure

Two domains: PGDSO and PAO (focus on PAO)

Top level of PAO: Plant structure, plant anatomical space, portion of plant substance

How terms are organized within the PAO:

(1)by structure, (2) with homology, if it is known

Aim for single inheritance, use multiple if necessary for users

Definitions

Genus-differentia form

-need to read the definition of the ancestor term to understand definition of child term

Relations are a part of the definition

Definitions and names are taxonomy-neutral; should fit any species in which that structure occurs

-comments and subsets help clarify when a term is only used in certain taxa

2. What are the most important changes that had to be made to accommodate mosses and other non-angiosperm plants?

Top level reorganization

Adding new categories to encompass all structures:

• collective plant structure

• cardinal organ part

• collective organ part structure

• embryonic plant structure

• rhizoid

• trichome

• plant anatomical space

Theses changes were important for all plants

New whole plant growth stages for plant life cycle phases

gametophytic phase and sporophytic phase

Use of participates_in relation allows us to specify structures that only occur in one generation

Redefining upper-level terms of the plant structure branch:

New definitions of plant cell, plant organ, portion of plant tissue, plus the new terms listed above, make these definitions appropriate for all plants

Mid-level and lower-level terms

Added important structures that were missing: sporangium, gametangium, protonema, gametophore, thallus

Redefined mid-level terms to fit broader range of taxa (often had to obsolete and replace, if definition was very different). Example: megagametophyte, microgametophyte, microsporangium,

Created general mid-level categories that fit all plants, with specific children for structures that differ among taxa.

Examples:

-sporangium>microsporangium>pollen sac

-apical cell>shoot apical cell>leaf apical cell>vascular or non-vascular leaf apical cell

-archesporial cell>male archesporial cell or female archesporial cell

Need to talk about parts of leaf, how to annotate to part, plus vascular and non-vascular leaf.