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?

These times work well for the group- will give them a choice of a few times on Monday or Tues next week 9am or 10am

Link to doodle poll

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 encourage them to submit gene expression annotations to us to link to the terms

-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

Expertise: Physcomitrella genomics, Moss Ontology

They are interested and available to do it and next Tuesday works for them.

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

Expertise: systematics, evolution, and ecology of bryophytes

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

Expertise: Moss systematics, pleurocarpous mosses, moss structural diversity

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

Expertise: liverworts, apical growth

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

Expertise: molecular systematics of bryophytes and lichens

• 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)

We decided that it would best to do this with the Physco group for now from Germany. They can interact with their community, the terms we added were specific to their project.

Topics

1. Organizing principles of the PO

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 homology, if it is known (2)by structural, developmental or positional similarity

For example:

We group sporangia together, because there is good evidence that they are homologous across land plants.

Flowers, inflorescences and strobili are grouped together as reproductive shoot systems. We don't know the exact evolutionary transformations between the different structures, but we know that they are all shoot systems that bare sporangia.

We group vascular leaves, petals, sepals and sporophylls together. They appear to be homologous, but more importantly, they share structural and developmental characteristics (all are lateral organs that develop from an SAM). We know that vascular and non-vascular leaves are not homologous, but we group them because of their structural and developmental similarity.

The PO is a hypothesis that can change as more information becomes available.

• Aim for single inheritance, use multiple inheritance if necessary for users. If possible, have only one asserted is_a parent, other should be inferred by cross products (this will not always be possible).

Definitions

• Genus-differentia form

-this means one needs to read the definition of the ancestor term to understand definition of a 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?

Describing the plant life cycle

• The new terms gametophyte phase (PO:0028003) and sporophyte phase (PO:0028002) were added to the PGDSO (during an earlier release).

Also added protonema phase, for bryophytes and pteridophytes. Other life cycle/growth phases will be added in future releases.

• The terms gametophyte and sporophyte were made obsolete, and added as synonyms of whole plant.

If one wants to describe a gametophyte, they should use whole plant (PO:0000003) in the gametophyte phase (PO:0028003).

• Use of the participates_in relation allows us to specify structures that only occur in one generation or the other.

For example, seta participates_in sporophyte phase, gametophore participates_in gametophyte phase.

New mid- to lower-level terms and reorganization to accommodate all plants

• Added important structures for non-angiosperms that were missing from the PO: sporangium, gametangium, protonema, gametophore, thallus, apical cell, seta

• Added new terms for structures that only occur in the gametophytic generation: antheridium, archegonium,

• 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>non-vascular leaf apical cell

-archesporial cell>male archesporial cell or female archesporial cell

• Added synonyms that are used for non-angiosperm plants:

Top-level classes were redefined, and new classes were added, to encompass all structures:

Theses changes were important for all plants, not just bryophytes

New upper-level classes:

• collective plant structure

• cardinal organ part

• collective organ part structure

• embryonic plant structure

• rhizoid

• trichome

• plant anatomical space

Redefined upper-level classes:

• in vitro plant structure

• plant cell

• plant organ

• portion of plant tissue

Organization: general terms and part_of children

Some classes that occur in both vascular and non-vascular plants (e.g. vascular leaf and non-vascular leaf) have parts that can occur in either type (e.g., leaf epidermis, leaf lamina). Creating separate part_of children for each type would lead to term inflation and an overly complex ontology structure.

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

3. Demonstration

Annotations

Searching for annotations

Contributing annotations

Source Forge

• Creating an account and logging in

• Setting preferences

• Requesting new terms

• Commenting on current trackers

5. Outreach

-Encourage Physco group to reach out to moss community to let people know about the PO.

-Encourage bryophyte researchers to contribute annotations to PO