Difference between revisions of "Plant Ontology Webinar- May 2011 release"

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==2. What are the most important changes that had to be made to accommodate mosses and other non-angiosperm plants?==
 
==2. What are the most important changes that had to be made to accommodate mosses and other non-angiosperm plants?==
  
===Top level reorganization===
+
===New whole plant growth stages for plant life cycle phases===
====New whole plant growth stages for plant life cycle phases====
 
  
 
gametophytic phase and sporophytic phase
 
gametophytic phase and sporophytic phase
Line 79: Line 78:
 
Also added protonema phase, for bryophytes and pteridophytes
 
Also added protonema phase, for bryophytes and pteridophytes
  
 +
===Mid-level and lower-level terms (this is the interesting stuff!)===
 +
 +
*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,
  
====New categories were added to encompass all structures:====
+
*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,
  
*collective plant structure
+
*Created general mid-level categories that fit all plants, with specific children for structures that differ among taxa.
 +
 
 +
Examples:
 +
 
 +
-sporangium>microsporangium>pollen sac
  
*cardinal organ part
+
-apical cell>shoot apical cell>leaf apical cell>non-vascular leaf apical cell
  
*collective organ part structure
+
-archesporial cell>male archesporial cell or female archesporial cell
  
*embryonic plant structure
+
*Added synonyms that are used for non-angiosperm plants:
  
*rhizoid
 
  
*trichome
+
===Top-level classes were redefined, and new classes were added, to encompass all structures:===
  
*plant anatomical space
+
Theses changes were important for all plants, not just bryophytes
  
Theses changes were important for all plants
+
'''New upper-level classes:'''
  
 +
*collective plant structure
  
====Upper-level terms of the plant structure branch were redefined so they would include all instances in all plants:====
+
*cardinal organ part
  
New definitions of plant cell, plant organ, portion of plant tissue, plus the new terms listed above, make these definitions appropriate for all plants
+
*collective organ part structure
  
===Mid-level and lower-level terms (this is the interesting stuff!)===
+
*embryonic plant structure
  
*Added important structures for non-angiosperms that were missing from the PO: sporangium, gametangium, protonema, gametophore, thallus, apical cell, seta
+
*rhizoid
  
*Added new terms for structures that only occur in the gametophytic generation: antheridium, archegonium,
+
*trichome
  
*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,
+
*plant anatomical space
  
*Created general mid-level categories that fit all plants, with specific children for structures that differ among taxa.
+
'''Redefined upper-level classes:'''
  
Examples:
+
*in vitro plant structure
  
-sporangium>microsporangium>pollen sac
+
*plant cell
  
-apical cell>shoot apical cell>leaf apical cell>non-vascular leaf apical cell
+
*plant organ
  
-archesporial cell>male archesporial cell or female archesporial cell
+
*portion of plant tissue
  
*Added synonyms that are used for non-angiosperm plants:
 
  
 
====Organization: general terms and part_of children====
 
====Organization: general terms and part_of children====

Revision as of 16:21, 17 May 2011

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:

Expertise: Physcomitrella genomics, Moss Ontology

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

Expertise: systematics, evolution, and ecology of bryophytes

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

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

Topics

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?

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

Also added protonema phase, for bryophytes and pteridophytes

Mid-level and lower-level terms (this is the interesting stuff!)

  • 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

4. Q&A