Difference between revisions of "Plant Ontology Webinar- May 2011 release"
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New definitions of plant cell, plant organ, portion of plant tissue, plus the new terms listed above, make these definitions appropriate for all plants | 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=== | + | ===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 important structures for non-angiosperms that were missing from the PO: sporangium, gametangium, protonema, gametophore, thallus, apical cell, seta | ||
| Line 117: | Line 117: | ||
-sporangium>microsporangium>pollen sac | -sporangium>microsporangium>pollen sac | ||
| − | -apical cell>shoot apical cell>leaf apical cell> | + | -apical cell>shoot apical cell>leaf apical cell>non-vascular leaf apical cell |
-archesporial cell>male archesporial cell or female archesporial cell | -archesporial cell>male archesporial cell or female archesporial cell | ||
*Added synonyms that are used for non-angiosperm plants: | *Added synonyms that are used for non-angiosperm plants: | ||
| + | |||
| + | ====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. | Need to talk about parts of leaf, how to annotate to part, plus vascular and non-vascular leaf. | ||
Revision as of 16:17, 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:
- 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
- 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)
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?
Top level reorganization
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
New categories were added 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
Upper-level terms of the plant structure branch were redefined so they would include all instances in all plants:
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 (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:
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.
