Difference between revisions of "Plant Ontology Webinar- May 2011 release"
| Line 15: | Line 15: | ||
==People to invite- potential Reviewers:== | ==People to invite- potential Reviewers:== | ||
| − | Stefan Rensing and Daniel Lang of the [http://plantco.de/ Physcomitrella group], University of Freiburg, Germany; | + | * Stefan Rensing and Daniel Lang of the [http://plantco.de/ Physcomitrella group], University of Freiburg, Germany; |
[http://www.cosmoss.org/ Cosmoss Moss Ontology] | [http://www.cosmoss.org/ Cosmoss Moss Ontology] | ||
| − | Brent Mishler, UC Berkeley, USA, [http://ucjeps.berkeley.edu/people/mishler.html Brent Mishler] (bmishler at berkeley.edu) | + | * Brent Mishler, UC Berkeley, USA, [http://ucjeps.berkeley.edu/people/mishler.html Brent Mishler] (bmishler at berkeley.edu) |
| − | Bill Buck (NYBG) [http://www.nybg.org/science/scientist_profile.php?id_scientist=5 William Buck] (bbuck at nybg.org) | + | * Bill Buck (NYBG) [http://www.nybg.org/science/scientist_profile.php?id_scientist=5 William Buck] (bbuck at nybg.org) |
| − | Barbara Crandall-Stotler, Department of Plant Biology Southern Illinois University [http://bryophytes.plant.siu.edu/index.html Bryophytes at SIU, home] (crandall at plant.siu.edu) | + | * Barbara Crandall-Stotler, Department of Plant Biology Southern Illinois University [http://bryophytes.plant.siu.edu/index.html Bryophytes at SIU, home] (crandall at plant.siu.edu) |
| − | Bernard Goffinet, University of Connecticut [http://www.eeb.uconn.edu/people/goffinet/ Goffinet Lab] (bernard.goffinet at uconn.edu) | + | * Bernard Goffinet, University of Connecticut [http://www.eeb.uconn.edu/people/goffinet/ Goffinet Lab] (bernard.goffinet at uconn.edu) |
| − | Scott Schuette (Southern Illinois University) [http://bryophytes.plant.siu.edu/scott.html Bryophytes at SIU, Schuette] (swschuette at gmail.com) | + | * Scott Schuette (Southern Illinois University) [http://bryophytes.plant.siu.edu/scott.html Bryophytes at SIU, Schuette] (swschuette at gmail.com) |
(will present talk on Physco bioinformatics at our symposium at the IBC) | (will present talk on Physco bioinformatics at our symposium at the IBC) | ||
Revision as of 22:26, 16 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.
People to invite- potential Reviewers:
- Stefan Rensing and Daniel Lang of the Physcomitrella group, University of Freiburg, Germany;
- 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)
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
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.
