POC Conf. Call 6-29-10

POC meeting, Webex Conference Call; Date: June 29th, 2010 10am (PDT)

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Absent: Alejandra Gandolfo, (Cornell University), Barry Smith (University at Buffalo, NY).

Collaborators: none

Acceptance of the minutes from the 6-23-10 meeting? All in favor? There were no additions, deletions or changes to last weeks minutes.

Workshop page: [Corvallis Workshop June 29th and 30th, 2010]

Agenda and Minutes for June 29th Conference Call:

The main goals of the meeting will be ontology development and preparation for a release, along with focused training on annotating genes and mappings.

*Curators discussion: Determine priorities for next release of PO:

1. Date of next release? July 2010? Aug 15th goal for live release

-What needs to be done before this release?

-Beta PSO release to users: TAIR, NASC, VirtualPlant, Gramene, SoyBase, Genevestigator, SGN, OryzaBase, MaizeGDB:Carolyn Lawrence, BRENDA, UniProt, PlantTribes, TraitNet

-send to po_announce and po-dev lists

-documentation of changes in the ontology, research paper,

-po-anatomy test will remain for development

Justin will set up a beta browser that will display the working ontology and will include annotations see: http://beta.plantontology.org:8080/amigo/go

• Panel of experts? set up review, 1 month period

Look for templates for reviews from experts

-FAQs and guiding principles -Need to update documentation on web page and wiki for next release -what we did and why we did it. This will also go in paper (see below). -highlight things we want people to review

Names: Sarah Hake, Quentin Cronk, Paula Rudall* (Kew Bot Garden), Sarah Matthews (Harvard), Elena Kramer (Harvard) Neelima Sinha (U C Davis), Chelsea Specht* (UC Berkeley), Rob Martienssen (Cold Spring Harbor), Peter Raven (MoBot) Gar Rothwell* (Ohio University), Peter Linder* (Switzerland), Chris Hardy* (Millersville University)

(*)plant anatomy experts

- meet with folks at the ASPB/BSA meeting- -organize a conflab?

Interaction with the Botanical Society- Structural and Developmental section, try to set up an interface with their website

Need to start work on an update of the Plant Physiology paper- goal for fall.

Need to update documentation on web page and wiki for next release - what we did and why we did it. This will also go in paper.

2. Is top level of Plant Structure ontology ready to go?

-Review of top level terms

-add 'plant structure system' with children 'shoot system','root system', 'vascular system' -will be defined based on CARO anatomical system

Discussion: problem that some terms like rhizoid is very different from roots. rhizoids single or multicellular?

• They can be both, but they do not form a system like roots so should not be under plant structure system.

Shoot system should have children vegetative and reproductive shoot systems

PJ- do we really need to have 'whole plant'??? -current def'n of 'plant structure' covers the whole plant already

CM- whole plant is needed for annotating traits such as 'whole plant weight' in TO for example -also present in other anatomical ontologies, such as FMA

• We decided that we should obsolete gametophyte and sporophyte, add the terms "gametophytic phase, sporophytic phase to the PGD Ontology.

-male and female gametophyte should be children of whole plant.

-will need to add the term: 'embryo sac'- parent term of egg terms. This will be a child of female gametophyte.

-get rid of 'seedling' is_a whole plant and refer to stage of development

- Looked at male gametophyte terms -- has no is_a children, and all part_of children can remain.

-CM- combine the PSO and the PGDO into one file such as GO does it, separate namespaces. Implementation?

-Chris and Justin are setting up a system to convert the PO anatomy editors file (po_anatomy_test) a deployed version, so we will have an editors version and deployed version.

Review of second level terms

- should focus on fixing 'plant cell' and 'portion of plant tissue', others are in decent shape

-Should structures have part_of relations (to gametophyte, sporophyte, or whole plant) whenever possible?

Taken care of because we no longer have gametophyte and sporophyte.

-Do we want to keep in vitro structures or send to OBI?

we will keep these terms in the the Plant Structure Ontology for now and that portion of the Ontology can be mirrored in their ontologies.

Discussion on 6/30/10 about whether or not in vitro structures should be is_a children of their in vivo structures (like cultured cell is_a plant cell) or not. For now, they are not; instead will have derived from relations to in vivo structures. Probably need to revisit this issue, because it will come up in other ontologies as well.

3. Status and goals for is_a completeness (Ramona can report)

- 136 terms without is_a parents

Based on definitions:

-73 of these terms have obvious parents (many of them some kind of portion of plant tissue)

-11 more terms could be assigned parents if new terms were created

-15 terms could be assinged parents with some consideration

-36 terms need discussion to determine parent terms (no obvious parent)

Ramona can make bulk Source Forge tracker items for these terms.

4. Should we aim to complete one branch of the ontology? For Example: leaves, in vitro terms or plant cells, specific type- axial cells for example hydroids and leptoids?

-We will focus on leaves- need mega and microphyll, gametophyll, sporophyll, have a term 'vascular leaf' and 'nonvascular leaf' -DWS- comment we need the terms heterophylly, isophylly

5. Changing lower-level terms to include cross products and genus-differentia definitions.

-How much can be done before release?

This will probably have to wait until the next release for the most part.

6. Goals and timetable for the next release:

Not discussed.

bud (PO:0000055)

All of the grand-children of bud . See SF tracker item for explanation and suggestions. This issue came up while working on the terms for tuber eye.

At 6-23-10 conference call, we decided to make only 'axillary bud' and 'terminal bud' direct children of bud to eliminate the problem of dual parentage.

Added new terms: terminal reproductive bud (PO:0025071) and axillary reproductive bud (PO:0025072).

This will allow annotations of reproductive buds from non-flowering plants and 'terminal floral bud' and 'axillary floral bud' will be children of these terms Therefore, the terms 'floral bud', 'vegetative bud' and 'inflorescence bud' were obsoleted.

To do: axillary inflorescence bud is_a axillary reproductive bud and terminal inflorescence bud is_a terminal reproductive bud

Tuber PO:0004543 (tuber)

On the 6-23 conference call, everyone agreed that tuber is_a stem,not a shoot.

proposed def'n: A swollen or enlarged storage stem with determinate growth. See discussion on 6-30-10 minutes

This would encompass both subterranean and aerial tubers.

• Tuber epidermis (PO:0025046): proposed def'n: A portion of stem epidermis that is part of a tuber.

• Aerial tuber epidermis (PO:0025047): A portion of tuber epidermis that is part of an aerial tuber.

• Subterranean tuber epidermis (PO:0025048): A tuber epidermis that is part of a subterranean tuber.

Comment: The skin of young potatoes is epidermis while the skin of mature potatoes is periderm. Related syn.: potato skin

tuber epidermis

New terms to deal with tuber epidermis:

• Tuber periderm (PO:0025043): A portion of stem periderm that is part of a tuber.

• Aerial tuber periderm (PO:0025044): A portion of tuber periderm that is part of an aerial tuber.

• Subterranean tuber periderm (PO:0025045): A portion of tuber periderm that is part of a subterranean tuber. Comment: The skin of young potatoes is epidermis while the skin of mature potatoes is periderm. Narrow syn.: potato skin

Can we close these items? We will work on the definitions of stem and shoot tomorrow morning.

hypodermis and endodermis

During the POC conference call on 6-23-10, it was decided that endodermis and hypodermis should be part_of cortex, but we needed to change the definition of cortex to allow this. Barry suggested that we define the parent terms as the maximal portion of a tissue, then the child terms can be part_of.

cortex (PO:0005708): A maximal portion of ground tissue between the vascular system and the epidermis in a plant.

revised def'n: A maximal portion of ground tissue between the vascular system and the epidermis in a plant.

hypodermis (PO:0005051): A portion of ground tissue that is the outermost layer of a portion of cortex. comment:A layer or layers of cells beneath the epidermis that is distinct in appearance from adjacent tissues.

endodermis: (PO:0000252)A portion of ground tissue that is the inner most layer of a cortex and has a casparian strip in its anticlinal cell walls. Comment: Forms a sheath around the vascular system. It may have secondary walls later, part_of cortex

Other types of cortex, for instance: embryo cortex, stem cortex, and several others then must also be defined as is_a ground tissue that is part_of cortex.

Terms from last week

These items were tabled for future discussions

1. fruit (See SF Tracker: fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.

Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it). Dbx ref to parthenogenesis: Medical subject heading Ontology D010312

Barry suggested that we reword the second half of the definition, because the final word 'it' was ambiguous about what it was referring to, and the use of the word 'other' was unclear. We agreed that the second part of the definition about other floral structures should go into the comments section. Started to discuss whether or not the seed should be included as part of the definition (fruit contains seed), but ran out of time. To be continued next meeting.

2. Embryo (See SF Tracker: embryo)

Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants

(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes -add a comment?

Relationships:

(1) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity (2) develops_from zygote (see comment above) Usually (3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)