Sunday Sept 11th, 2011

Detailed agenda for Sunday Sept 11th, 2011

Back to main agenda for POC_Meeting_at_NYBG;_Sept_10th-11th,_2011.

Review of the Physcomitrella presentation:

There were some suggestions for changes, so those were made and the final version is linked here: Moss 2011 Meeting- PO presentation

Next steps for the PO:

PJ: presented the PO at NSF as part of the Gramene application

As part of publication process of paper authors will be encouraged/required to annotate to the PO and GO and ...?, Initially starting with Plant cell

• text mining: associate to GO, PO and TO *Textpresso

expression, phenotype, interactions

PJ: Update from NSF person, we will need a one-page description of future directions (this fall? when?)

• plant phenotypes focus of interest, new directions

• Problems with lack of plant annotations coming to GO (JB), PO will be the gatekeeper and coordinate them

GO model genome and Gramene

Cathy Wu- Protein Ontology- use their pipeline?

Freelance annotators @ Plant Cell (soon Plant Physiology)

Need robust plant phenotype Ontology (TO?), Environment Ontology (EnvO), Plant Disease Ontology (PDO), GAZ, PRO

NSF: Interorganismal and Environment Systems

allergies, food, symbionts, toxins, ecology, pathogens

BS: Need to find money for development of the Plant Disease Ontology

Infectious Disease Ontology (IDO): human disease, need to be able to link to the PDO

Apply to USDA/NIH/NSF? what is the best route?

PRO- no resources for plant protein ontology dev. apply for additional $$?

BS: presenting: Environment Ontology (EnvO) at 12th Genomic Standard Consortium

Trait Ontology

see the TO on Trait Ontology on Gramene

Discussion of the Pheno RCN

Discussion of the Ellis book on leaf architecture. It is appropriate for draft ontology of leaf characters, even though it may be missing characters that are needed for non-dicot leaves.

Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of general qualities (characters) are categorical character states, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".

Plans for upcoming Release

See details at Summary_of_Changes_to_PO_September_2011

Major changes for this release were:

1. Inclusion of Spanish synonyms. They seem to be working fine, except that we still should have the descriptor "(Spanish:)" preceding them. Look up notes from meeting...

Not clear if this is a problem with just the dev browser.

Need to follow up on this.

2. Eliminating_Zea/Poaceae_terms_from_PO

More or less complete. PGDSO may change as we go forward, but we can use as is for now.

3. New annotation files:

• Should we wait for MaizeGDB to send all their new annotations? Yes. At least get the PAO annotations in.

• Addition of new annotations for grape (LC working on) and [strawberry]

4. Other changes

• Japanese synonyms?

Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO.

Japanese synonyms are not currently in the editors' file. Should be added.

Target dates:

We discussed having a release in September, 2011

• Finish all edits: 9/23/2011

• Update annotation files and test on beta browser:

• Other tasks?

• Final release: End of September?

Outstanding edits to finish before release

See Items_for_future_meetings

PGDSO

Edits requested by MS for MaizeGDB

coleoptile emergence

From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be:

suggested def'n: coleoptile emergence (PO:0007045): Emergence of coleoptile from the seed. (rather than above ground)

This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.

PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence(PO:0007030) is defined as "Shoot or leaf breaks through soil surface."

• All of the sibling terms to cotyledon emergence (coleoptile, epicotyl, and hypocotyl emergence) are also defined as when they break through the soil surface, so if we change one, we should change all of them.

Do we all agree that it is better to define terms relative to other plant structures instead of to the environment?

We will keep the existing terms that reference emergence from the soil, but rename as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.

PJ suggested that we don't need to obsolete and replace the terms, but RW feels that this is exactly the kind of change in definition that warrants obsoleting the term and creating a new one.

Adding the replaced_by link would make moving existing annotations straightforward. There are 133 annotations on shoot emergence, including 1 from coleoptile emergence and 2 from cotyledon emergence.

Also, all of these terms should be renamed as stages rather than as developmental processes - so, for example, PO:0007045 should be called coleoptile emergence stage, rather than coleoptile emergence. The definitions should reflect the fact that they are stages, not developmental processes.

Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. We should fix these while we're redefining the terms.

current structure:

current and proposed definitions

current: seedling growth (PO:0007131): Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination

Seedling growth stage should begin after germination, not after imbibition. Imbibition is part of germination, and a seedling does not exist until after germination.

proposed: seedling growth stage A vegetative growth stage that begins with germination and ends with the development of the first adult leaves.

Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.

new proposed name and def.: seedling development stage: A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.

Note: After the PGDSO is revised, the parent of this term will be sporophyte vegetative development stage, so definition will change slightly.

Note: all of the definitions below describe only a single point in time, when they should describe an interval. New definitions will be posted on Source Forge.

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence stage (new number): A vegetative growth stage that occurs when a part of a shoot system emerges from a seed.

Comment: This terms is used only for seed plants.

new proposed names and definitions:

shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that occurs when a part of a shoot system emerges from the growth medium.

shoot emergence from seed coat development stage (new number): A seedling growth stage that occurs when a part of a shoot system emerges from a seed coat.

current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence stage (new number): A shoot emergence stage that occurs when a coleoptile emerges from a seed.

Comment: This terms is used only for seed plants.

See SF tracker for new proposed terms and definitions.

current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]

proposed: cotyledon emergence stage (new number): A shoot emergence stage that occurs when a cotyledon emerges from a seed.

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.

See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.

See SF tracker for new proposed terms and definitions.

current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: epicotyl emergence stage (new number): A shoot emergence stage that occurs when a epicotyl emerges from a seed.

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.

See SF tracker for new proposed terms and definitions.

current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: hypocotyl emergence stage (new number): A shoot emergence stage that occurs when a hypocotyl emerges from a seed.

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.

See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.

See SF tracker for new proposed terms and definitions.

Could also add terms for feeder emergence for some gymnosperms.

5 fruit formation; FF.00 fruit size 10%

Initial Comment from MS:

"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view. Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size. For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."

current def'n:FF.00 fruit size 10% (PO:0007032): The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]

Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green

All the other sizes are defined similarly.

There are actually annotations on 3 of the 5 fruit size stages.

proposed def'n.: (based on Mary's suggestion): A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.

Comment: This stage can only be used when the final size of the fruit is known.

We agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.

RW: When does formation of a fruit occur? Should we say fertilization of an ovary instead?

Legume terms

requested by Austin Mast

banner, wing and keel

reference: Lawrence, Taxonomy of Vascular Plants (1955)

Banner (as in a legume flower) - suggest using name banner petal

Proposed def: A petal that is the top-most petal of a papilionaceous corolla.

Comment: Usually larger than the adjacent wing petals. Found in the flowers of some Fabaceae.

Synonyms vexillum (exact), standard (broad)

Okay to add banner petal.

Wing (as in a legume flower) - suggest using name wing petal

Proposed def: One of two lateral petals that is adjacent to the banner petal of a papilionaceous corolla .

Comment: The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.

Okay to add wing petal.

Keel (as in a legume flower) - suggest using name corolla keel and adding term for keel petal.

Two new terms:

corolla keel: A boat-shaped collective phyllome structure that consists of the two lowest petals of a papilionaceous corolla.

Comment: The two petals of the keel are often fused at the apex and free at the base. The keel projects toward the front of the flower. Found in the flowers of some Fabaceae.

is_a collective phyllome structure, part_of corolla

New proposed name: keel

We need to reword the definition of corolla (and other collective phyllome structures), because technically, the keel is a corolla (it consists of two or more petals). New definition should be the maximal set of petals or whatever in a flower.

keel petal: A petal that is one of the two lowest petals of a papilionaceous corolla.

Comment: The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other. Each petal is shaped like half a boat and projects toward the front of the flower.

Okay to add keel petal.

phyllode

This was tabled for discussion at a future meeting:

See more details at: Items_for_future_meetings

Calyptra perianth types

This was tabled for discussion at a future meeting:

See more details at: Items_for_future_meetings

Images in the PO

See: Plantsystematics.org

from MAG (by email): "I am taking with me not only lots of "annotated" photos for Pankaj but also I will demonstrate everything we did with Plantsystematics.org and the PO photos. We are using the list I translated (the English version of course) and added them as keywords in Plantsystematics.org as a search engine as well."

Some slides have 8 images, some have 16. More than 3000 slides.

Make each image and xml file so metadata is associated.

Some discussion of copyright issues. PO material must be open access (according to grant), but users need to get credit for their photos. PJ suggested putting a watermark on the images with the credit for the photographer, then people can contact photographer for image without water mark if they want to use it.

BS suggested contacting Phil Bourne from UCSD re. nano-publishing.