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 at NSF as part of the Gramene application

As part of publication process of paper - text mining:associate to GO, PO and TO

• Textpresso

expression, phenotype, interactions 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 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

- Ellis book is appropriate for morphotype:

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.

2. Eliminating_Zea/Poaceae_terms_from_PO

3. New annotation files:

• Should we wait for MaizeGDB to send all their new annotations?

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

4. Other changes

• Japanese synonyms?

Target dates:

We discussed having a release in September, 2011

• Finish all edits: 9/16/2011?

• 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?

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: 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.

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 shoot system emerges from a seed.

Comment: This terms is used only for seed plants.

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.

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.

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.

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.

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 the fruit and ends when then fruit has reached 10% of its final size.

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

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)

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.

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

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.

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

Make each image and xml file so metadata is associated.

Phil Bourne nano-publishing UCSD