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

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 there 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.

phyllode

Last week, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.

Background on Phyllode:

Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:

"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."

The main reference people cite for phyllodes is: D.R. Kaplan 1980, Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.

Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."

Some more contemporary uses of the term phyllode:

Gardner et al. 2005 (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):

"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles."

and later in the paper:

"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.

"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."

Leroy and Heuret 2007 (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by a type of foliar organ called a phyllode." and "...the different transitional forms range from pinnate leaves to phyllodes..."

See fig. 1 in this paper. They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.

Yang et al. 2008 (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.

Forster and Bonser 2009, Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."

RW did not find any contemporary papers that said that a phyllode is a petiole.

Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.

Unifacial leaf as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311). Might be better to make a parent term ensiform leaf which has children phyllode and unifacial leaf.

Proposed terms and definitions:

vascular leaf

>unifacial leaf

>>terete leaf (round in cross section)

>>ensiform leaf (flat in cross section)

>>>phyllode

unifacial leaf: A vascular leaf that has increased activity of either the adaxial or abaxial meristem early in development, leading to abscense of the opposite surface on the leaf. (ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)

Comment: A unifacial leaf may be round in cross-section (terete) or it may be laminar (ensiform), in which case lamina development is in a median plane (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Unifacial leaves may be bifacial at the leaf base. Many unifacial leaves develop by reduced (or absent) activity of the marginal meristems and increased activity of the adaxial meristem early in development, leading to mature leaves with only an adaxial surface (e.g., Acacia, most monocots?). However, some develop by increased activity of the abaxial meristem early in development, leading to mature leaves with only an abaxial surface.

RW: need to check and add references for all of these

terete leaf: A unifacial leaf that is round in cross section due throughout all of part of the length of the leaf.

Comment: The surface of a terete leaf correspond to either the adaxial or abaxial surface of a normal leaf.

ensiform leaf: A unifacial leaf that is flat in cross section due to a lamina that develops in a median plane (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout all of part of the length of the leaf.(ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)

Comment: Common in many monocots and some dicots. Both sides of an ensiform leaf correspond to only one of either the adaxial or abaxial surface of a normal leaf.

RW: Maybe phyllode should just be a narrow synonym of ensiform leaf.

phyllode: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in develop.

Comment: Common in legumes of the genus Acacia. Similar development occurs in some monocot leaves (ensiform leaves), but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, phyllode-type transition leaf). In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not. Phyllodes are generally xeromorphic.

is_a ensiform leaf, is_a adult leaf

phyllode-type transition leaf: A transitional vascular leaf in which the basal portion of the leaf has lamina development is a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.

Comment: Common in seedlings of legumes of the genus Acacia. May also occur later, after the plant has begun to produce phyllodes.

is_a transitional leaf, is_a vascular leaf

bristle

(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)

Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should request terms needed to PATO.

See more details at Items_for_future_meetings#bristle

Calyptra perianth types

This was raised at the POC meeting POC_Conf._Call_8-23-11

Existing terms:

• fruit operculum (PO:0025298): A collective organ part structure that is the apical part of a circumsessile capsular fruit that separates from the rest of the capsule during dehiscence. [source: POC:curators]

Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.

and

• calyptra perianth (PO:0025299): A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary. [source: POC:curators]

Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra.

Synonyms: related: floral operculum; exact: angiosperm calyptra; exact: floral calyptra (suggest we add flower operculum as related and flower calyptra as exact)

Proposed changes: More specific terms for calyptra

At least week's meeting, there was a request for more specific terms for calyptras formed of fused petals or fused sepals.

In Eucalyptus, there may be one or two calyptras: an inner operculum or calyptra composed of fused petals and an outer operculum or calyptra composed of fused sepals. In many species, the sepals to do not fuse, and there is no outer operculum.

Our current definition of calyptra perianth includes fused tepals, which would encompass the existing term "fused collective tepal structure" (PO:0025138), but to my knowledge, tepals are not present in Eucalyptus. (The ANBG provides EUCLID, an excellent resource for description of Eucatypus morphology.)

Suggest adding a new term "fused perianth", that is consistent with our other terms such as "fused collective tepal structure". This would be a more general term, and could include perianths that are partially fused.

Proposed new terms and ontology structure:

• need to open a SF tracker for these

perianth

> fused perianth (new)

>> fused collective tepal structure (PO:0025138)

>> calyptra perianth (flower operculum) (PO:0025299)

>>> calyptra calyx (outer operculum) (new)

>>> calyptra corolla (inner operculum) (new)

• Should we also add terms for fused petal and fused sepal (already have fused tepal)?

terms and definitions

• fused perianth: A perianth that is composed of two or more fused perianth parts (sepals, petals or tepals).

Comment: Perianth parts may be partially or wholly fused.

• calyptra perianth (PO:0025299): A fused perianth that is composed of fused sepals or petals and located on top of a gynoecium that contains an inferior ovary.

Comment: Found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra or fruit operculum. Use the more specific term (calytra corolla or calytra calyx) if possible. Species of the subgenera Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development.

Synonyms: flower operculum, floral operculum, floral calyptra; angiosperm calyptra

• calyptra calyx: A calyptra perianth composed of fused sepals.

Comment: Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused.

Synonyms: outer operculum, calyx operculum

• calyptra corolla: A calyptra perianth composed of fused petals.

Comment: Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla).

Synonyms: inner operculum, corolla operculum

• fused collective tepal structure (PO:0025138), calyptra calyx and calyptra corolla all have dual parentage (is_a fused perianth and is_a collective tepal structure, calyx, or corolla. If we were to import PATO:0000642 (fused with), we could make cross product definitions and infer one of the relations.

Images in the PO via Plantsystematics.org (11:00 AM - 12:30 PM)

• 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."