POC Conf. Call 8-30-11

POC meeting, Webex Conference Call; Date: Tuesday Aug 30th, 2011 10am (PDT)

In attendance:

POC members:

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_8-23-11?

New children of calyptra perianth

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

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

In Eucalyptus, there may be one or two calyptra: 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.)

I 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:

ontology structure:

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)

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.

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.

Update on addition of new MaizeGDB Annotations

• This was discussed on the conference calls: [POC Conf. Call 8-2-11] and [POC Conf. Call 8-23-11], as well as the webex meeting with Mary Schaeffer on Aug. 11th, see: Submission of Association files for the Kaeppler gene expression data from MaizeGDB- Aug 2011

Loading annotation files

Any updates? LC fixed the annotation file and resubmitted it to the SVN, JE loaded onto beta browser

Now there are 25,004 annotations showing up that are associated with style (PO:0009074)

• RW is working on a list of Zea/Poazeae terms that have been merged and have annotations associated with them.

Merging maize-specific terms and other changes to the ontology

See Eliminating_Zea/Poaceae_terms_from_PO

PAO terms

• All terms with Zea and Poaceae in their names have been merged or renamed (except hull, see below). Most of the related terms (parts of the florets) have also been merged. Still need to add comments to some of the affected terms.

• Renamed ear and tassel "ear inflorescene" and "tassel inflorescence", as decided at last week's meeting.

• Kept spikelet and its subtypes, and floret and its subtypes.

Poaceae hull

Poaceae hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from the dried lemma and palea.

Would be best to give this term a name without "Poaceae" in it, but just "hull" could lead to confusion with other uses of the word hull. Any suggestions?

lemma

Existing def: lemma (PO:0009037): In a grass floret, the lower of two bracts enclosing a flower. [source: APWeb:Glossary, GR:pj]

Proposed def: A flower bract that is part of a spikelet and is the lower of two bracts enclosing a spikelet floret.

Comment: Found in Poaceae such as Zea mays. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding spikelet type. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).

Was part_of Poaceae floret, but made part_of spikelet, because it is a bract, and by definition, bracts are not part of a flower.

floret

The current definition for floret (PO:0009082) is: Small flowers, especially of the spikelets of Poaceae and Cyperaceae

The current definition for Poaceae floret is: A floret that is part of a spikelet. [source: POC:curators] Comment: Found in Poaceae. It is not clear what the lemma, palea and lodicule correspond to in conventional flowers, therefore we are not making any assumptions of homology at the present time.

Poaceae floret was part of spikelet. After merging the terms, I made floret part_of spikelet, because florets in both Cyperaceae and Poacae occur in spikelets (PMID:20197291 and others).

Suggest that we rename PO:0009082 "spikelet floret". This would distinguish it the way floret is used in the Asteraceae. The word "floret" can then be a narrow synonym of flower and be used annotation for flowers in Asteraceae (which don't have the special parts that florets in grasses have and therefore don't need a special sub-class, although we could add terms for them if the need arises).

Proposed name and definition:

spikelet floret (PO:0009082): A small flower that is part of a spikelet.

Comment: Found in Poaceae and Cyperaceae. Lemma, palea and lodicule are part of a spikelet floret, but since it is not clear what they correspond to in conventional flowers, no assumptions of homology are made at the present time. To describe a ray or disk floret of the Asteraceae, use flower (PO:0009046).

Added "ray floret" and "disk floret" as narrow synonyms of flower.

PGDSO terms

We have 5 open SF trackers for PGDSO terms for MaizeGDB. We can fix these without having to redo the whole PGDSO structure.

IL.03 full infloresecence length reached

Add two related synonyms:

3.4 late vegetative (maize)

VT (maize)

Also add to the comment: In US cornbelt maize, the tassel fully emerges about 2-3 days prior to silk emergence from husk leaves. At this time the ear and husk may still be enclosed within its leaf sheath depending on the variety and environmental conditions.

LP.18 eighteen leaves visible

Under synonyms add: related: VT vegetative transition in maize (US cornbelt)

3 infloresence visible - rework the tree, add a term

Current structure:

From Mary: Humble suggestions for reworking this part of the ontology so that very early stages of all species can be lumped, and to make it easier to annotate.

(1) PO:0007047 3 inflorescence visible should be redefined to include early stages where it may be visible (e.g. booting) but not yet emerged. One might rename the visible to ‘detectable’ and define appropriately.

current definition: The stage at which plant is producing inflorescence(s). is_a B reproductive growth

proposed definition, 3 inflorescence detectable phase: A reproductive growth phase during which one or more inflorescences is detectable.

Comment: This includes the time when inflorescence may be developing (e.g. booting in Zea) but not yet emerged. Includes times when inflorescences are detectable only by assay or with a microscope.

(2) PO:0007006 IL.00 inflorescence just visible should include the booting stage, etc. Perhaps rename to - IL.00 inflorescence just detectable. This will permit lumping with similar stages in Arabidopsis for example. Basically, all the developmental programs are in place and the structure is growing, even if only visible as a bulge in the sheath, or by stripping off the vegetative parts to view.

RW: What Mary describes is still visible (if the structure is actually growing), with manipulation of the plant or aid of a microscope. Use of the word detectable includes times when it could be detected by assay, but not visible. I think if we want a phase that describes that, we should add a separate phase: "inflorescence just detectable", for times when the inflorescence can be detected, but not seen, but only if people need it.

current definition: Inflorescence just visible to the naked eye.

proposed definition, IL.00 inflorescence just visible phase: An inflorescence detectable phase during which one or more inflorescences is just visible to the naked eye but not yet developed.

Comment: Includes the time when the inflorescence can be seen by removing outer leaves or bracts, or when the inflorescence is detectable as a swelling of the outer leaves or bracts, such as booting in Zea.

(3) PO:00070411 inflorescence emergence from flag leaf sheath would now have a direct is_a relationship with 3 inflorescence visible.

Additional comment from Mary: "the term 'emergence from flag leaf sheath' be made more global and be called something like inflorescence emergence (eg from flag leaf sheath, from leaf sheath) with appropriate definition. This way all terms save 2 (per above) would be retained."

current definition, inflorescence emergence from flag leaf sheath: The stage at which the inflorescence emerges from the flag leaf sheath.

proposed definition, inflorescence emergence phase: An inflorescence visible phase during which an inflorescence emerges from sheathing leaves or bracts.

Comment: Includes emergence of a Zea inflorescence from a flag leaf.

(4) PO:0007014 booting would be merged to the term PO:0007006 inflorescence just detectable.

Suggest merging PO:0007014 booting with PO:0007006 IL.00 inflorescence just visible phase. All children of booting would stay under PO:0007006 (inflorescence just visible, with synonym booting).

(5) Obsolete PO:0007012 Poaceae inflorescence visible as it would no longer be required.

Suggest merging PO:0007012 into inflorescence detectable stage, rather than obsoleting it. Descendants of PO:0007012 (booting and inflorescence emergence from flag leaf sheath) are already moved to other parents, see above.

coleoptile emergence -- definition

If we have time to discuss this, details are at Items_for_future_meetings#coleoptile_emergence_--_definition

5 fruit formation; FF.00 fruit size 10%

If we have time to discuss this, details are at Items_for_future_meetings#5_fruit_formation.3B_FF.00_fruit_size_10.25

Upcoming meetings 2011:

• POC Meeting at New York Botanic Garden Dates, Sept 10th-11th, 2011

The PO meeting will be on Saturday Sept. 10 and Sunday Sept. 11th.

RW has reserved the NYBG apartment for the nights of Sept. 9 and 10th, but it looks like the Hotel in Yonkers will work better for LC, PJ and BS -Reservation for the Garden apartment has been cancelled.

We are working on developing the agenda: See: POC Meeting at NYBG; Sept 10th-11th, 2011