POC Conf. Call 8-30-11

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_8-23-11? no additions, deletions, or changes

link to Webex recording

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 test annotation file

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

-MS is correcting her script for creating the files. What is the size recommendation for the next set of files?

Now there are 25,004 annotations showing up that are associated with style (PO:0009074) (which is part_of ear floret (PO:0006354); noted in Col 16)

This makes more sense in terms of the number of gene models.

• Remaining Issues:

Are these propagating correctly? Why are these also on plant cell?

RW: because associations (incorrectly) get passed through all relations. Same reason they are on portion of plant tissue. See this image: Media:style_to_cell.jpg

The annotations are being passed through both has_part and develops_from and the annotations are showing up on plant cell and are also on portion of plant tissue.

Why is there nothing in the "Associated To:" column? not sure. LC will email CM and JE to investigate

Do we need to add additional lines to associate these with ear floret? Yes, Mary will add these, RW will follow up with her.

This will also be the case for about 10 of the other tissues that MS is annotating to, especially the leaf terms

Need to fix links to MaizeGDB pages for gene models and the tissue pages LC will follow up.

Merging maize-specific terms and other changes to the ontology

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

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 inflorescence" 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?

How about caryposis hull?

Okay to change name to caryopsis hull.

lemma and palea

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. A lemma subtends an individual floret while glumes subtend the pair of florets. 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).

Note: This was part_of Poaceae floret, but made it part_of spikelet, because it is a bract, and by definition, bracts are not part of a flower. We are actually making a homology assumption by saying it is a bract.

All of the above also applies to palea (PO:0009038).

The above changes were approved.

RW will email MS and ask her to look at the specific Source Forge items for maize.

glume

See Eliminating_Zea/Poaceae_terms_from_PO#glume for more details.

glume (PO:0009039, PO:0006026)

current def: A "bract" in the inflorescence of a grass, sedge or similar plant.

proposed def: One of a pair of inflorescence bracts that is part of a spikelet and subtends the two florets.

Comment: Found in Poaceae and Cyperaceae. Glumes subtends the pair of florets while a lemma or palea subtend the individual florets.

glume of ear spikelet (PO:0006367)

current def: A bract in the ear inflorescence of a maize plant, subtending two florets.

proposed def: A glume that is part of an ear spikelet.

intersection_of: is_a glume and part_of ear spikelet

glume of tassel spikelet (PO:0006368)

current def: A bract in the tassel inflorescence of a maize plant, subtending two florets.

proposed def: A glume that is part of a tassel spikelet.

intersection_of: is_a glume and part_of tassel spikelet

The above changes are okay. Will keep the different types of glumes.

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.

These should be "ray flower" and "disk flower", however, people sometimes use floret, so we could add "ray flower", "disk flower" and "floret" as synonyms of flower. Also, "ray floret" and "disk floret" could be added as related synonyms

Floret is also used in the Hammemilidaceae, for example Witch hazel .

There should be a lot of genomics work going on in Asteraceae like safflower and sunflower, so we may need to readdress the terminology.

Should also add "spikelet flower" as synonym of "spikelet floret".

We will need to work on definition of spikelet, because it is not just in grasses. Spikelets occur throughout the Poales. RW will make SF tracker.

PJ asked about the case of date palms. Sometimes the word "spikelet" is used to describe inflorescence branches, as in oil palms. We could add spikelet as a related synonym of inflorescence branch.

PJ: See link: Phyllotaxis in the Oil Palm: Arrangement of Male/Female Spikelets on the Inflorescence Stalk

DWS and MAG will look into the description of oil palms by ???,,, please fill in. RW will open a SF tracker for spikelet

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 inflorescence 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.

Will ask MS if she could supply citations for these synonyms, because they are likely to confuse people who don't work on maize.

Comment may not apply to every variety of US cornbelt maize. Need to ask Mary if there should be specific varieties listed. Add SF comment about this- is this true for B73?

LP.18 eighteen leaves visible

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

add citation

3 inflorescence visible

Suggestion to rework the tree, add a term:

From Mary Schaefffer: 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.

Current structure:

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 def'n: 3 inflorescence detectable phase: A reproductive growth phase during which one or more inflorescence is detectable.

LC: I think we should stick to using the singular case; will post comment on SF

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.

New name and definition are okay. Add "3 inflorescence visible" as a synonym.

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 def'n: IL.00 inflorescence just visible phase: An inflorescence detectable phase during which one or more inflorescence 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.

Next stage is 1/4 inflorescence length reached, so this stage could go from just visible until it has reached 1/4 of its length.

Of course, you may not know what final length will be. This may be hard to apply across all taxa. We need to think of more comparable landmarks in development, like initiation of carpel, etc.

We will keep the current stages for now, but look into more general terms across taxa.

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 def'n: inflorescence emergence phase: An inflorescence detectable phase during which an inflorescence emerges from sheathing leaves or bracts.

Comment: Includes emergence of a Zea mays inflorescence from a flag leaf, following booting.

Okay to make this change. Add word "mays" to comment.

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).

We will keep booting and its children. Booting will be a child of PO:0007006 inflorescence just detectable.

Keeping this because booting is a grass specific term. Need to make it clear that this term should only be used for grasses.

We need to make a written policy statement describing when we choose to add/keep certain growth stages that are specific to particular taxa. Criteria: when there is no one-to-one correspondence between growth stages in one taxa (or a set of taxa) and in others. Examples: booting stages in Poaceae, rosette stages in Brassicaceae (and other taxa).

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.

Okay to merge this into "3 inflorescence detectable phase". Inflorescence emergence phase (see #3 above) will be child of "3 inflorescence detectable" and booting will be a child of IL.00 inflorescence just visible phase (see #4 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

Items arising from last week's meeting:

New children of calyptra perianth

Will update SF tracker for these terms so people can comment on them there.

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.

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 canceled.

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

Probably start the first day talking about the PGDSO, then go from there.

The PO meeting will be all day Saturday Sept. 10 and morning of Sunday Sept. 11. DWS, PJ, BS, LC, MAG and RW will attend

RW and LC should work on a presentation/proposal for changes to PGDSO.

* Virtual PO presentation for Moss 2011 Meeting in Germany Date: Sept 12, 2011 8am EDT from NYBG

See: Moss 2011 PO page

Abstract has been submitted

More details: TBA

Note from DWS: Moss 2012 will be at the NYBG next summer