POC Conf. Call 7-12-11

POC meeting, Webex Conference Call; Date: Tuesday July 12th, 2011 10am (PDT)

In attendance:

POC members: Absent:

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_7-05-11?

Plant Physiology Publication

RW and LC are working on a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PO in the past year, focusing on restructuring of PAO. Will focus on how PO is now applicable to a wider range of plant species.

Discussion items arising from manuscript:

• Last week, we agreed to use "type" and "term" in the way BS suggested based on the Hill et al. 2008 gene annotation paper, rather than using "class"

Type = A universal, represents the entity or stage/phase in reality.

Term = the thing in the PO that corresponds to a PO id.

• Prefixing some of the term names with "plant" (e.g. plant cell, plant embryo)

CM:"So I see you've decided to prefix many terms with "plant". I don't think this is necessary (we decided this at the JAX CL meeting), and no other ontology does anything similar. I guess if this is just for the upper level terms (which should be hidden from view in most applications) then the user-unfriendliness doesn't matter. It's also a little curious as the terms that have the potential to cause confusion in a pan-eukaryotic context (epidermis, cuticle) are _not_ prefixed. I would recommend omitting all "plant" prefixes. For details on automatic assignment of obo foundry unique labels, see our paper from WOMBO/ICBO this year."

Do we want to add "plant" as prefix to terms like epidermis, cuticle, vascular system? Probably should be consistent.

Do we want to remove other plant prefixes?

RW: I think they make sense for the upper level terms, because they are only defined in terms of plants (e.g., a plant anatomical entity is an AE that is in a plant)

• Use of noun form in term names: Is it nb that it is consistent across the ontology? (We decided this at the POC conf call POC_Conf._Call_5-17-11#Items_arising_from_previous_meetings:.)

CM: "I would say "embryonic plant structure" rather than "embryo plant structure", the relational adjective form is far more common in other ontologies, but horses for courses.

Should we change this? It does sound better.

• The defense of the "portion of" prefix doesn't sound very convincing.

Current text: "Although the phrase “portion of plant substance” is not part of everyday language, that name was chosen, rather than plant substance, to clearly express that this class can include any portion of a plant substance (such as xylem sap) found anywhere in the world, be it all of the xylem sap in the world, all of the xylem sap in any whole plant, or just the xylem sap found in one particular branch of one particular plant."

Suggestions for better wording?

• The reflexive part_of case is interesting (trichomes). What is in the manuscript is 100% correct. However, it is worthwhile bringing this up on the RO list.

• Never say "children" or "parents" if you can be more specific (subtype, part_of)???

• Should PAO and PGDSO should be referred to as branches, rather or as sub ontologies

• Use of "relation" versus "relationship": is there a rule about when to use these words?

[1]

User requests, Plant Anatomy Ontology:

TraitNet requests:

corm

proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.

child of stem (PO:0009047).

pneumatophore

definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves

proposed def: A root that is erect and protrudes above the soil.

Comment: Pneumatophores are found in trees that live in flooded habitats such as mangroves. May provide oxygen to below ground roots growing in flooded soils.

tendril

Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.

tendrils can be (evolutionarily) derived from multiple types of structures. Suggest we make separate terms:

branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.

leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaflet tendril (child of leaflet): A leaflet that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar. Aids plant in climbing.

Can add other types of tendrils if they come up or users need them.

This is the way we defined spine (no parent class spine, only leaf spine and stipule spine with is_a relations to leaf and stipule).

Alternative is to create a parent 'tendril'(is_a plant structure) with children that are part_of the other structures:

tendril: A plant structure that is slender and coiling. Comment: Aids plant in climbing.

branch tendril is_a tendril part_of branch

leaf tendril is_a tendril part_of leaf

leaflet tendril is_a tendril part_of leaflet

leaf apex tendril is_a tendril part_of leaf apex

The part_of relations are technically correct (not proper part), but I don't think it conveys the proper meaning. Also, according to the formal definitions, a leaflet tendril or a leaf apex tendril would be a leaf tendril as well.

Maize GDB

transition leaf - definition

From Mary at MaizeGDB: It would be helpful to add some insights on the transition leaf. For example - Leaves that have mosaics of juvenile and adult tissues. In maize, the juvenile will be at the tip, which differentiates first, with adult at the base. Other grasses may have other arrangements, eg Brachypodium, which may have both juvenile and adult across the breadth of a leaf. Provided by Erin Irish, who references t his paper: Irish, E. E. and Karlen, S. (1998) Restoration of juvenility in maize shoots by meristem culture. International Journal of Plant Science 159, 695-701. The Brachy. information is more recent.

Suggest adding to the comment of juvenile leaf, transition leaf and adult leaf: Many species have juvenile leaves are at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves will be at the tip of the stem, which differentiates first, with adult at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenille and adult tissues, as in Brachypodium.

Can add Irish and Karlen reference to definition dbxrefs if it is appropriate.

leaf base

See tracker item for details.

I think Mary's questions have been answered, and this item can be closed. We can add a comment to it once we resolve the issue of transferring annotations for parts of leaf.

style, silk, Poaceae style

From Mary at MaizeGDB: Suggest that you merge these, keeping style, obsoleting silk and Poaceae style. Do the same for other floral parts that have a species spin on them, but are really the same as other more generic names for flower parts.

From PJ: Poaceae / Zea was necessary in some terms because often detail structures referred to parts of tassel/ear floret and it has conflict with floret compositeae besides the spatial aspects.

Rather than working on this piecemeal, we need to have an organized approach to eliminating the Poacaeae/Zea terms. Need to look at the structure from the top down and ensure part_of relations remain correct. Do we want to allocate time to this now or wait for next release?

See page for Eliminating Zea/Poaceae terms from PO

42 terms in PAO with Poaceae in the name.

28 terms in PAO with Zea in the name.

Only on Poaceae terms in PGDSO, and it is on today's agenda to merge with another term.

User requests: PGDSO:

Maize GDB

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 (eg 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 detect, 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 booting.

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

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

coleoptile emergence -- definition

See next week's agenda.

Upcoming meetings 2011:

• Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.

Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).

DWS is attending, but will not present. Many people from the BSA will be at the IBC meeting in Melbourne.

• ICBO 2011 Second International Conference on Biomedical Ontology

July 26-30, 2011 Buffalo, New York ICBO

-LC will present the PO on Friday July 29th, 3:30pm in the session: "Parallel Sessions on Special Topics: The OBO Foundry, featuring discussions of the Infectious Disease Ontology, the Ontology for Biomedical Investigations, the Ontology for General Medical Sciences and the Plant Ontology"

Link to program: [2]

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Date: July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

• Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Gramene and Plant Ontology are hosting a [Data Curation Workshop] again, focusing on pathway curations.

LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Plant_Biology_2011_Outreach_Booth and we are invited to take part. We are hosting the website.

• International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

• POC Meeting at New York Botanic Garden Tentative dates, Sept 9th-11th, 2011

DWS will look into booking the apartments at the NYBG for accommodations

More details TBA....