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?
User requests, Plant Anatomy Ontology:
Legume terms submitted by Austin Mast
Remaining:
phyllode
Last week, we looked at examples of leaves where the petiole is a phyllode, 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.
See references by Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) and
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.
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)."
Boke (1940) 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. Pin- nate leaves and transition forms possess an apical pointlet like that of the phyllode."
Proposed def: A vascular leaf in which the laminar development is a median plane (perpendicular to the axis), rather than the more common state of in a transverse plane (tangent to the axis).
Comment: Lamina development in a phyllode may occur in the region of the leaf that would normally develop into a petiole. In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not.
Unifacial leaf as synonym? No- not the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311).
TraitNet requests:
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
child of stem (PO:0009047).
Their comment: is synonym to tubercle (even though they define tubercle differently)
podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
proposed def: A modified leaf base
Comment: Functions as the photosynthesising organ in some cacti and other succulents.
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.
Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
tendrils can 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 the problem is that according to the formal definitions, a leaflet tendril or a leaf apex tendril would be a leaf tendril as well.
Publications
- Plant Physiology: 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 manuuscrip:
Last week, we agreed to use "type" and "term" in the way BS suggested based on the Hill et al. 2008 gene annotation paper.
From 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.
Do we want to remove other plant prefixes? I (RW) 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).
"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.
- Short topics paper for American Journal of Botany
The editor of AJBOT asked Dennis to put together a short paper for them- can focus on PO. This would be consistent with the goals of the Phenotype RCN to reach out more to the botany community.
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: [1]
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
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....
