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"
- Prefixing the 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."
LC: this was not my understanding of what was decided at the JAX CL meeting.
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 on....
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?
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.
podarium
Their comment: is synonym to tubercle (but it isn't exactly the same)
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. podarium: A modified leaf base (under construction)
Comment: Functions as the photosynthesising organ in some cacti and other succulents.
proposed def. tubercle: (under construction)
Legume terms submitted by Austin Mast
Remaining:
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:
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.
Proposed terms and definitions:
phyllode: An adult 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). (ref: Lawrence)
Comment: Common in legumes of the genus Acacia. Lamina development in a phyllode occurs from activity of the abaxial meristem early in development, similar to unifacial leaves. Similar development occurs in some monocot 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, transitional phyllode-type 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 vascular leaf, is_a adult leaf
Unifacial leaf as synonym? No- not 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.
phyllode-type transition leaf: A transitional vascular leaf in which the basal portion of the leaf has lamina development 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.
bristle
More complicated, because it is a phenotype term, and applies to structures other than stipules.
Will discuss at a future meeting.
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....
