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."
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 enlarged modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
[This article] describes podaria and tubercles (as synonyms) as a swelling of the stem (cladode) fused with the base of a leaf:
"Tubercles (or podaria) are swellings below the conic leaves of the pad (long-shoot). The upper part of the conic leaf is the blade, which abscises in a week or two at a notch. The leaf base, or petiole, and adjacent stem tissues are fused together forming the tubercle. The tubercle may elongate and swell such as in species of pincushion cacti (Mammillaria spp.). If the raised tubercles align vertically around the stem they can coalesce with those directly above and below forming ribs, like those of the saguaro."
proposed def. podarium or tubercle: under construction
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....
