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?
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
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
The definition stipulates adding annotating also to either vascular or non-vascular leaf if annotating to this one. The rationale for this is not clear. It seems to me that annotating to another vascular leaf term: adult, transition or juvenile leaf, accomplishes the same purpose, or does it? The same issue holds also for leaf apex and possibly leaf tip.
This question was answered, but she an additional question:
"But would you explain what happens if I forget to add vascular leaf? Curious about why there are not just two terms for leaf base - one for vascular and one for non-vascular."
From RW:
In answer to "what happens if I forget to add vascular leaf?": We are working on a script that will read in the taxon id for any annotation to a part of a leaf, and automatically copy that annotation to vascular or non-vascular leaf, depending on the species. In the mean time, it is better if curators can annotate to both.
In answer to "why there are not just two terms for leaf base - one for vascular and one for non-vascular.": The problem is that leaf has 15 is_a descendents and about 30 part_of descendents, and as more types of leaves are described, we need a way to describe the parts of all of them. This would create a lot of term inflation. You can see more discussion of this on our minutes at: http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_6-28-11#Items_arising_from_previous_meetings:_Dealing_with_children_of_leaf
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
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?
User requests: PGDSO:
Maize GDB
IL.03 full infloresecence length reached
Add to synonyms: related: 3.4 late vegetative, aka VT, tassel but not ear in maize
LP.18 eighteen leaves visible
Under synonyms add: related: VT vegetative transition in maize (US cornbelt)
coleoptile emergence -- definition
It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed (rather than above ground) . This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.
PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence(PO:0007030) is defined as "Shoot or leaf breaks through soil surface."
All of the sibling terms to cotyledon emergence (coleoptile, epidcotyl, and hypocotyl emergence) are also defined as when they break through the soil surface, so if we change one, we should change all of them.
Do we all agree that it is better to define terms relative to other plant structures instead of to the environment?
PJ suggested that we don't need to obsolete and replace the terms, but RW feels that this is exactly the kind of change in definition that warrants obsoleteling the term and creating a new one. Adding the replaced_by link would make moving existing annotations straightforward.
Also, all of these terms should be renamed as stages or phases rather than developmental processes - so it should be called coleoptile emergence stage, rather than coleoptile emergence - and the definitions modified accordingly.
An alternative solution is to leave existing terms defined as is (but to create a new set of terms for the stages when structures emerge from a seed. PO:0007030 could be renamed "shoot emergence from the soil stage" and we could create a new term "shoot emergence from the seed" with children like "coleoptile emergence from the seed".
3 infloresence visible - rework the tree, add a term
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.
(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.
(3) PO:00070411 inflorescence emergence from flag leaf sheath would now have a direct is_a relationship with ‘3 inflorescence visible’.
(4) PO:0007014 booting would be merged to the term PO:0007006 infloresence just detectable.
(5) Obsolete PO:0007012 Poaceae inflorescence visible as would no longer be required.
Re Add a term. One thought was to add a term specific for the ear on maize,
but on second thought I prefer lumping, so that 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.
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....
