POC Conf. Call 1-17-12
POC meeting, Webex Conference Call; Date: Tuesday Jan 17th, 2012 10:30am (PST)
In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University), Barry Smith (University at Buffalo, NY)
Absent: Pankaj Jaiswal (OSU), Justin Elser (OSU), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab)
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-10-12? No additions, deletions, or changes.
Back to POC Meetings Minutes
Term Requests from users
freely ending veinlet: Part of leaf vein. Higher order veins that are only connected to other veins at one end.
proposed definition: A leaf vein above the first order that is connected to another vein only at one end.
comment: May be branched or simple. Usually used with third order or higher veins. If vein order is known, an additional annotation should be place on secondary vein (PO:0020140), tertiary vein (PO:0008021), quaternary vein (PO:0008022), or higher order vein (PO:0008023).
Note: PO currently does not have a term for first order or primary vein, but we have this term requested under Items_for_future_meetings#leaf_vein.2C_midrib.2C_costa
ref.: Ellis et al.
DWS: We need a term for tracheoidal idioblast.
What about leaves with repetative dichotomies? Are they all first order veins? No, defined by caliper of vein. We should put a comment on the different order veins that they are not appropriate for dichtomously branching vein patterns (like some ferns or gymnosperms).
From Shawna Thompson.
From FNA glossary: A set of one or more awns (aristae, bristles, setae) or scales at the summit of an inferior ovary just beneath or outside the free portion of the corolla; persisting in the fruit (cypsela) and often aiding wind or animal dispersal; in Asteraceae (Compositae). Considered by some to be an evolutionarily modified upper calyx portion, the lower portion having been incorporated into the floral tube casing adnate to the ovary wall; considered by others to be an outgrowth from the ovary wall.
From Harris and Harris: The modified calyx of the Asteraceae, consisting of awns, scales, or bristles at the apex of the achene.
proposed definition, pappus: A collective organ part structure that has a parts one or more pappus elements (scales, awns, or bristles) at the apex of an inferior ovary just beneath or outside the free portion of the corolla.
Comment: Found in flowers and fruits (cypsela) of the Asteraceae. May aid in dispersal by wind or animals. Considered by some to be an evolutionarily modified upper calyx portion, the lower portion having been incorporated into the floral tube casing adnate to the ovary wall; considered by others to be an outgrowth from the ovary wall.
Modified definition: ...beneath or outside a corolla. (not just outside the free portion)
FNA also has a term for "pappus scale": A pappus element that is more or less planate and relatively thin and broad; may terminate in one or more awn- or bristle-like appendages. I suggest we add a term for pappus element, with pappus scale, pappus awn, and pappus bristle as narrow synonyms.
proposed definition, pappus element: A cardinal organ part that is a segment of a pappus.
comment: May be awn-, scale-, or bristle-shaped.
synonyms: pappus scale, pappus awn, pappus bristle; part_of pappus
Should we refer to PATO terms for awn-, scale-, or bristle-shaped? Probably, but it is difficult because they don't really have terms for that right now. We could suggest them.
May want to add a subset for Asteraceae if we keep adding terms specific to them.
GO refers to these terms, but they are absent from PO.
GO has floral organ development: The process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure.
They also have a request for floral organ senescence. They would like a PO term for cross referencing.
Also, PO has the term: 3 flower organ development stage (PO:0007600).
Proposed def., floral organ: An plant organ that is part of a flower.
comment: Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores.
intersection_of: is_a plant organ and part_of:flower
No direct children. All subtypes will be inferred.
synonym: flower organ
GO has "floral whorl development": The process whose specific outcome is the progression of a floral whorl over time, from its formation to the mature structure. A floral whorl is a circular arrangement of parts of a flower arising from a stem of a plant.
floral whorl in PO is a narrow synonym for: PO:0025023 ! collective phyllome structure
Should we add a term for floral whorl as a subtype of collective phyllome structure?
From PJ: I think the term usage of whorl is coming in the GO development section is for annotating the genes involved in the ABC model of flower development. There are set of genes that are involved in expressing and initiating the development of 'floral organs' (More appropriate than whorls) http://aob.oxfordjournals.org/content/100/2/155.full. Though we have individual types of whorl as stand alone terms there is no bin term floral whorl.
Perhaps it would be best to just keep "floral whorl" as a narrow synonym of collective phyllome structure. GO can still reference PO:0025023 and call their term "floral whorl development" if they want. However, they may want to consider if the annotations would be better on "floral organ development".
We will not add a separate term for floral whorl, but GO can continue to use it, because it is a synonym of collective phyllome structure. Also suggest that it would be better for people to annotate to either floral development or to corolla, calyx, etc. development.
New terms and changes arising from previous discussions
During a discussion at the POC meeting on 10-18-11, we realized that it would be best to have seed be a subtype of plant structure.
Current def.: A propagating organ formed in the reproductive cycle of gymnosperms and angiosperms, derived from the ovule and enclosing an embryo. [source: APWeb:Glossary, GR:Pankaj_Jaiswal] comment: The seed is representative of a next generation of sporophyte.
New proposed def.: A plant structure that develops from an ovule and contains an embryo enclosed in a seed coat.
Comment: A seed generally develops from an ovule after fertilization, but may develop without fertilization in the case of adventitious embryos, somatic embryos, or other embryos that arise through apogamy. A seed is a reproductive unit of seed plants (gymnosperms and angiosperms).
develops_from ovule, has_part embryo
Also removed seed part_of fruit relation, added seed to subsets for gymnosperms and angiosperms.
Definition should say "has as parts..." rather than contains.
New proposed comment: A seed generally develops from an ovule after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms).
Should we put PO id in the definitions? For now, will only put ids in the comments, but in the definition, we should be sure to use the term names. What would be great is to have AmiGO recognize the text string of PO terms and automatically create links, so definition is legible to people and not cluttered with numbers, but still links to terms.
May want to review this next week. May need to be more specific in definition. Maybe add something about the exine.
Spore is_a cell, which is correct, but it is also a whole plant. Just as we changed the definition of plant zygote to reflect its dual nature, I suggest we change spore. Also suggest that we rename it plant spore, for consistency.
Current definition: A plant cell that arises through meiosis and develops into a gametophyte.
New proposed name and definition, plant spore: A single-celled whole plant that arises through meiosis and develops into a multi-celluar gametophyte.
Need to check if gametophytes are always multicellular in green algae. - Yes in green algae. Not for some other algae, but they are not covered by PO.
Actually, spores can be multicellular, so spore should not be a subtype of plant cell.
Revised definition: A whole plant that arises through meiosis and develops into a gametophyte.
Put comment that it is single-celled in homosporous ferns and may be multicellular in heterosporous plants.
proposed definition: A gametophyte development stage that occurs during the interval between meiosis and the germination of a spore.
comment: The plant spore stage ends with the first cell division of a spore. Includes the stage when a megaspore is present before it develops into a megagametophyte or embryo sac and the stage when a microspore is present before it develops into a microgametophyte or pollen.
intersection of is_a gametophyte development stage, has_participant spore
Get rid of comment that says "ends with the first cell division of a spore" because sometimes the spore divides before it germinates. Add comment: There may be cell division in a spore before it germinates.
proposed definition: A gametophyte dormant stage during which a spore participates in a dormancy process.
Comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.
is_a gametophyte dormant stage, has_participant spore
Because plant spore stage is an XP of is_a gametophyte development stage and has_participant spore, this will be inferred to be is_a plant spore stage.
Check if GO has spore germination term, and make sure it is appropriate for plants.
proposed definition: A sporophyte dormant stage during which a plant embryo participates in a dormancy process.
Comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. In seed plants, a plant embryo dormant stage may be part of a seed dormant stage.
is_a sporophyte dormant stage, has_participant plant embryo
Since plant embryo stage is an XP of is_a sporophyte development stage and has_participant plant embryo, this will be inferred to be is_a plant embryo stage.
Also added seed dormant stage has_ part plant embryo dormant stage. Can't add the inverse part_of relation, because not all embryo dormancy occurs in seeds. Question for Barry or Chris: Is this the correct usage of part_of for development stages? Yes. Future RO/BFO will have different part_of relations for continuants and occurrents.
May want to review definitions of lamina (PO:0025060) and leaf lamina. Others are okay.
Leaf lamina is defined as any lamina that is part of a leaf, so petiole lamina is a subtype of leaf lamina. At least week's meeting, we decided that lamina should be defined exclusive of the petiole. That is how most people think of it.
We may want to make a parent term phyllome lamina, because we will eventually need to add terms for petal lamina, etc. Are there laminae in structures other than phyllomes? There can be, like stem wings or seed wings.
lamina (PO:0025060): A regional part of an anatomical structure that is enlarged through lateral growth.
Sometimes people refer to a part of a leaf as the lamina, even though it is not flat, like in Alium or Proteacea with needle-like leaves. We should put a comment on leaf lamina that it may not be flat.
Can't use the phrase "lateral growth" in the definition, because that refers to e.g., growth from the vascular cambium.
New proposed definition of lamina: A part of a plant structure that is thin and flat.
Should add PATO terms to comment, if possible.
proposed new term, phyllome lamina (PO:0025396): A lamina that is part of a phyllome.
current definition, leaf lamina: A lamina that is part of a leaf, usually dorsiventrally flattened and expanded.
proposed definition, leaf lamina: A phyllome lamina that is the flat part of a leaf, exclusive of the petiole or sheath, if either is present.
Comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333).
New proppsed definitin: A phyllome lamina that is the part of a leaf exclusive of the petiole or sheath, if either is present.
Comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae.
Petiole lamina (PO:0025129, A lamina that is part of a petiole) should be made is_a phyllome lamina, instead of is_a leaf lamina.
Post-poned until next week's discussion. Details moved to Items for future meetings
Upcoming meetings and Presentations 2011/2012:
January 14-18, 2012, San Diego, California
PO will be represented at the following events:
- Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data. We have 5 speakers and time at the end for a panel discussion.
PJ will give the introductory remarks at the Ontology workshop, and hopefully take part in the Panel Discussion.
For more info, see the PAG 2012 Ontology workshop wiki page.
- LC is also presenting in the Non-Seed Plant Workshop on Saturday, Jan 14th, (3:50pm-6pm) and in the Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am).
- We will also do a computer demo Monday 12:50 pm for the PO.
- The PO will also take part in an Outreach booth organized by MaizeGDB- schedule TBA
-Do we want to host the wiki page for the booth again?
Phenotype RCN meeting, 23-25 February 2012
The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.
It will be held again at NESCent (Durham, NC).
RW has a friend there she can stay with and is interested in going.
This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.
The projects of the Plant Working Group that we started in CO will be worked on during the next meeting.
Eva said that they can cover RW's plane fare from NY.
Maize Genetics Meeting, March 15-18, 2012
The maize meetings are being held in Portland, OR this year.
For more info see: Maize Genetics Meeting 2012
Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.
Deadlines: Advance meeting registration is due by January 31, 2012.
April 2-4, 2012, Washington DC
• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.
• Notification date: February 3, 2012
From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?
Annual meeting of the Society for the Preservation of Natural History Collections
Yale University, New Haven Connecticut June 11-16, 2012
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).
From PJ: If we can show progress in the FNA work or Morphobank yes we should
July 7 - 11, 2012 - Columbus, Ohio
Call for Symposia, Colloquia and Workshops:
RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.
Proposal was submitted, waiting for news.
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.
We should also consider hosting an outreach booth.
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)
• 2 months of Rotating Banner Ads in the online American Journal of Botany
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin
• A Rotating Banner Ad on the Botany 2012 abstract submission site
• A Rotating Banner Ad on the 2012 Conference Registration site.
PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.
JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX
Registration scheduled to open first week in January.
Early Bird Registration: by May 11
Advance Discounted: May 12-June 15
International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria
co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)
- Jan. 31st, 2012: Paper submission deadline
- Feb. 28th, 2012: Notification of paper acceptance
- March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
- April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
- June 30th 2012: Deadline for all camera-ready copies for the proceedings
BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.
RW will circulate a draft of a manuscript for a plant disease extension of the Infectious Disease Ontology. Must be submitted by Jan. 31, 2012.
RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts