POC Conf. Call 1-3-12
POC meeting, Webex Conference Call; Date: Tuesday Jan 3rd, 2012 10am (PST)
In attendance:
POC members:
Absent:
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-20-11?
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PSDS Revisions: Whole plant development stages
Review of PO terms for gametophyte/sporophyte dormant stage
These were accepted at the POC Conf. Call 12-13-11, but we are waiting for the revisions from GO to complete them.
sporophyte dormant stage (PO:0007132): A sporophyte development stage during which a sporophyte participates in an multicellular organism dormancy process (GO:xxxx).
comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy of a plant may be preceded by the senescence of its parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Resurrection plants are in andormant stage when they become dessicated. Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.
gametophyte dormant stage (PO:0025342): A gametophyte development stage during which a gametophyte participates in a organism dormancy process (GO:xxxx). link to dev
Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are a moss that has undergone dessication (a resurrection plant) or the female gametophyte of Ginkgo biloba, which is dormant before fertilization. Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.
Note: need to check on details of Ginkgo, We can put the general term for dormancy process (GO:0022611) in the comment until a new term for organism dormancy is added.
Why are these def'ns differnt?
Resolve the issue about the existing synonyms of sporophyte dormant stage
Are these actually appropriate as synonyms for sporophyte dormant stage (PO:0007132, was dormancy, which was a subtype of whole plant growth stage)?
10.05-seed dormant in barley
10.05-seed dormant in oat
10.05-seed dormant in Triticeae
10.05-seed dormant in wheat
10.06-viable seed germination in barley
10.06-viable seed germination in oat
10.06-viable seed germination in Triticeae
10.06-viable seed germination in wheat
10.07-seed not dormant in barley
10.07-seed not dormant in oat
10.07-seed not dormant in Triticeae
10.07-seed not dormant in wheat
They all come from GRO.
Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.
Updates to GO terms for Dormancy Process terms:
Link to discussion on GO SF Tracker
Most of our suggestions were accepted, except that they did not see the need for "multicellular organism dormancy process"
Agreed upon def'ns and comments:
dormancy process (GO:0022611): 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.
comment: In plants and animals, dormancy may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. In plants, dormancy may involve the formation of dormant buds, and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system [in] herbaceous perennials. The end of dormancy [or "exit from dormancy", to parallel the symbiont terms] in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium.
Dbxrefs: GOC:PO_curators [to be added to the curators' initials file]
Paola had a question about the PO_ref: "how should I enter this? I haven't found any other PO_REF in GO or in the GO>references file"
They are willing to add multicellular organism dormancy process as a narrow synonym, if needed.
The process in which a dormant state is induced, maintained or broken. Dormancy is characterized by a suspension of physiological activity. (They also have a term for seed dormancy.)
proposed new definition for dormancy process: A developmental process in which a dormant state is induced, maintained or broken.
Comment: A dormant state is characterized by a suspension of most physiological activity, and in plants, a suspension of growth.
Should say dormancy, instead of dormant state.
New comment: Dormancy is a suspension of most physiological activity and growth that can be reactivated.
Will check with animal people at GO to see if comment applies only to plants and if there are other comments needed for animals.
Dormancy is defined in the comment; is different from dormancy process; sometimes called a dormant state. Need to check with GO if they want to define dormancy as a separate term, of just keep it in the definition of dormancy process, as we have here.
seed dormancy (GO:0010162): The process in which a dormant state is induced, maintained and broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated.
proposed new definition for seed dormancy: A dormancy process that has as participant a seed.
comment: Seed dormancy is characterized by a suspension of physiological activity that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.
should be called seed dormancy process.
Should say dormancy, instead of dormant state.
New comment: Seed dormancy is a suspension of physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.
organism dormancy (new term): A dormancy process that has as participant a whole organism.
Comment: A dormant state in an organism is characterized by a suspension of most physiological activity. In plants, organism dormancy is marked by a suspension of growth and generally involves the formation of dormant buds. These may be above ground (in woody plants), at ground level (in herbaceous plants), or underground (in plants with tubers, bulbs, corms, or perennating rhizomes). Organism dormancy in plants may be preceded by the senescence of other plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. The end of organism dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium. Organism dormancy in plants is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, although environmental stimuli may not be necessary for the onset of dormancy.
should be called "multicellular organism dormancy process
New comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. In plants, multicellular organism dormancy may involve the formation of dormant buds and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. The end of organism dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium. May be a response to environmental conditions such as seasonality or extreme heat, drought, or cold.
We may also want to request GO terms like bud dormancy process and spore dormancy process.
Existing synonyms
Are these actually appropriate as synonyms for sporophyte dormant stage (PO:0007132, was dormancy), which was a subtype of whole plant growth stage?
Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.
10.05-seed dormant in barley
10.05-seed dormant in oat
10.05-seed dormant in Triticeae
10.05-seed dormant in wheat
10.06-viable seed germination in barley
10.06-viable seed germination in oat
10.06-viable seed germination in Triticeae
10.06-viable seed germination in wheat
10.07-seed not dormant in barley
10.07-seed not dormant in oat
10.07-seed not dormant in Triticeae
10.07-seed not dormant in wheat
They all come from GRO.
review of definitions for embryo stage and plant embryo
embryo stage
We already had a term PO:0007631, embryo development stages, is_a seed development stage. This term was renamed embryo stage and made is_a sporophyte vegetative stage.
proposed def.:
embryo stage (PO:0007631): A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.
Comment: An embryo stage generally starts after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it begins after the division of a single cell that is not a zygote. The end of an embryo stage varies among taxa.
plant embryo
Now that we have a working term for embryo stage, we can define plant embryo in terms of the stage.
existing def. plant embryo (PO:0009009): A whole plant in the early part of a sporophytic phase after the first cell division.
proposed def. plant embryo (PO:0009009): A whole plant that participates in the embryo stage (PO:0025369).
comment (basically the same as existing comment): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.
-change from participates_in sporophyte development stage to participates_in embryo stage
We had a discussion a few weeks ago whether is better to define stages in terms of structures or structures in terms of stages. We agreed that in general, it is better to define stages in terms of structures. This works well for terms like trichome development stage which have a trichome as a primary participant. However, in the case of embryo stage (and other whole plant growth stages), the primary participant is a whole plant that is undergoing certain processes, and the stage is a more fundamental term that defines what those processes are. It would be circular to define the embryo stage as a stage that has as participant an embryo, then define the embryo as a whole plant during a certain time. Better to define the embryo stage as a stage that has as participant a whole plant that is undergoing certain processes (in this case, everything between first cell division and the other events that mark the end of embryo stage).
We agreed that in the case of embryo and zygote (and probably other whole plant stages), it is better to define the stage first, then define the whole plant as participating in that stage.
zygote stage
We already have a term "A zygotic stage" (PO:0001097), is_a embryo stage. This was renamed zygote stage and made is_a sporophyte development stage.
current def. zygote stage (PO:0001097): One cell stage that results from fertilization.
proposed def. zygote stage: A sporophyte development stage that occurs during the interval between syngamy and the first cell division.
Comment: Succeeds syngamy and precedes the embyro stage.
As with the embryo stage/embryo, RW thinks it would be better to define the stage, then define a zygote as a whole plant that participates the zygote stage, rather than the other way around.
We had some discussion of whether it was better to name this plant zygote or zygote. Zygotes in plants are the same thing as zygotes in animals, so why call them something different? Reason to name it plant zygote is to disambiguate it from terms that are named zygote in other ontologies.
RW after meeting: Embryo stage and zygote stage be probably be plant embryo stage and plant zygote stage too.
gametophyte/sporophyte senescent stage
Senescence and aging in GO
PO has the following terms: sporophyte senescent stage (PO:0007017), gametophyte senescent stage (PO:0025343), H anther senescence (PO:0001036), and 4 leaf senescence stage (PO:0001054), plus 6 ripening (PO:0007010). Rather than writing out the definition senescence in every term, we would like to be able to refer to a GO biological process term.
Go had the general term:
senescence GO:0010149: OBSOLETE. A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed.
but, as their comment says: "This term was made obsolete because its name is ambiguous and it is covered by the two more specific terms: 'organ senescence ; GO:0010260' and 'cell aging ; GO:0007569'."
The POC needs a term for whole organism senescence, and we feel that the existing definitions of aging is not appropriate for plants, or even for GO:cell aging and GO:cellular senescence.
Revisions to existing GO terms
GO tree view:
aging
>cell aging
>>cellular senescence
>multicellular organismal aging
>organ senescence
>>leaf senescence
See References/notes, below, for source of definitions.
aging (GO:0007568)
current definition: The inherent decline over time, from the optimal fertility and viability of early maturity, that may precede death and may be preceded by other indications, such as sterility.
proposed definition: A developmental process that is a deterioration and loss of function over time.
Comment: Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death (GO:0016265) and may succeed developmental maturation (GO:0021700). May be preceded by other indications, such as sterility in animals. (RW: Isn't sterility part of aging? GO has a term for aging-dependend sterility, synonym of chromatin silencing at silent mating-type cassette.)
Note: GO:biological process already states that this applies is "pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms", and GO:developmental process states that it is a "progression of an integrated living unit... over time from an initial condition to a later condition".
We only had time for a quick discussion of senescence. Will go over it more next week.
We agreed that comment about sterility should probably come out.
cell aging (GO:0007569)
Postponed until the 12-20-11 meeting.
cellular senescence (GO:0090398)
Postponed until the 12-20-11 meeting.
multicellular organismal aging (GO:0010259):
Postponed until the 12-20-11 meeting.
organ senescence (GO:0010260)
Postponed until the 12-20-11 meeting.
leaf senescence (GO:0010150)
Postponed until the 12-20-11 meeting.
ripening (GO:0009835)
Postponed until the 12-20-11 meeting.
PO senescent stage terms
Postponed until the 12-20-11 meeting.
Mistake in the CL/PO coordination
CM raised the issue below: spot the inconsistency:
/ PO:0025131 ! plant anatomical entity is_a PO:0009011 ! plant structure is_a PO:0000004 ! in vitro plant structure is_a PO:0000005 ! cultured plant cell *** is_a PO:0009002 ! plant cell [xref: GO:0005623] is_a PO:0000005 ! cultured plant cell ***
/ CL:0000000 ! cell [xref: FMA:68646] [xref: GO:0005623 "cell"] [xref: KUPO:0000002] [xref: WBbt:0004017] [xref: XAO:0003012]
is_a CL:0000003 ! cell in vivo
is_a CL:0000004 ! cell by organism
is_a CL:0000255 ! eukaryotic cell
is_a CL:0000610 ! plant cell *** [xref: PO:0009002]
if the xrefs are equivalent and in vivo is (presumably) disjoint from in vitro, then plant cell is unsatisfiable.
Link to CL:0000610 plant cell on CL.
They should be using our definition of plant cell as well: "A cell which is a plant structure. [source: GO:0005623, POC:Curators]"
- SOLUTION 1:
With it's current placement, CL:0000610 must really be equivalent to a PO:0009002 that is in-vivo - this doesn't correspond to a named class in PO. We could rename CL:0000610 to "in vivo plant cell" and have a bridging axioms that says this is a subclass of PO:0009002
- SOLUTION 2:
obsolete CL:0000610, with a consider link (not replaced by) to PO:0009002
add an xref to PO:0009002 to CL:0000000 (just as we have for the other taxon-centric AOs).
Remove: 'treat-xrefs-as-equivalent: PO'
Add: 'treat-xref-as-genus-differentia: PO part_of NCBITaxon:nnnnn ! viridiplantae'
- SOLUTION 3:
move CL:0000610 ! plant cell to be a direct child of CL:0000000 ! cell
we would probably want to move CL:0000255 ! eukaryotic cell at the same time
From CM:
"I don't like solution 1. Neutral w.r.t. 2 and 3."
"Note that whatever the solution, we need a consistent cross-ontology naming strategy. I don't think it's necessary to prefix every in-vivo class with "in-vivo". But we need to be consistent. At the moment "eukaryotic cell" means "eukaryotic in vivo cell", whereas "plant cell" (in PO) means "plant cell, in vivo or in-vitro".
"How about this: if we have a taxonomic qualification, it doesn't imply in-vivo. If we have a named cell type (e.g. "neuron") or some other qualification, it implies in-vivo?"
CL should us the PO definition of plant cell. We should put it on the CL plant tracker.
The problem is if someone tries to import PO into CL, because of the conflict with in vivo cell. This should be address in the document from MH proposing changes to CL.
PJ raised an issue with experimentally modified cell -- you can experimentally modify a cell then stick it back in an organism, so it is in vivo.
Not everyone received Melissa's document. RW will circulate to PO internal, and we will review it before we discuss this more.
Wood Anatomy Ontology Meeting
Please see the Wood_Anatomy and the Wood anatomy ontology meeting, 2012 at NYBG, agenda wiki pages for more information.
Tentative dates are Feb. 5th-7th, 2012 (Sun-Tues)
Update and status:
Invitation letter went out 12/15/11 from DWS, to experts (below) signed by all three Co-PIs, along with Jill Wegrzyn of the TreeGenes Database at UCDavis (Bioinformatics) and Andrew Groover Geneticist, USDA Forest Service, Institute of Forest Genetics, Davis CA. Deadline for their response was Dec 31st 2011.
- Frederic Lens: Netherlands Centre for Biodiversity Naturalis
- Barb Lachenbruch link
- Elisabeth Wheeler (paleobotanist and wood anatomist at NC State
- Rachel Spicer Connecticut College
- John Carlson (jec16@psu.edu) link
- Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the Fagaceae Genomics Web
So far, Fredich Lens, Meg Staton, Barb Lachenbruch and Rachel Spicer have responded positively, and RW has followed up with them. John Carlson has declined to attend as he is having surgery at the end of January.
Still waiting to hear from Elisabeth Wheeler, who has been out of town. Maybe Ale could follow up with her?
Travel forms have been sent to all to confirmed domestic invitees and LC is collecting them. So far we have received them from Jill and Andrew.
The paperwork for FL has been submitted to the dept and is in progress.
BS is available to give his presentation on Sunday morning (see: Wood anatomy ontology meeting, 2012 at NYBG, agenda). He suggested that this presentation may be of interest to others in the NYC area. He will advertise it to a wider audience, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.
Upcoming meetings and Presentations 2011/2012:
PAG 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.
Any news??
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.
5th International Biocuration Conference
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.
See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf
• Notification date: February 3, 2012
From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?
SPNHC 2012
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
Botany 2012
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.
exhibitor's booth
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.
Annotation wiki
JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.
ASPB Plant Biology 2012
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
ICBO 2012
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)
Relevant dates
- 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
We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?
Possible topics: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?
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.
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts
