POC Conf. Call 12-13-11

POC meeting, Webex Conference Call; Date: Tuesday Dec 13th, 2011 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_12-6-11?

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PDSO Revisions: Whole plant development stages

gametophyte/sporophyte dormant stage

GO terms

GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.

dormancy process (GO:0022611): 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.

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.

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.

PO terms

sporophyte dormant stage (PO:0007132): A sporophyte development stage during which a sporophyte participates in an organism dormancy process (GO:xxxx).

comment: 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, although a sporophyte dormant stage 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). Dormancy 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 dormancy is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, even though environmental stimuli may not be necessary for the onset of dormancy.

gametophyte dormant stage (PO:0025342): A gametophyte development stage during which a gametophyte participates in a dormancy process (GO:0022611).

comment: This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, even though environmental stimuli may not be necessary for the onset of dormancy.

References:

Vegis; Dormancy in Higher Plants ARPP 1964

paper on sporophyte dormancy in a bryophyte

Dormancy of gemmae in a liverwort: DOI: 10.1034/j.1600-0706.2001.940314.x. In this case, the gemma is a whole plant.

Dessication tolerance in resurrection plants: DOI: 10.1080/07352680591008583. A kind of dormancy?

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: The 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 the 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 in terms of stages. In general, it is better to define stages in terms of structures. This works well for terms like trichome development stage. However, in the case of embryo stage, the structure is really a whole plant that is undergoing certain processes, and the stage is a more fundamental term.

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.

proposed def. zygote stage (PO:0001097):A sporophyte development stage that occurs during the interval between syngamy and the first cell division.

As with the embryo stage/embry, 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.

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".

cell aging (GO:0007569)

current definition: Progression of the cell from its inception to the end of its lifespan. Source: GOC:jh, PMID:12044934

proposed definition: An aging process that has as participant a cell.

Comment: Occurs after a cell has stopped dividing. Precedes cell death (GO:0008219) and may succeed cell maturation (GO:0048469). Aging includes processes like cellular senescence, but is more inclusive.

cellular senescence (GO:0090398)

current definition: A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest. Source: GOC:BHF

proposed definition: A cellular aging process in which a cell permanently loses the ability to participate in the cell cycle (GO:0007049). (Go has the term cell cycle arrest GO:0007050, but the definition sounds more like a temporary suspension of the cell cycle.)

Comment: Cellular senescence is accompanied by other cell aging processes, such as wear and tear or the dismantling of cellular components. May be a response to cellular stress or other stimuli, whereby normal cells lose the ability to divide through irreversible cell cycle arrest (post-mitotic senescence), or it may be intrinsic, in cells that have a finite capacity for division (mitotic senescence).

We may want to make two new subtypes, mitotic cellular senescence and post-mitotic cellular senescence.

multicellular organismal aging (GO:0010259):

current definition: The inherent decline of a multicellular organism 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. Source: GOC:dph, GOC:isa_complete, GOC:mtg_sensu, GOC:sm

proposed definition: An aging process that has as participant a whole multicellular organism.

Comment: Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism 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.)

Synonym: multicellular organism senescence; we may want to add monocarpic senescence as a narrow synonym or as a new subtype (see notes below).

organ senescence (GO:0010260)

current definition: The process that occurs in an organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism. An example of this process is found in Arabidopsis thaliana. Source: GOC:mtg_sensu, GOC:sm

proposed definition: An aging process that has as participant an organ.

Comment: May succeed organ maturation (GO:0048799) and precede the death of the organ. Includes processes such as cellular senescence (GO:0090398) and an overall decline in metabolism (GO:0008152). Occurs in plant organs such as leaves or petals.

leaf senescence (GO:0010150)

current definition: The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. Source: ISBN:0387987819

proposed definition: An organ senescence that has as participant a leaf.

Comment: Has as participant a leaf (PO:0025034), or, more specifically, a vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075). May succeed maturation and precede death of the leaf. Includes processes such as cellular senescence (GO:0090398) and an overall decline in metabolism (GO:0008152).

ripening (GO:0009835)

GO has the term ripening: The series of events causing changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) to make it more attractive to animals and/or aid in seed dispersal.

Ripening is_a anatomical structure maturation, but it should probably be an aging, with the synonym fruit senescence.

proposed definition: An aging process that has as participant a fruit.

comment: Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.

synonym: fruit senescence

References/notes

Google definitions:

se·nes·cence, Noun:

  1. The condition or process of deterioration with age.
  2. Loss of a cell's power of division and growth.

de·gen·er·a·tion, Noun:

  1. The state or process of being or becoming degenerate; decline or deterioration.
  2. Deterioration and loss of function in the cells of a tissue or organ.

wordnetweb.princeton.edu/perl/webwn:

viability:

(of living things) capable of normal growth and development. (note that this would include 
senescence, since it is a "normal" developmental process)

Nooden and Leopold, 1988, Senescence and Aging in Plants:

Senescence and aging are both degenerative processes. Aging is passive and senescence is active.

Aging: wear and tear

Senescence: internal dismantling of cells, tissues, and organs

Gan, 2010, in Senescence Processes in Plants (Annual Plant Reviews):

ISBN:9781405139847

When cells lose the ability to divide further (either intrinsically or through stress), they begin to age and degenerate. This process is called "cellular aging", "postmitotic aging", or "postmitotic senescence". In plants, postmitotic senescence occurs in leaves/flowers/fruits and involves active but slow degenerative processes, or may be a hypersensitive response, involving an active and very quick degenerative process.

Two types of senescence (for cells or organs):

mitotic senescence: When cells that could divide a finite number of time stop dividing, e.g., arrest of apical meristem or arrest of cell divisions early in fruit development. Also called proliferative senescence. Similar to replicative senescence in yeast and animals.

post-mitotic senescence: Occurs in (cells in) organs like leaves and petals that, once formed, rarely undergo cell division, although the cells retain the ability to divide. Usually involves predominantly somatic tissue, and is similar to cellular senescence in Drosophila and C. elegans

Organism aging or organism senescence: "At the organismal level, when an organism's ability to respond to stress declines, its homeostasis becomes increasingly imbalnaced, and its risk of disease increase with age, which lead to the ultimate death of the whole organism. Although cellular senescence may contribute to organismal senescence, the latter is much more inclusive."

Monocarpic senescence: senescence associated with a monocarpic life history - a single (sporophytic) reproductive event in the life cycle. Includes three coordinated processes:

1. senescence of organs and tissues such as leaves (post-mitotic senescence)

2. arrest of the SAM (mitotic or proliferative senescence)

3. permanent suppression of axillary buds

PO terms

See initial discussion at Saturday_Sept_10th,_2011#Task_4._Work_existing_upper-_to_mid-level_terms_into_the_hierarchy_determined_in_task_3., where we decided that even though a plant may die from other causes before the end of normal senescence, the senescent stage of a whole plant ends with death.

sporophyte senescent stage (PO:0007017): A sporophyte development stage during which a sporophyte participates in multicellular organism senescence (GO:xxxx).

comment:

gametophyte senescent stage (PO:0025343): A gametophyte development stage during which a gametophyte participates in multicellular organism senescence (GO:xxxx).

comment:

Upcoming meetings and Presentations 2011/2012:

Sematic web conference focused on life science

JP will attend the SWAT4LS meeting in December. Folks such as TW from NCBO will be there.

Poster presentation: "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes link

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).

• LC will also do a computer demo for the PO, unless one of the Justins is there and wants to do it.

• The PO will take part in an Outreach booth organized by MaizeGDB.

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.

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

Call for abstracts is now open:

There are three submission categories for abstracts:

1. Talk or Poster (with consideration for oral presentation) (LC would prefer a talk)

2. Poster only

3. Workshop only

• Submission deadline December 9, 2011

• Notification of acceptance February 3, 2012

Instructions

There are seven topic sessions from which submitters are invited to select:

1. Ontologies, standards and best practices, including gold standard datasets.

2. Protein annotation; sequences, structures and pathways.

3. Community annotation and Wikis.

4. Genomics and metagenomics data curation.

5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.

6. Literature collection, text mining and curation.

7. Tools to assist curation, including automated pipelines.

PJ planning to attend and will be running a biocuration workshop, LC and RW can go, DWS will be away,

'From 9-27-11: PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide.

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.

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012)

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

22-25 July 2012; Graz, Austria.

Conference Web site: http://purl.bioontology.org/ICBO/

• The consensus with CM, MH and DOS was not to organize an Anatomy Ontology Workshop this year.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts.

Could also consider organizing a phenotype ontology workshop.

Relevant dates

31 December 2011: Workshop and tutorial proposal submission deadline

25 January 2012: Notification of acceptance of workshops and tutorials

31 January 2012: Paper submission deadline

28 February 2012: Notification of paper acceptance

15 March 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline

15 April 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance

30 June 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.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX