POC Conf. Call 12-20-11

From Plant Ontology Wiki
Jump to navigationJump to search

POC meeting, Webex Conference Call; Date: Tuesday Dec 20th, 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_12-13-11?

Back to POC Meetings Minutes

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?"

PSDS Revisions

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).

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".

At least week's call, we agreed that comment about sterility should probably come out. GO has a term for aging-dependend sterility, synonym of chromatin silencing at silent mating-type cassette.

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). Cell aging includes 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).

Comment: Cellular senescence may be 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.

Go has terms for quiescence (GO:0070314 and GO:0070317) and cell cycle arrest (GO:0007050). The definitions of cell cycle arrest is quite general, and could include cellular senescence. We need to make GO aware of this.

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 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

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."

PO senescent stage 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:0010259).

comment: The sporophyte senescent stage is often preceded by the sporophyte reproductive stage, and it ends with death of the sporophyte, either as a result of senescence or some other cause. The sporophyte senescent stage always succeeds the sporophyte reproductive stage in monocarpic plants. This stage is distinct from sporophyte dormant stage (PO:0007132), in which many organs senesce, but some parts of the plant remain alive. Multicellular organism senescence (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 it is more inclusive.

Suggest adding to comment of sporophyte reproductive stage: The sporophyte senescent stage always succeeds the sporophyte reproductive stage in monocarpic plants.

gametophyte senescent stage (PO:0025343): A gametophyte development stage during which a gametophyte participates in multicellular organism senescence (GO:0010259).

comment: The gametophyte senescent stage is often preceded by the gametophyte reproductive stage, and it ends with death of the gametophyte, either as a result of senescence or some other cause. This stage is distinct from gametophyte dormant stage (PO:0007132), in which many organs senesce, but some parts of the plant remain alive. Multicellular organism senescence/aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms senescence/aging includes processes like cellular senescence and organ senescence, but it is more inclusive.

Status of New Annotation Files for data release in Dec:

Last week we added two new sets of annotations:

Physcomitrella Annotations

LC has been working extensively with DL and SR to get the Physcomitrella annotations added.

Last week, before JE left, we loaded their association file with ~224,652 annotations on three PO terms: spore, protonema and gametophore

These are available for preview on the beta browser


Outstanding issues: we are still sorting out a few problems with linking and displaying the new annotations. Hopefully these can be resolved when JE returns in a week.

Cotton (Gossypium)

LC has been working with collaborators at AgBase to add these on our new trichome development terms

  • seed trichome (PO:0004511)
  • petal (PO:0009032)
  • root (PO:0009005)
  • anther (PO:0009066)
  • leaf (PO:0025034)- should be vascular leaf (PO:0009025)


Example link for Dbxref:

http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=3633&database=UniProtKB/TrEMBL&uid=Q8VWP8_GOSHI&gb_acc=Q8VWP8

Updating the Gramene Annotations

During the last release cycle, LC worked with the Gramene collaborators to get their files updated. They were also going through a release as well. Have not received any new annotations, even though they said they should be coming from Gramene in the next 1-2 weeks


Updates?

Others

Strawberry

Potato Annotations

LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.

From Dr. Richard Finker (Wageningen, The Netherlands):

"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."

This will go in the next release, do they have expression data- RNA Seq?

Status of new DbxRefs:

  • Need links for Physco (Cosmoss page), Gossypium and strawberry

Annotation Guidelines

Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators


Trichome development stages

Need to address outstanding issues and wrap this up.


References:

Arabidopsis leaf trichomes: http://www.nature.com/nrm/journal/v5/n6/full/nrm1404.html (consistent with existing definitions of leaf trichome stage)

Alvin F. Reeves II. (1977) Tomato trichomes and mutation affacting their development. Amer. J. Bot. 64(2): 186-189. http://www.jstor.org/stable/2442106

Wood Anatomy and Forest Trees

Wood anatomy Ontology Development: PO will work with a group of scientists to develop ontology terms to describe wood anatomy and development.

Please see the Wood_Anatomy and the Wood anatomy ontology meeting, 2012 at NYBG, agenda wiki pages for more information.

Three Goals:

  • Develop terms for wood structure in the PAO
  • Develop terms and ontology structure for wood formation,the time course of development
  • Terms to describe wood quality and phenotype, traits- go into TO?

Update and status: Plan is hold the meeting at the NYBG during the first 2 weeks of Feb.

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: Dec 31st 2011

So far, Fredich Lens, Meg Staton, and Rachel Spicer have responded positively, and RW has followed up with them. Still waiting to hear from other invitees. If necessary, we can follow up with them.

We should ask Jill Wegrzyn to follow up with John Carlson. MAG can follow up with Elizabeth Wheeler, and LC with Barb Lachenbruch.

Would be nice to set tentative dates before leaving for the holiday.

Vascular tissue terms

RW, MAG, and DWS have been working on the existing PO terms for vascular tissue and cell types. See Items_for_future_meetings#Vascular_tissues_and_cell_types.

These terms will need to be fixed before the Wood Ontology meeting in February. Proposed definitions and structures are almost ready, so we can start working on them during the POC meetings in January.

FNA

See previous minutes for details of the mappings (POC_Conf._Call_11-1-11#FNA)

We had a conference call with FNA on Nov 18th, 2011.

Next steps:

  • add 364 synonyms to existing terms - many of these are plural forms
  • fix several errors that were discovered while doing the mappings (minor things, like definitions of ariloid versus strophiole).
  • add 143 unique new terms, plus their synonyms

-FNA provides definitions, so this will be relatively easy

  • work with FNA to create an official mapping file

-FNA will provide unique IDs for their terms. This is needed especially for FNA terms that have the same name but different meaning.

-FNA terms that map to >1 PO term should have multiple lines in the mapping file. Whenever the FNA term matches a general term plus its subtypes, should only map to the general term. They can use reasoner to infer mapping to more specific subtypes. We can create some new general terms like "organ apex".

-Some of their terms that are just too general for PO. For these, when HC does the next round of text mining, she will pull out more meaning from context, e.g., use the term leaf base instead of just base.

  • begin work on phenotype/character terms, including the 101 from this list plus all of the FNA character terms

Upcoming meetings and Presentations 2011/2012:

PAG 2012

January 14-18, 2012, San Diego, California

PO will be represented at the following events:

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.

  • We will also do a computer demo Monday pm (tentatively) for the PO, perhaps JP would like to do this.
  • 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

Next meeting scheduled for Tuesday, Jan. 3rd, 2012 at 10am PST/1pm EST

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_12-20-11&oldid=13919"