POC Conf. Call 12-20-11
POC meeting, Webex Conference Call; Date: Tuesday Dec 20th, 2011 10am (PST)
POC members: Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell University), Barry Smith (University at Buffalo, NY), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab), Pankaj Jaiswal (OSU)
Absent: Dennis Stevenson (NYBG)
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-13-11? No additions, deletions, or changes.
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
"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.
Senescence and aging in GO
RW will send link to GO trackers for senescence and dormancy process to PO internal, so others can comment on them.
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:
>multicellular organismal aging
See References/notes, below, for source of definitions.
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.
CM: General comment on structure: This depends on repetition of a common process that is repeated in child terms. Puts a lot of weight on the definition of the parent term. There are other kinds off deterioration and loss of functions that are not aging (RW: but are there other kinds of developmental processes that are deterioration and loss of functions?). Maybe aging should be a kind of grab bag for cellular aging, organ aging, and organism aging, and make more specific definitions for those. Onotology structure would be identical, but would affect definitions.
Some discussion of the difference between aging and getting older. Does aging always follow maturity?
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 after a cell has stopped dividing.
Comment: 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.
Comment from DWS outside meeting: Cells can stop dividing and be specialized, then dedifferentiate and start to divide again (totipotency). From RW: In this case, the cell has not lost its capacity to divide, so it is not going through senescence. However, it may not always be able to tell if a cell is quiescent of senescent.
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).
Synonym: multicellular organism senescence; we may want to add monocarpic senescence as a narrow synonym or as a new subtype (see notes below).
BS: We need to make note of terms like monocarpic that should be defined in other ontologies. CM suggested that it could go in PATO.
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.
Is there organ senescence in animals? Perhaps in things that metamorphosize.
PO will also need a term for anther senescence, is_a organ senescence, to correspond to the PO stage term.
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).
Because of the all-some nature of has_paricipant relation, GO would have to say leaf senescence has_participant leaf, but in every individual instance, the relation would be to vascular leaf or non-vascular leaf.
At this point, the call was temporarily interupted by Darth Vader, be we were able to resist the temptation of the dark side.
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
Rename this "fruit ripening" for clarity.
This term already has a taxon restriction on parent (for Angiospermae, presumably).
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):
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.
Even though the existing GO terms are not perfect for our needs, we will go ahead with the new definitions, and add a comment that we have reqested new definitions from GO, which we can get rid after GO updates their definitions.
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 processes like cellular senescence, organ senescence, and wear and tear.
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 processes like cellular senescence, organ senescence, and wear and tear.
Status of New Annotation Files for data release in Dec:
Last week we added two new sets of annotations:
These are available for preview on the beta browser
The Dbxrefs.txt has been updated with new stanzas for these two groups- see below.
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 four PO terms: spore, protonema, protoplast 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. Waiting for a response from DL @ the links.
Then these could be uploaded to the main database for a data release, as all the necessary terms are in the current live file.
In the future, we will also have annotations for Physco for PSDS terms.
LC has been working with collaborators at AgBase to add these on our new trichome development terms. This is a smaller set of a ~100 associations.
- seed trichome (PO:0004511)
- petal (PO:0009032)
- root (PO:0009005)
- anther (PO:0009066)
- vascular leaf (PO:0009025)
- seed trichome development stage (PO:0025369)
- seed trichome elongation stage (PO:0025371) 
- seed trichome initiation stage PO:0025371 
- seed trichome secondary wall biosynthesis stage (PO:0025372) 
- embryo stage (PO:0007631)
- endosperm development stages (PO:0007633)
- anther developmental stages (PO:0001004)
- leaf development stages (PO:0001050)
- root development stages (PO:0007520)
- petal differentiation and expansion stage (PO:0007611)
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. (eg: missing colon in reference)
Then will have to go into the next release, as most of the necessary terms are in the editor's file, unless we decide to .
Updating the Gramene Annotations
LC has been working with MM and KY-C to get the Gramene annotations updated and fixed for the data release. Also have made significant progress on updating our information and links on their site (finally!)
The Gramene files on our SVN (http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/) contain annotations to terms that have been replaced with other terms (thus now they are alt ids). When we did the release in the fall, this caused errors.
Here is the text of the email from JE @ them:
On 10/12/2011 2:37 PM, Justin Elser wrote: "This is the list of ids that amigo had problems with. They all seem to be from the file po_anatomy_gene_oryza_gramene.assoc and po_anatomy_qtl_oryza_gramene.assoc"
PO:0006318 PO:0006329 PO:0006384 PO:0006441 PO:0006442 PO:0006444 PO:0006445 PO:0006446 PO:0006449 PO:0006450 PO:0006451 PO:0006452 PO:0006455 PO:0006456 PO:0006457 PO:0006462 PO:0006463 PO:0006464 PO:0006465 PO:0006472 PO:0006497 PO:0006508
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.
- 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.
- 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 (email@example.com) link
- Meg (Margeret) Staton (firstname.lastname@example.org) Clemson University (the lead on both the hardwoods website and the Fagaceae Genomics Web
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.
Elisabeth Wheeler has been out of town. LC will follow up with Barb Lachenbruch and RW will ask Jill to follow up with John Carlson.
Tentative dates are Feb. 5-7 (Sun-Tues).
BS is available to give his presentation on Sunday morning. 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.
RW will send out travel forms to domestic invitees for them to sign and make sure they get to LC.
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.
Okay to start adding these synonyms to the ontology. Don't need group discussion, since they are just synonyms of existing terms. Will have FNA:glossary as reference. Link to Google Doc listing them is on the SF tracker for 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.
- add 364 synonyms to existing terms - Many of these are plural forms. See list of synonyms on Google Docs
- 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:
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.
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
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