Difference between revisions of "POC Conf. Call 12-13-11"

From Plant Ontology Wiki
Jump to navigationJump to search
 
(75 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
'''POC meeting, Webex Conference Call; Date: Tuesday Dec 13th, 2011 10am (PST)'''
+
'''POC meeting, Webex Conference Call; Date: Tuesday Dec 13th, 2011 10:30am (PST)'''
  
 
In attendance:  
 
In attendance:  
  
−
POC members:
+
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), Dennis Stevenson (NYBG)
−
 
 
−
Absent:
 
  
 +
Absent:  Chris Mungall (Lawrence Berkeley National Lab), Pankaj Jaiswal (OSU)
  
 
Collaborators: none
 
Collaborators: none
  
 +
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_11-29-11]]? ''No additions, deletions, or changes.''
  
−
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_12-6-11]]?
+
Back to [[POC Meetings Minutes]]
  
−
Back to [[POC Meetings Minutes]]
 
  
 +
=PO Glossary=
 +
Looked at the new glossary page again see: [http://dev.plantontology.org:8080/db/glossary/glossary1 Plant Anatomy Glossary]
  
 +
''Comments: Looks good, suggest having a search box, if it is possible''
  
−
=PDSO Revisions: Plant structure development stages=
+
=PSDS Revisions: Whole plant development stages=
−
==Whole plant development stages==
+
==[https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]==  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]===  
+
===GO terms===
−
====GO terms====
 
 
GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.
 
GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.
  
Line 27: Line 28:
 
'''proposed new definition for dormancy process:'''  A developmental process in which a dormant state is induced, maintained or broken.  
 
'''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, by a suspension of growth.
+
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.  
 
'''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.  
Line 34: Line 42:
 
'''proposed new definition for seed dormancy:'''  A dormancy process that has as participant a seed.
 
'''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.(''work on comment'')
+
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.
 
'''organism dormancy (new term):''' A dormancy process that has as participant a whole organism.
  
−
====PO terms====
+
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.
−
'''sporophyte dormant stage (PO:0007132):''' A sporophyte development stage during which a sporophyte participates in an organism dormancy process (GO:xxxx).
+
 
 +
''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.''
 +
 
 +
===PO terms===
 +
'''sporophyte dormant stage (PO:0007132):''' A sporophyte development stage during which a sporophyte participates in an multicellular 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.
 
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).
+
''New 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 may be preceded by the senescence of plant 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 a dormant stage when they become dessicated.
 +
 
 +
'''gametophyte dormant stage (PO:0025342):''' A gametophyte development stage during which a gametophyte participates in a organism dormancy process (GO:xxxx).
  
 
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.
 
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.
  
 +
''New 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 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, which is dormant before fertilization. (need to check on details of Ginkgo)''
 +
 +
'''Note:''' We can put the general term for dormancy process (GO:0022611) in the comment until a new term for organism dormancy is added.
 +
 +
''Definitions and comments should focus on helping users to choose the correct stage, so information on what marks the beginning or end of a stage is most useful.''
 +
 +
''Would be good to include some examples for each type, e.g., gametophyte in Gingko, resurrection plants.''
  
 
References:  
 
References:  
Line 59: Line 90:
 
Dessication tolerance in resurrection plants: DOI: 10.1080/07352680591008583. A kind of dormancy?
 
Dessication tolerance in resurrection plants: DOI: 10.1080/07352680591008583. A kind of dormancy?
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3432979&group_id=76834&atid=835555 gametophyte/sporophyte senescent stage]===
+
===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)?
 +
 
 +
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
  
−
Work on these terms is ongoing. Will present new definitions and GO proposal for senescence at a future meeting.
+
10.07-seed not dormant in barley
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3439459&group_id=76834&atid=835555 embryo stage] and [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo]===
+
10.07-seed not dormant in oat
−
====embryo stage====
+
 
 +
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.
 +
 
 +
==review of definitions for [https://sourceforge.net/tracker/?func=detail&aid=3439459&group_id=76834&atid=835555 embryo stage] and [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555 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.
 
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.
  
Line 71: Line 130:
 
'''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.
 
'''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.
+
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====
+
===plant embryo===
 
Now that we have a working term for embryo stage, we can define '''plant embryo''' in terms of the stage.
 
Now that we have a working term for embryo stage, we can define '''plant embryo''' in terms of the stage.
  
Line 84: Line 143:
 
-change from participates_in sporophyte development stage to participates_in embryo stage
 
-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.''
+
''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).''
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3439450&group_id=76834&atid=835555 zygote 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.''
 +
 
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3439450&group_id=76834&atid=835555 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.
 
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.
 
  
 +
'''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.''
 +
 +
==[http://sourceforge.net/tracker/?func=detail&aid=3432979&group_id=76834&atid=835555 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: [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008150#lineage GO:biological process] already states that this applies is "pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms", and [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0032502#lineage 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.''
  
−
=Upcoming meetings and Presentations 2011/2012:=
+
===PO senescent stage terms===
 +
''Postponed until the 12-20-11 meeting.''
 +
 
 +
=Updating PO relations=
 +
 
 +
*derives_by_manipulation:
 +
This was discussed on the [[POC_Conf._Call_10-18-11]]
 +
 
 +
*has_participant:
  
−
==Sematic web conference focused on life science==
+
This was discussed on the [[POC_Conf._Call_11-29-11]]
  
−
JP will attend the [http://www.swat4ls.org/workshops/london2011/ SWAT4LS] meeting in December. Folks such as TW from NCBO will be there.
+
''These relations are in the developers' file so they can be viewed in the dev browser. Still need icons.''
  
−
Poster presentation: "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes [http://wiki.plantontology.org:8080/images/6/62/SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf link]
+
=Other - personel=
 +
MAG will have an undergraduate working on the PO starting in the spring.
 +
 
 +
=Upcoming meetings and Presentations 2011/2012:=
  
 
==[http://www.intl-pag.org/ PAG 2012]==
 
==[http://www.intl-pag.org/ PAG 2012]==
Line 117: Line 256:
 
*LC is also presenting in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1046.html Non-Seed Plant Workshop] on Saturday, Jan 14th, (3:50pm-6pm) and in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes] workshop on Sunday, Jan. 15th, (8:00am - 10:10am).
 
*LC is also presenting in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1046.html Non-Seed Plant Workshop] on Saturday, Jan 14th, (3:50pm-6pm) and in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html 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.
+
*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
  
−
*The PO will take part in an Outreach booth organized by MaizeGDB.
+
-Do we want to host the wiki page for the booth again?
  
 
==Phenotype RCN meeting, 23-25 February 2012==
 
==Phenotype RCN meeting, 23-25 February 2012==
Line 128: Line 269:
  
 
RW has a friend there she can stay with and is interested in going.
 
RW has a friend there she can stay with and is interested in going.
 +
 +
''Any news??''
  
 
==Maize Genetics Meeting, March 15-18, 2012==
 
==Maize Genetics Meeting, March 15-18, 2012==
Line 146: Line 289:
 
April 2-4, 2012, Washington DC
 
April 2-4, 2012, Washington DC
  
−
Call for abstracts is now open:
+
• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.
−
 
 
−
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
+
See link: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf‎]]
  
−
•   '''Submission deadline December 9, 2011'''
+
• Notification date: February 3, 2012
  
−
•    Notification of acceptance February 3, 2012
+
From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?
−
 
 
−
[http://pir.georgetown.edu/biocuration2012.html/instructions.html 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.
 
  
 
==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==
 
==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==
Line 226: Line 340:
 
JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.
 
JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.
  
−
==ICBO 2012==
+
==[http://my.aspb.org/?page=Meetings_PB2012  ASPB Plant Biology 2012]==
−
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012])
 
  
−
co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)
+
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX
  
−
22-25 July 2012; Graz, Austria.
+
Registration scheduled to open first week in January.
  
−
Conference Web site: http://purl.bioontology.org/ICBO/
+
Early Bird Registration: by May 11
 +
 +
Advance Discounted: May 12-June 15
  
−
*The consensus with CM, MH and DOS was not to organize an Anatomy Ontology Workshop this year.
+
==ICBO 2012==
−
 
+
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria
−
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
+
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)
−
 
 
−
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
 
  
 +
'''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?
 
We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?
Line 264: Line 368:
 
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 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
+
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts
  
 
=Next meeting scheduled for Tuesday, Dec. 20th, 2011 at 10am PST/1pm EST=
 
=Next meeting scheduled for Tuesday, Dec. 20th, 2011 at 10am PST/1pm EST=

Latest revision as of 19:43, 8 March 2012

POC meeting, Webex Conference Call; Date: Tuesday Dec 13th, 2011 10:30am (PST)

In attendance:

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), Dennis Stevenson (NYBG)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Pankaj Jaiswal (OSU)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-29-11? No additions, deletions, or changes.

Back to POC Meetings Minutes


PO Glossary

Looked at the new glossary page again see: Plant Anatomy Glossary

Comments: Looks good, suggest having a search box, if it is possible

PSDS 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.

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.

PO terms

sporophyte dormant stage (PO:0007132): A sporophyte development stage during which a sporophyte participates in an multicellular 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.

New 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 may be preceded by the senescence of plant 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 a dormant stage when they become dessicated.

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

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.

New 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 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, which is dormant before fertilization. (need to check on details of Ginkgo)

Note: We can put the general term for dormancy process (GO:0022611) in the comment until a new term for organism dormancy is added.

Definitions and comments should focus on helping users to choose the correct stage, so information on what marks the beginning or end of a stage is most useful.

Would be good to include some examples for each type, e.g., gametophyte in Gingko, resurrection plants.

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?

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)?

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.

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.

Updating PO relations

  • derives_by_manipulation:

This was discussed on the POC_Conf._Call_10-18-11

  • has_participant:

This was discussed on the POC_Conf._Call_11-29-11

These relations are in the developers' file so they can be viewed in the dev browser. Still need icons.

Other - personel

MAG will have an undergraduate working on the PO starting in the spring.

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, Dec. 20th, 2011 at 10am PST/1pm EST

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_12-13-11&oldid=15614"