Difference between revisions of "POC Conf. Call 1-3-12"

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In attendance:
 
In attendance:
  
−
POC members:
+
POC members: ''Laurel Cooper (OSU),  Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab)'',
−
 
 
−
Absent:
 
  
 +
Absent: ''Marie Alejandra Gandolfo (Cornell University), Pankaj Jaiswal (OSU)
 +
''
  
 
Collaborators: none
 
Collaborators: none
  
  
−
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-20-11?
+
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-20-11? ''No additions, deletions, or changes.''
  
 
Back to [[POC Meetings Minutes]]
 
Back to [[POC Meetings Minutes]]
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including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leaching of inhibitors.
 
including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leaching of inhibitors.
  
−
comment:?
+
''RW: This should say "A dormancy process..." instead of "A developmental process...". I suggested this on GO SF tracker.''
  
 
related synonym: seed dormancy
 
related synonym: seed dormancy
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Comment: Bud dormancy may precede dormancy of the whole plant.
 
Comment: Bud dormancy may precede dormancy of the whole plant.
  
 +
''RW: This should say "A dormancy process..." instead of "A developmental process...". I suggested this on GO SF tracker.''
  
 
Paola: To make it clear that this term refers to plant buds only, and to avoid confusion with other buds i.e. those resulting from asexual reproduction, I'd add a taxon constraint. Plant experts, please advise if this should be to Viridiplantae, Embryophyta or Spermatophyta.
 
Paola: To make it clear that this term refers to plant buds only, and to avoid confusion with other buds i.e. those resulting from asexual reproduction, I'd add a taxon constraint. Plant experts, please advise if this should be to Viridiplantae, Embryophyta or Spermatophyta.
  
−
From RW: I think the taxon restriction should be for Embryophyta, but I will check into whether or not the term bud is used for green algae.  
+
From RW: I think the taxon restriction should be for Embryophyta, but I will check into '''whether or not the term bud is used for green algae'''.  
 +
 
 +
''Ken Karoll of NYBG walked into the meeting for a minute and confirmed that the term budding is used to describe a particular type of cell division that leads to branches in green algae, so the taxon restriction should go on Viridiplantae.''
  
 
RW noted: "You could add an xref: bud dormancy process (GO:0010162 has_participant bud (PO:0000055)."
 
RW noted: "You could add an xref: bud dormancy process (GO:0010162 has_participant bud (PO:0000055)."
Line 65: Line 68:
  
 
(Paola: BTW, to do too:  GO:0042751 estivation, add exact synonym: aestivation)
 
(Paola: BTW, to do too:  GO:0042751 estivation, add exact synonym: aestivation)
 +
 +
''BS: Should we also request GO terms for process that induce, maintain, or release dormancy. The underlying mechanisms for each are so different. We could add a comment that people who need these processes should request them on the GO tracker, or maybe it should go on the GO definition.''
 +
 +
''We were concerned that the range of process in these terms is so broad. Do our users need more specific terms? So far no one has requested them. We should probably request them in terms.''
 +
 +
''RW will follow up on GO request for spore dormancy -- someone else already created a tracker for it.''
  
 
===Review of PO terms for [https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]===
 
===Review of PO terms for [https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]===
  
−
These were accepted at the [[POC Conf. Call 12-13-11]], but we are waiting for the revisions from GO to complete them. See below:
+
These were accepted at the [[POC Conf. Call 12-13-11]], but will need to be revised based upon the revisions of the GO terms to complete them. See below:
−
 
 
  
 
'''sporophyte dormant stage (PO:0007132):''' A sporophyte development stage during which a sporophyte participates in an '''multicellular organism dormancy process (GO:xxxx)'''.   
 
'''sporophyte dormant stage (PO:0007132):''' A sporophyte development stage during which a sporophyte participates in an '''multicellular organism dormancy process (GO:xxxx)'''.   
Line 75: Line 83:
 
[http://dev.plantontology.org:8080/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0007132&session_id=6522b1311285460 link to dev]
 
[http://dev.plantontology.org:8080/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0007132&session_id=6522b1311285460 link to dev]
  
−
comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy of a plant may be preceded by the senescence of its parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Resurrection plants are in andormant stage when they become dessicated. Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.
+
Revised def'n: '''sporophyte dormant stage (PO:0007132):''' A sporophyte development stage during which a sporophyte participates in an dormancy process.  [source:GO:0022611]
 +
 
 +
Revised comment: Dormancy process (GO:0022611)is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy of a plant may be preceded by the senescence of its parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Resurrection plants are in '''andormant''' stage when they become dessicated.  
 +
 
 +
take off: 'Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.'
  
 
'''gametophyte dormant stage (PO:0025342):''' A gametophyte development stage during which a gametophyte participates in a '''organism dormancy process (GO:xxxx)'''.  
 
'''gametophyte dormant stage (PO:0025342):''' A gametophyte development stage during which a gametophyte participates in a '''organism dormancy process (GO:xxxx)'''.  
 
[http://dev.plantontology.org:8080/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0025342&session_id=6522b1311285460 link to dev]
 
[http://dev.plantontology.org:8080/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0025342&session_id=6522b1311285460 link to dev]
  
−
Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are a moss that has undergone dessication (a resurrection plant) or the female gametophyte of Ginkgo biloba, which is dormant before fertilization. Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.
+
Revised def'n: '''gametophyte dormant stage (PO:0025342):''' A gametophyte development stage during which a gametophyte participates in a dormancy process. [source:GO:0022611]
 +
 
 +
Revised comment: Dormancy process (GO:0022611) is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are a moss that has undergone dessication (a resurrection plant) or the female gametophyte of Ginkgo biloba, which is dormant before fertilization.  
 +
 
 +
remove:  Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.
  
  
−
'''Note:''' Need to check on details of Ginkgo,  
+
''RW: Comments should refer to GO definition of dormancy process. Note that dormancy, not a dormancy process, is the suspension of growth and activity.''
−
We can now use the revised general term for dormancy process (GO:0022611).
 
  
−
These def'ns will need to be revised now.
+
''New proposed comments:''
 +
 
 +
sporophyte dormant stage (PO:0007132), comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy of a plant may be preceded by the senescence of its parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte
 +
is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Resurrection plants are in a dormant stage when they become dessicated.
 +
 
 +
gametophyte dormant stage (PO:0025342), comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.  This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are a moss that has undergone dessication (a resurrection plant) or the female gametophyte of Ginkgo biloba, which is dormant before fertilization.
 +
 
 +
''We should add specific examples (species names) of what are resurrection plants. Examples for mosses: Andreas (look up), for sporophyte: Selaginella lepidophylla, Craterostigma plantagineum. Also, Polytrichum have annual growth marks, because they are dormant during the winter and aquatic ferns with sporocarps, where gametophytes are dormant. We can provide a number of examples illustrating not only the taxonomic diversity but the diversity of mechanisms.''
 +
 
 +
''RW, after meeting: Polytrichum commune is a moss that is dessicated-dormant (PMCID: PMC343055). The boreal moss Polytrichum alpestre has shoot systems with annual growth segments due to a period of dormancy during the winter (JSTOR:3242212). Spores are also in the gametophyte stage (according to our definition), so spore dormancy is a type of gametophyte dormancy. See SF tracker for new comments.''
  
 
===Resolving the issue about the existing synonyms of sporophyte dormant stage===
 
===Resolving the issue about the existing synonyms of sporophyte dormant stage===
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10.07-seed not dormant in wheat
 
10.07-seed not dormant in wheat
  
−
They all come from GRO.
+
They all come from [http://www.gramene.org/db/ontology/search?id=GRO:0007199 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.
 
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.
  
 +
''Presumably, these synonyms are here in case anyone is still using the old GRO and searching for them. However, there was general agreement that these terms are extraneous. We thought it would be best to get rid of them, and either create subsets for the different species (which we may already have) and/or add comments about the different dormant stages in the different species.'
 +
 +
''We are going to remove these synonyms from dormant stages. Will probably want to remove them from the other development stage terms as well.''
 +
 +
 +
'''Need new PSDS term: [https://sourceforge.net/tracker/index.php?func=detail&aid=3468651&group_id=76834&atid=835555 seed dormant stage]:'''
 +
 +
'''New proposed definition, seed dormant stage:''' A seed development stage during which a seed participates in a seed dormancy process.
 +
 +
Comment: A seed dormancy process (GO:0010162) is a dormancy process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a seed. Seed dormancy is a suspension of most physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leaching of inhibitors. Not all seeds go through a seed dormant stage.
 +
 +
''We agreed that this term should be added.''
 +
 +
''During a seed dormant stage, does a seed need to be dormant? According to this definition, a seed is a dormant stage as soon as it starts to undergo dormancy initiation, and it stays in one until it has finished all of the dormancy breaking processes. There will be times when seeds are both maturing and in a dormant stage. This overlap of stages is universal, because the boundaries are not discrete.''
 +
 +
''RW after meeting: GO already has terms for maintenance of seed dormancy and release of seed dormancy, plus acquisition of dessication tolerance (of seed).''
 +
 +
''Some seeds go dormant before the embryo develops cotyledons and other not. Also, the seed coat may go dormant before the embryo. We need to see what subtypes users need before we create too many specific terms.''
 +
 +
''We should add a term for embryo dormant stage (is_a sporophyte dormant stage, maybe part_of seed dormancy, but ferns, etc. can also have dormant embryos). Maybe later we can add seed coat dormant stage if it is needed.''
 +
 +
''Seed dormancy is usually a one-off process, but many whole plants will go dormant many times (except for biennials).''
 +
 +
''GO term should be added as a definition dbxref.''
 +
 +
 +
These synonyms should be moved here (or gotten rid of):
 +
 +
10.05-seed dormant in barley
 +
 +
10.05-seed dormant in oat
 +
 +
10.05-seed dormant in Triticeae
  
 +
10.05-seed dormant in wheat
  
  
−
==[http://sourceforge.net/tracker/?func=detail&aid=3432979&group_id=76834&atid=835555 gametophyte/sporophyte senescent stage]==
+
'''Existing term:  seed germination stage (PO:0007057):''' The resumption of growth by the embryo in a seed. [source: GR:Anuradha_Pujar, ISBN:047124529]  
−
This section was copied from POC 12-20-11 and needs to be revised
 
  
−
Put in the link to GO SouceForge tracker:
+
related synonyms:
 +
germination in maize
  
−
===Senescence and aging in GO===
+
0 germination in Solanaceae
−
''RW will send link to GO trackers for senescence and dormancy process to PO internal, so others can comment on them.''
+
 
 +
0 Germination in soybean
 +
 
 +
00-germination in maize
 +
 
 +
01-germination in barley
 +
 
 +
01-germination in oat
 +
 
 +
01-germination in rice
 +
 
 +
01-germination in Triticeae
 +
 
 +
01-germination in wheat
 +
 
 +
BBCH principal growth stage 0
 +
 
 +
germination in Arabidopsis
 +
 
 +
maize growth stage-0
 +
 
 +
rice growth stage-1
 +
 
 +
 
 +
 
 +
Could also move these synonyms there:
 +
 
 +
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 ??
  
−
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.
+
10.07-seed not dormant in oat  ??
  
−
Go had the general term:
+
10.07-seed not dormant in Triticeae  ??
  
−
'''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.
+
10.07-seed not dormant in wheat  ??
  
−
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'."
+
==[http://sourceforge.net/tracker/?func=detail&aid=3432979&group_id=76834&atid=835555 gametophyte/sporophyte senescent stage] terms==
 +
Even though the existing GO terms are not perfect for our needs, we decided last week to go ahead with the new definitions, and add a comment that we have requested new definitions from GO, which we can get rid after GO updates their definitions.
  
−
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.
+
'''sporophyte senescent stage (PO:0007017):''' A sporophyte development stage during which a sporophyte participates in multicellular organism senescence (GO:0010259).  
  
−
===Revisions to existing GO terms===
+
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.
−
'''GO tree view:'''
 
  
−
aging
+
Suggest adding to comment of sporophyte reproductive stage: The sporophyte senescent stage always succeeds the sporophyte reproductive stage in monocarpic plants.
  
−
>cell aging
+
''Need to rethink the comment on monocarpic plants -- there a plants like agave that are considered monocarpic, but in fact it is only the shoot system that dies, and other shoots grow out from the base. Should say something like "The sporophyte senescent stage may succeed the sporophyte reproductive stage in monocarpic plants"'' or remove the comment. RW will look into monocarpic definitions.''
  
−
>>cellular senescence
+
'''gametophyte senescent stage (PO:0025343):''' A gametophyte development stage during which a gametophyte participates in multicellular organism senescence (GO:0010259).
  
−
>multicellular organismal aging
+
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.
  
−
>organ senescence
+
See also 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.
  
−
>>leaf senescence
+
===Senescence and aging in GO===
 +
''Should these terms have process at the end of the name? Maybe yes for clarity and consistency, but most of us agreed that it was somewhat redundant in the name. CM felt that the GO editors probably wouldn't go for it.''
  
−
See References/notes, below, for source of definitions.
+
''CM: Should we try to define all of the specific terms in terms of the general one, or be more general with the definition of aging, then provide more specific definitions for each one.''
  
−
====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.
+
We discussed these new definitions for GO last week. The following changes were suggested on the [https://sourceforge.net/tracker/?func=detail&aid=3468945&group_id=36855&atid=440764 GO SourceForge tracker]:
  
−
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).
+
'''aging (GO:0007568)'''
  
−
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".
+
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.
  
−
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''.
+
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).
  
−
''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.''
+
Note: There are many processes that are a deterioration and loss of function over time, but not all of them are aging. However, aging is a subtype of GO:biological process,which states that it is "pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms", and GO:developmental process, which states that it is a "progression of an integrated living unit... over time from an initial condition to a later condition".  These inherited properties make the definition of aging more specific.
  
−
''Some discussion of the difference between aging and getting older. Does aging always follow maturity?''
 
  
−
====cell aging (GO:0007569)====
+
'''cell aging (GO:0007569)'''
  
−
'''current definition:''' Progression of the cell from its inception to the end of its lifespan.
+
Current definition: Progression of the cell from its inception to the end of its lifespan. Source: GOC:jh, PMID:12044934
−
Source: GOC:jh, PMID:12044934
 
  
−
'''proposed definition:''' An aging process that has as participant a cell after a cell has stopped dividing.
+
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.
+
Comment: Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest  (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
  
−
====cellular senescence (GO:0090398)====
+
''Can remove clause "after a cell has stopped dividing" from the definition, because the comment covers it.''
  
−
'''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.
+
''Need to say "has principle cell", because otherwise, you can have a whole organism that has as participant a cell that, but it is not going through a cell aging process.''
−
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).  
+
''Also important to add: every time a cell divides, it ages, because that is when damage to the telomeres occurs.''
  
−
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).
+
''Cells can age during very brief periods when they are not dividing, between each division.''
  
−
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.
+
'''cellular senescence (GO:0090398)'''
  
−
''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.''
+
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
  
−
====multicellular organismal aging (GO:0010259):====
+
proposed definition: A cellular aging process in which a cell permanently loses the ability to participate in the cell cycle (GO:0007049).
  
−
'''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.
+
Comment: Cellular senescence may be accompanied by other cell aging processes, such as wear and tear or the dismantling of cellular components. Cellular senescence 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 stress-induced premature senescence, GO:0090400), or it may be intrinsic, in cells that have a finite capacity for division (mitotic senescence or replicative senescence, GO:0090399).
−
Source: GOC:dph, GOC:isa_complete, GOC:mtg_sensu, GOC:sm
 
  
−
'''proposed definition:''' An aging process that has as participant a whole multicellular organism.
+
Also add the following synonyms:
  
−
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).
+
mitotic cellular senescence as a synonym of stress-induced premature senescence (GO:0090400)
  
−
'''Synonym: multicellular organism senescence'''; we may want to add '''monocarpic senescence''' as a narrow synonym or as a new subtype (see notes below).
+
post-mitotic cellular senescence as a synonym of replicative senescence (GO:0090399)
  
−
''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)====
+
'''multicellular organismal aging (GO:0010259)'''
−
'''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.
+
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
  
−
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.
+
Proposed definition: An aging process that has as participant a whole multicellular organism.
  
−
''Is there organ senescence in animals? Perhaps in things that metamorphosize.''
+
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).
  
−
''PO will also need a term for anther senescence, is_a organ senescence, to correspond to the PO stage term.''
+
As with aging, we felt that comment about sterility should come out, because sterility is a sign of aging, not something that precedes it.  
  
−
====leaf senescence (GO:0010150)====
+
Please add the following synonym: multicellular organism senescence (exact), monocarpic senescence (narrow)
−
'''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).
+
'''organ senescence (GO:0010260)'''
  
−
''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.''
+
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
  
−
''At this point, the call was temporarily interupted by Darth Vader, be we were able to resist the temptation of the dark side.''
+
Proposed definition: An aging process that has as participant an organ.
  
−
====ripening (GO:0009835)====
+
Comment: Includes processes such as cellular senescence (GO:0090398) and an overall decline in metabolism (GO:0008152). May succeed organ maturation (GO:0048799) and precede the death of the organ. Occurs in plant organs such as leaves or petals.
−
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.
+
'''leaf senescence (GO:0010150)'''
  
−
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.
+
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
  
−
synonym: fruit senescence
+
Proposed definition: An organ senescence that has as participant a leaf.
  
−
''Rename this "fruit ripening" for clarity.''
+
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).
  
−
''This term already has a taxon restriction on parent (for Angiospermae, presumably).''
+
Note: Because of the all-some nature of the has_paricipant relation, the GO definition has to say leaf senescence has_participant leaf, but in every individual instance, the relation would be to vascular leaf or non-vascular leaf.  
  
−
====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.
+
'''ripening (GO:0009835)'''
  
−
Aging: wear and tear
+
GO has the term ripening, which we suggest renaming "fruit ripening". Ripening is_a anatomical structure maturation, but it should be a subtype of aging, with the synonym "fruit senescence".
  
−
Senescence: internal dismantling of cells, tissues, and organs
+
Current definition: 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.
  
−
'''Gan, 2010, in Senescence Processes in Plants (Annual Plant Reviews):'''
+
Proposed definition: An aging process that has as participant a fruit.
  
−
ISBN:9781405139847
+
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.
  
−
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.
+
synonym: fruit senescence
  
−
Two types of senescence (for cells or organs):
+
This term already has a taxon restriction on parent (for Angiospermae, presumably).
  
−
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
+
'''floral organ senescence (new term)'''
  
−
'''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."
+
Note that there is an open tracker for [https://sourceforge.net/tracker/index.php?func=detail&aid=3425355&group_id=36855&atid=440764 flower senescence]. RW will add a comment to that tracker that it is not a type of organ senescence, because a flower is not a plant organ. Also, although the term flower senescence is used, it is not really the whole flower that senesces, but the petals or tepals.
  
−
===PO senescent stage terms===
+
''Other organs besides petal senesce too, like stamens.''
−
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.''
+
See also PO SF tracker for [https://sourceforge.net/tracker/?func=detail&aid=3464416&group_id=76834&atid=835555 floral organ].
  
−
'''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.
+
All of the above definitions and synonyms could use POC:curators and Gan, 2010, in Senescence Processes in Plants (Annual Plant Reviews), ISBN:9781405139847 as reference.
  
−
Suggest adding to comment of sporophyte reproductive stage: The sporophyte senescent stage always succeeds the sporophyte reproductive stage in monocarpic plants.
+
=Term Requests from [http://www.agron-omics.eu/ Agron-Omics]=
 +
At the recent EBI Crop Ontology meeting PJ met with [http://atidb.org/group/projects.html Sean Walsh]
  
−
'''gametophyte senescent stage (PO:0025343):''' A gametophyte development stage during which a gametophyte participates in multicellular organism senescence (GO:0010259).  
+
[http://www.agron-omics.eu/ Arabidopsis GROwth Network integrating OMICS technologies]
  
−
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.
 
  
−
===PO senescent stage terms===
+
please see [[Items_for_future_meetings]]
−
''Postponed until the 12-20-11 meeting.''
 
  
 
=Mistake in the CL/PO coordination=
 
=Mistake in the CL/PO coordination=
Line 343: Line 419:
 
''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.''
 
''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.''
+
''RW: This is ok in MH's new proposal, because experimentally modified cell and multicellular organism cell are independent categories.''
 +
 
 +
Proposed format from Melissa's document:
 +
 
 +
[[File:MH_cell_heirarchy.jpg]]
 +
 
 +
PO cell would be a subtype of either cell (CL:0000000) or multicellular organism cell (new) depending on how plant is defined (viridiplantae versus embryophyta). ''PO defines plant as viridiplantae, so we should use CL:0000000.''
 +
 
 +
''Discussed the use of ex situ or in situ. Perhaps they used ex environment and ex vivo instead, to deal with the two different meanings of ex situ.''
 +
 
 +
''BS: The CL should be restricted to those terms that apply to cells in general, and used for cross products to cells that occur in particular organism. PO could then use the CL to talk about plant cells ex vivo, etc.''
 +
 
 +
==proposed solution==
 +
BS (via email) said that he was very much in favor of 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 has been done for the other taxon-centric AOs).
 +
 
 +
Remove from CL: 'treat-xrefs-as-equivalent: PO'
 +
 
 +
Add to CL: 'treat-xref-as-genus-differentia: PO part_of NCBITaxon:nnnnn ! viridiplantae'
 +
 
 +
''All present agreed that solution 2 was the preferred solution.''
  
 
=Wood Anatomy Ontology Meeting=
 
=Wood Anatomy Ontology Meeting=
Line 361: Line 460:
 
*Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the [http://www.fagaceae.org/ Fagaceae Genomics Web]  
 
*Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the [http://www.fagaceae.org/ Fagaceae Genomics Web]  
  
−
So far, Fredich Lens, Meg Staton, Barb Lachenbruch and Rachel Spicer  have responded positively, and RW has followed up with them. John Carlson has declined to attend as he is having surgery at the end of January.
+
So far, Fredich Lens, Meg Staton, Barb Lachenbruch, Elizabeth Wheeler and Rachel Spicer  have responded positively, and RW has followed up with them. John Carlson has declined to attend as he is having surgery at the end of January.
  
−
Still waiting to hear from Elisabeth Wheeler, who has been out of town. Maybe Ale could follow up with her?
+
Travel authorization forms have been sent to all to confirmed domestic invitees and LC is collecting them. So far we have received them from Jill, EW and Andrew.
−
 
 
−
Travel forms have been sent to all to confirmed domestic invitees and LC is collecting them. So far we have received them from Jill and Andrew.
 
  
 
The paperwork for FL has been submitted to the dept and is in progress.   
 
The paperwork for FL has been submitted to the dept and is in progress.   
  
 
BS is available to give his presentation on Sunday morning (see: [[Wood anatomy ontology meeting, 2012 at NYBG, agenda]]). He suggested that this presentation may be of interest to others in the NYC area. He will advertise it to a wider audience, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.
 
BS is available to give his presentation on Sunday morning (see: [[Wood anatomy ontology meeting, 2012 at NYBG, agenda]]). He suggested that this presentation may be of interest to others in the NYC area. He will advertise it to a wider audience, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.
 +
 +
''RW will follow up with Barb, Rachel, and Meg about the travel paperwork.''
  
 
=Upcoming meetings and Presentations 2011/2012:=
 
=Upcoming meetings and Presentations 2011/2012:=

Latest revision as of 19:44, 8 March 2012

POC meeting, Webex Conference Call; Date: Tuesday Jan 3rd, 2012 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab),

Absent: Marie Alejandra Gandolfo (Cornell University), Pankaj Jaiswal (OSU)

Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-20-11? No additions, deletions, or changes.

Back to POC Meetings Minutes

PSDS Revisions: Whole plant development stages

Updates to GO terms for Dormancy Process terms:

Link to discussion on GO SF Tracker

Most of our suggestions were accepted, except that they did not see the need for "multicellular organism dormancy process". These changes should take effect early in the New Year.


Agreed upon def'ns and comments:

dormancy process (GO:0022611): A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.

comment: In plants and animals, dormancy may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. In plants, dormancy may involve the formation of dormant buds, and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system [in] herbaceous perennials. The exit from dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium.

Dbxrefs: GOC:PO_curators [to be added to the curators' initials file]

Paola had a question about the PO_ref: "how should I enter this? I haven't found any other PO_REF in GO or in the GO>references file"

They are willing to add 'multicellular organism dormancy process' as a narrow synonym.

seed dormancy process (new name)(GO:0010162): A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a seed. Seed dormancy is a suspension of most physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leaching of inhibitors.

RW: This should say "A dormancy process..." instead of "A developmental process...". I suggested this on GO SF tracker.

related synonym: seed dormancy

Dbxrefs as above

RW noted: "You could add an xref: seed dormancy process (GO:0010162) has_participant seed (PO:0009010)

TB:In GO, we do not currently use has_participant outside of the go_xp_chebi.obo file,


New term: bud dormancy process (GO:xxxxxxx): A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a bud. Bud dormancy is a suspension of most physiological activity and growth that can be reactivated. It may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. The exit from bud dormancy is marked by the resumed growth of the bud. Comment: Bud dormancy may precede dormancy of the whole plant.

RW: This should say "A dormancy process..." instead of "A developmental process...". I suggested this on GO SF tracker.

Paola: To make it clear that this term refers to plant buds only, and to avoid confusion with other buds i.e. those resulting from asexual reproduction, I'd add a taxon constraint. Plant experts, please advise if this should be to Viridiplantae, Embryophyta or Spermatophyta.

From RW: I think the taxon restriction should be for Embryophyta, but I will check into whether or not the term bud is used for green algae.

Ken Karoll of NYBG walked into the meeting for a minute and confirmed that the term budding is used to describe a particular type of cell division that leads to branches in green algae, so the taxon restriction should go on Viridiplantae.

RW noted: "You could add an xref: bud dormancy process (GO:0010162 has_participant bud (PO:0000055)."

see comment from TB, above.

(Paola: BTW, to do too: GO:0042751 estivation, add exact synonym: aestivation)

BS: Should we also request GO terms for process that induce, maintain, or release dormancy. The underlying mechanisms for each are so different. We could add a comment that people who need these processes should request them on the GO tracker, or maybe it should go on the GO definition.

We were concerned that the range of process in these terms is so broad. Do our users need more specific terms? So far no one has requested them. We should probably request them in terms.

RW will follow up on GO request for spore dormancy -- someone else already created a tracker for it.

Review of PO terms for gametophyte/sporophyte dormant stage

These were accepted at the POC Conf. Call 12-13-11, but will need to be revised based upon the revisions of the GO terms to complete them. See below:

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

link to dev

Revised def'n: sporophyte dormant stage (PO:0007132): A sporophyte development stage during which a sporophyte participates in an dormancy process. [source:GO:0022611]

Revised comment: Dormancy process (GO:0022611)is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy of a plant may be preceded by the senescence of its parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Resurrection plants are in andormant stage when they become dessicated.

take off: 'Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.'

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

Revised def'n: gametophyte dormant stage (PO:0025342): A gametophyte development stage during which a gametophyte participates in a dormancy process. [source:GO:0022611]

Revised comment: Dormancy process (GO:0022611) is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are a moss that has undergone dessication (a resurrection plant) or the female gametophyte of Ginkgo biloba, which is dormant before fertilization.

remove: Refers to GO0022611 (dormancy process). Have requested term for multicellular organism dormancy in GO.


RW: Comments should refer to GO definition of dormancy process. Note that dormancy, not a dormancy process, is the suspension of growth and activity.

New proposed comments:

sporophyte dormant stage (PO:0007132), comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy of a plant may be preceded by the senescence of its parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Resurrection plants are in a dormant stage when they become dessicated.

gametophyte dormant stage (PO:0025342), comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are a moss that has undergone dessication (a resurrection plant) or the female gametophyte of Ginkgo biloba, which is dormant before fertilization.

We should add specific examples (species names) of what are resurrection plants. Examples for mosses: Andreas (look up), for sporophyte: Selaginella lepidophylla, Craterostigma plantagineum. Also, Polytrichum have annual growth marks, because they are dormant during the winter and aquatic ferns with sporocarps, where gametophytes are dormant. We can provide a number of examples illustrating not only the taxonomic diversity but the diversity of mechanisms.

RW, after meeting: Polytrichum commune is a moss that is dessicated-dormant (PMCID: PMC343055). The boreal moss Polytrichum alpestre has shoot systems with annual growth segments due to a period of dormancy during the winter (JSTOR:3242212). Spores are also in the gametophyte stage (according to our definition), so spore dormancy is a type of gametophyte dormancy. See SF tracker for new comments.

Resolving the issue about the existing synonyms of sporophyte dormant stage

Are these actually appropriate as synonyms for sporophyte dormant stage (PO:0007132, was dormancy, which was a subtype of whole plant growth stage)?

10.05-seed dormant in barley

10.05-seed dormant in oat

10.05-seed dormant in Triticeae

10.05-seed dormant in wheat

10.06-viable seed germination in barley

10.06-viable seed germination in oat

10.06-viable seed germination in Triticeae

10.06-viable seed germination in wheat

10.07-seed not dormant in barley

10.07-seed not dormant in oat

10.07-seed not dormant in Triticeae

10.07-seed not dormant in wheat

They all come from GRO.

Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.

Presumably, these synonyms are here in case anyone is still using the old GRO and searching for them. However, there was general agreement that these terms are extraneous. We thought it would be best to get rid of them, and either create subsets for the different species (which we may already have) and/or add comments about the different dormant stages in the different species.'

We are going to remove these synonyms from dormant stages. Will probably want to remove them from the other development stage terms as well.


Need new PSDS term: seed dormant stage:

New proposed definition, seed dormant stage: A seed development stage during which a seed participates in a seed dormancy process.

Comment: A seed dormancy process (GO:0010162) is a dormancy process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a seed. Seed dormancy is a suspension of most physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leaching of inhibitors. Not all seeds go through a seed dormant stage.

We agreed that this term should be added.

During a seed dormant stage, does a seed need to be dormant? According to this definition, a seed is a dormant stage as soon as it starts to undergo dormancy initiation, and it stays in one until it has finished all of the dormancy breaking processes. There will be times when seeds are both maturing and in a dormant stage. This overlap of stages is universal, because the boundaries are not discrete.

RW after meeting: GO already has terms for maintenance of seed dormancy and release of seed dormancy, plus acquisition of dessication tolerance (of seed).

Some seeds go dormant before the embryo develops cotyledons and other not. Also, the seed coat may go dormant before the embryo. We need to see what subtypes users need before we create too many specific terms.

We should add a term for embryo dormant stage (is_a sporophyte dormant stage, maybe part_of seed dormancy, but ferns, etc. can also have dormant embryos). Maybe later we can add seed coat dormant stage if it is needed.

Seed dormancy is usually a one-off process, but many whole plants will go dormant many times (except for biennials).

GO term should be added as a definition dbxref.


These synonyms should be moved here (or gotten rid of):

10.05-seed dormant in barley

10.05-seed dormant in oat

10.05-seed dormant in Triticeae

10.05-seed dormant in wheat


Existing term: seed germination stage (PO:0007057): The resumption of growth by the embryo in a seed. [source: GR:Anuradha_Pujar, ISBN:047124529]

related synonyms: germination in maize

0 germination in Solanaceae

0 Germination in soybean

00-germination in maize

01-germination in barley

01-germination in oat

01-germination in rice

01-germination in Triticeae

01-germination in wheat

BBCH principal growth stage 0

germination in Arabidopsis

maize growth stage-0

rice growth stage-1


Could also move these synonyms there:

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 ??

gametophyte/sporophyte senescent stage terms

Even though the existing GO terms are not perfect for our needs, we decided last week to go ahead with the new definitions, and add a comment that we have requested 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.

Need to rethink the comment on monocarpic plants -- there a plants like agave that are considered monocarpic, but in fact it is only the shoot system that dies, and other shoots grow out from the base. Should say something like "The sporophyte senescent stage may succeed the sporophyte reproductive stage in monocarpic plants" or remove the comment. RW will look into monocarpic definitions.

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.

See also 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.

Senescence and aging in GO

Should these terms have process at the end of the name? Maybe yes for clarity and consistency, but most of us agreed that it was somewhat redundant in the name. CM felt that the GO editors probably wouldn't go for it.

CM: Should we try to define all of the specific terms in terms of the general one, or be more general with the definition of aging, then provide more specific definitions for each one.


We discussed these new definitions for GO last week. The following changes were suggested on the GO SourceForge tracker:

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: There are many processes that are a deterioration and loss of function over time, but not all of them are aging. However, aging is a subtype of GO:biological process,which states that it is "pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms", and GO:developmental process, which states that it is a "progression of an integrated living unit... over time from an initial condition to a later condition". These inherited properties make the definition of aging more specific.


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: Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).

Can remove clause "after a cell has stopped dividing" from the definition, because the comment covers it.

Need to say "has principle cell", because otherwise, you can have a whole organism that has as participant a cell that, but it is not going through a cell aging process.

Also important to add: every time a cell divides, it ages, because that is when damage to the telomeres occurs.

Cells can age during very brief periods when they are not dividing, between each division.


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. Cellular senescence 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 stress-induced premature senescence, GO:0090400), or it may be intrinsic, in cells that have a finite capacity for division (mitotic senescence or replicative senescence, GO:0090399).

Also add the following synonyms:

mitotic cellular senescence as a synonym of stress-induced premature senescence (GO:0090400)

post-mitotic cellular senescence as a synonym of replicative senescence (GO:0090399)


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).

As with aging, we felt that comment about sterility should come out, because sterility is a sign of aging, not something that precedes it.

Please add the following synonym: multicellular organism senescence (exact), monocarpic senescence (narrow)


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

Note: Because of the all-some nature of the has_paricipant relation, the GO definition has to say leaf senescence has_participant leaf, but in every individual instance, the relation would be to vascular leaf or non-vascular leaf.


ripening (GO:0009835)

GO has the term ripening, which we suggest renaming "fruit ripening". Ripening is_a anatomical structure maturation, but it should be a subtype of aging, with the synonym "fruit senescence".

Current definition: 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.

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

This term already has a taxon restriction on parent (for Angiospermae, presumably).


floral organ senescence (new term)

Note that there is an open tracker for flower senescence. RW will add a comment to that tracker that it is not a type of organ senescence, because a flower is not a plant organ. Also, although the term flower senescence is used, it is not really the whole flower that senesces, but the petals or tepals.

Other organs besides petal senesce too, like stamens.

See also PO SF tracker for floral organ.


All of the above definitions and synonyms could use POC:curators and Gan, 2010, in Senescence Processes in Plants (Annual Plant Reviews), ISBN:9781405139847 as reference.

Term Requests from Agron-Omics

At the recent EBI Crop Ontology meeting PJ met with Sean Walsh

Arabidopsis GROwth Network integrating OMICS technologies


please see Items_for_future_meetings

Mistake in the CL/PO coordination

CM raised the issue below: spot the inconsistency: 

/ PO:0025131 ! plant anatomical entity 
 is_a PO:0009011 ! plant structure 
  is_a PO:0000004 ! in vitro plant structure 
   is_a PO:0000005 ! cultured plant cell ***  
  is_a PO:0009002 ! plant cell [xref: GO:0005623] 
   is_a PO:0000005 ! cultured plant cell ***

/ CL:0000000 ! cell [xref: FMA:68646] [xref: GO:0005623 "cell"] [xref: KUPO:0000002] [xref: WBbt:0004017] [xref: XAO:0003012] 

 is_a CL:0000003 ! cell in vivo
  is_a CL:0000004 ! cell by organism
   is_a CL:0000255 ! eukaryotic cell
    is_a CL:0000610 ! plant cell ***  [xref: PO:0009002]

if the xrefs are equivalent and in vivo is (presumably) disjoint from in vitro, then plant cell is unsatisfiable.

Link to CL:0000610 plant cell on CL.

They should be using our definition of plant cell as well: "A cell which is a plant structure. [source: GO:0005623, POC:Curators]"

  • SOLUTION 1:

With it's current placement, CL:0000610 must really be equivalent to a PO:0009002 that is in-vivo - this doesn't correspond to a named class in PO. We could rename CL:0000610 to "in vivo plant cell" and have a bridging axioms that says this is a subclass of PO:0009002

  • SOLUTION 2:

obsolete CL:0000610, with a consider link (not replaced by) to PO:0009002

add an xref to PO:0009002 to CL:0000000 (just as we have for the other taxon-centric AOs).

Remove: 'treat-xrefs-as-equivalent: PO'

Add: 'treat-xref-as-genus-differentia: PO part_of NCBITaxon:nnnnn ! viridiplantae'

  • SOLUTION 3:

move CL:0000610 ! plant cell to be a direct child of CL:0000000 ! cell

we would probably want to move CL:0000255 ! eukaryotic cell at the same time

From CM:

"I don't like solution 1. Neutral w.r.t. 2 and 3."

"Note that whatever the solution, we need a consistent cross-ontology naming strategy. I don't think it's necessary to prefix every in-vivo class with "in-vivo". But we need to be consistent. At the moment "eukaryotic cell" means "eukaryotic in vivo cell", whereas "plant cell" (in PO) means "plant cell, in vivo or in-vitro".

"How about this: if we have a taxonomic qualification, it doesn't imply in-vivo. If we have a named cell type (e.g. "neuron") or some other qualification, it implies in-vivo?"

CL should us the PO definition of plant cell. We should put it on the CL plant tracker.

The problem is if someone tries to import PO into CL, because of the conflict with in vivo cell. This should be address in the document from MH proposing changes to CL.

PJ raised an issue with experimentally modified cell -- you can experimentally modify a cell then stick it back in an organism, so it is in vivo.

RW: This is ok in MH's new proposal, because experimentally modified cell and multicellular organism cell are independent categories.

Proposed format from Melissa's document:

MH cell heirarchy.jpg

PO cell would be a subtype of either cell (CL:0000000) or multicellular organism cell (new) depending on how plant is defined (viridiplantae versus embryophyta). PO defines plant as viridiplantae, so we should use CL:0000000.

Discussed the use of ex situ or in situ. Perhaps they used ex environment and ex vivo instead, to deal with the two different meanings of ex situ.

BS: The CL should be restricted to those terms that apply to cells in general, and used for cross products to cells that occur in particular organism. PO could then use the CL to talk about plant cells ex vivo, etc.

proposed solution

BS (via email) said that he was very much in favor of 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 has been done for the other taxon-centric AOs).

Remove from CL: 'treat-xrefs-as-equivalent: PO'

Add to CL: 'treat-xref-as-genus-differentia: PO part_of NCBITaxon:nnnnn ! viridiplantae'

All present agreed that solution 2 was the preferred solution.

Wood Anatomy Ontology Meeting

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

Tentative dates are Feb. 5th-7th, 2012 (Sun-Tues)

Update and status:

Invitation letter went out 12/15/11 from DWS, to experts (below) signed by all three Co-PIs, along with Jill Wegrzyn of the TreeGenes Database at UCDavis (Bioinformatics) and Andrew Groover Geneticist, USDA Forest Service, Institute of Forest Genetics, Davis CA. Deadline for their response was Dec 31st 2011.

So far, Fredich Lens, Meg Staton, Barb Lachenbruch, Elizabeth Wheeler and Rachel Spicer have responded positively, and RW has followed up with them. John Carlson has declined to attend as he is having surgery at the end of January.

Travel authorization forms have been sent to all to confirmed domestic invitees and LC is collecting them. So far we have received them from Jill, EW and Andrew.

The paperwork for FL has been submitted to the dept and is in progress.

BS is available to give his presentation on Sunday morning (see: Wood anatomy ontology meeting, 2012 at NYBG, agenda). He suggested that this presentation may be of interest to others in the NYC area. He will advertise it to a wider audience, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.

RW will follow up with Barb, Rachel, and Meg about the travel paperwork.

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 12:50 pm for the PO.
  • The PO will also take part in an Outreach booth organized by MaizeGDB- schedule TBA

-Do we want to host the wiki page for the booth again?

Phenotype RCN meeting, 23-25 February 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

RW has a friend there she can stay with and is interested in going.

Any news??

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.


Deadlines: Advance meeting registration is due by January 31, 2012.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• Notification date: February 3, 2012

From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:


RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

Annotation wiki

JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

ASPB Plant Biology 2012

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

Registration scheduled to open first week in January.

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

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

Relevant dates

  • Jan. 31st, 2012: Paper submission deadline
  • Feb. 28th, 2012: Notification of paper acceptance
  • March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
  • April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
  • June 30th 2012: Deadline for all camera-ready copies for the proceedings

We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?

Possible topics: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.


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

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

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