Difference between revisions of "POC Conf. Call 6-30-10"

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POC meeting, Webex Conference Call; Date: June 30th, 2010 10am (PDT)
+
'''POC meeting, Webex Conference Call; Date: June 30th, 2010 10am (PDT)'''
  
−
In attendance: POC members:  
+
In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Chris Mungall (Lawrence Berkeley National Lab), Alejandra Gandolfo, (Cornell University)
  
−
Collaborators:  
+
Absent: Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY).
  
−
Absent:  
+
Collaborators: none
  
−
Acceptance of the minutes from the 6-29-10 meeting? All in favor?
+
Acceptance of the minutes from the 6-29-10 meeting? All in favor? ''There were no additions, deletions or changes to th minutes of yesterday's meeting.''
  
 +
Workshop page: [[http://wiki.plantontology.org:8080/index.php/POC_Meeting_and_Workshop_June_29th_and_30th,_Corvallis,_OR#Questions:  Corvallis Workshop June 29th and 30th, 2010]]
 +
o
 +
===*Work on items from Tuesday morning:===
 +
-Ontology development
  
 +
'''Updates of upper level terms'''
 +
 +
Reviewed changes from yesterday and will keep what we decided on at that meeting.
 +
 +
'''bud'''
 +
 +
Reviewed changes from yesterday and will keep what we decided on at that meeting.
 +
 +
'''Tuber'''
 +
 +
Decided that tuber is_a axillary shoot system. This changed during the course of the day's discussion. See additional notes below under stem, shoot, etc.
 +
 +
'''cortex- hypodermis and endodermis'''
 +
 +
Decided to put changes from yesterday's meeting into an obo file so we can look at them later.
  
 
===Terms from open SourceForge Trackers===
 
===Terms from open SourceForge Trackers===
  
  
−
'''1. stem and shoot''' (See SF Tracker [https://sourceforge.net/tracker/?func=detail&aid=2982923&group_id=76834&atid=835555/ stem] and need to add SF item for shoot)
+
===1. stem (PO:0009047)===
 +
[https://sourceforge.net/tracker/?func=detail&aid=2982923&group_id=76834&atid=835555/ stem]
  
−
Problem: Stem has no is_a parent- should be a collective plant structure?
+
Problem: Stem has no is_a parent- should be a collective plant structure or a plant organ?
  
 
Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]
 
Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]
 +
  
 
Synonyms: cane, culm,  stalk, trunk
 
Synonyms: cane, culm,  stalk, trunk
Line 24: Line 45:
 
OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.
 
OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.
  
 +
Stem proposed def'n: A shoot axis that has parts nodes and internodes
 +
 +
Comment: may bear leaves and buds.
 +
 +
 +
Decided to make new parent term axis which is_a plant organ.
 +
 +
parentage:-
 +
plant organ
 +
>axis
 +
>shoot axis, sibling root axis
 +
>> stem, siblings branch, stolon, pedicel, etc.
 +
 +
branch is synonymous with secondary, tertiary axis, etc.
 +
 +
RW notes are somewhat different. Say that stem is the primary axis, branch is all second or higher order axes. Therefore, definition of stem is: A shoot axis that is the primary axis of a plant. If you define stem by having nodes and internodes, that does not exclude secondary axes.
 +
 +
===2. Shoot (PO:0009006)=== 
 +
[https://sourceforge.net/tracker/?func=detail&aid=3011039&group_id=76834&atid=835555 shoot]
 +
 +
current def'n: Part of the sporophyte composed of the stems and leaves, and includes shoot apical meristems. [source: POC:curators]
 +
 +
Problem: Shoot has no is_a parent- should be a collective plant structure or a plant organ?
 +
 +
merges into shoot system (new term)
 +
 +
proposed def'n: The axial system of a plant that only includes shoot apical meristems and the structures that arise from them.
 +
 +
Comment: may bear leaves and buds.
 +
 +
parentage:
 +
plant system
 +
>shoot system
 +
>>vegetative  shoot system  (new term),
 +
 +
vegetative shoot system  proposed def'n: A shoot system that only bears vegetative structures.
 +
 +
Note: the root system and shoot system have no parts in common.
 +
 +
plant system
 +
>shoot system
 +
>reproductive shoot system (new term):
 +
proposed def'n: A shoot system that bears reproductive structures.
 +
 +
===3. Tuber terms(PO:0004543)===
 +
[https://sourceforge.net/tracker/?func=detail&aid=3017726&group_id=76834&atid=835555 tuber]
 +
 +
see comments from 6-29 meeting
 +
 +
new proposed def'n: A swollen or enlarged storage stem.
 +
 +
comment: may have with determinate growth.
 +
 +
We will look into whether or not tubers are determinate or not, vs rhizomes
 +
 +
proposed def'n:  A swollen or enlarged storage axillary shoot system.
 +
 +
 +
* '''Subterranean tuber (PO:0004547)'''
 +
 +
is_a 'tuber' and part_of 'rhizome'
 +
 +
current def'n: A swollen rhizome or a part of the rhizome with determinate growth. [source: POC:curator]
 +
 +
proposed def'n: A tuber that is part of a rhizome.
  
−
Shoot def: Part of the sporophyte composed of the stems and leaves, and includes shoot apical meristems. [source: POC:curators]
 
  
 +
* '''aerial tuber (PO:0004548)'''
  
−
'''Tubers, rhizomes and stolons''' should be stems and not shoots.
+
current def'n: An axillary shoot with a swollen stem.
  
−
Stolon PO:0003024 is defined as 'A slender, prostrate or trailing above-ground stem which produces roots and sometimes erect shoots at its nodes. [source: APWeb:Glossary]' but it is classified as a shoot.
+
proposed def'n: A tuber that is above ground
  
−
Tuber is defined as 'Swollen storage shoot with determinate growth. [source: POC:curators]' while
+
===4. rhizome (PO:0004542)===
 +
(need to add link to SF tracker)- under 'stem'
  
−
subterranean tuber is 'A swollen rhizome or a part of the rhizome with determinate growth. [source: POC:curator]' and
+
Current def'n: Underground shoot. [source: POC:curators]'
  
−
rhizome is 'Underground shoot. [source: POC:curators]'
+
proposed def'n: A stem that grows horizontally and produces shoots above and roots or rhizoids below.
  
−
Subterranean tuber is_a tuber and part_of rhizome, so its definition should be 'A tuber that is part of a rhizome.' Tuber is already defined as determinate growth.
+
Comment: Usually produces scale-like leaves, may produce rhizoids, especially in ferns or Pteridophytes.
  
−
Tuber could be defined as 'A swollen stem with determinate growth that has part portion of storage parenchyma.'
+
===5. Stolon (PO:0003024)===
 +
(need to add link to SF tracker)
  
−
We should request the term determinate from PATO.
+
current def'n: A slender, prostrate or trailing above-ground '''stem''' which produces roots and sometimes erect shoots at its nodes. [source: APWeb:Glossary]
  
 +
but it is classified as a shoot.
  
−
'''2. stalk''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972224&group_id=76834&atid=835555/ stalk])
+
===6. stalk (PO:0025066)===
 +
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972224&group_id=76834&atid=835555/ stalk])
  
 
This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.
 
This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.
  
−
def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.
+
current def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.
  
 
Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.
 
Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.
  
−
-made a cardinal organ part (as per its definition) rather than an organ.
+
-made it a child of cardinal organ part (as per its definition) rather than an organ.
 +
 
 +
 
  
 
'''Proposed children of stalk: (Test: do all of these fit the definition?)'''  
 
'''Proposed children of stalk: (Test: do all of these fit the definition?)'''  
  
−
*filament: The stalk of a stamen.(stamen:organ)
+
*'''filament:''' The stalk of a stamen.(stamen:organ)
 +
 
 +
*'''petiole:''' The stalk of a leaf. (leaf:organ)
 +
 
 +
*'''petiolule:''' The stalk of a leaflet (leaflet:cardinal organ part)
 +
 
 +
*'''funicle:''' The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)
 +
 
 +
*'''gynophore:''' The stalk at the base of the ovary.

(ovary: cardinal organ part)
 +
 
 +
 
 +
 
 +
*'''leaf rachis:''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972235&group_id=76834&atid=835555/ leaf rachis])
 +
current def'n: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ) 
 +
 
  
−
*petiole: The stalk of a leaf. (leaf:organ)
+
*'''peduncle:''' ([https://sourceforge.net/tracker/?func=detail&aid=2972231&group_id=76834&atid=835555/ peduncle])
  
−
*petiolule: The stalk of a leaflet (leaflet:cardinal organ part)
+
current def'n: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves.
  
−
*funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)
+
proposed def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition). 
  
−
*gynophore: The stalk at the base of the ovary.

(ovary: cardinal organ part)
 
  
−
*leaf rachis: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ)  (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972235&group_id=76834&atid=835555/ leaf rachis])
+
*'''pedicel:''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2975275&group_id=76834&atid=835555/ pedicel])
  
−
*peduncle: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves. (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972231&group_id=76834&atid=835555/ peduncle])
+
current def'n: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]  
  
−
propose revised def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).
+
proposed def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).
  
−
*pedicel: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]
 
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2975275&group_id=76834&atid=835555/ pedicel])
 
  
−
propose revised def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).
 
  
 
'''Note: We also have the term 'stem''''.  We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.
 
'''Note: We also have the term 'stem''''.  We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.
Line 82: Line 184:
  
  
−
'''3. More 'new is_a children of cardinal organ part''''  (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2971884&group_id=76834&atid=835555/ new is_a children of cardinal organ part])
 
  
−
Several weeks ago, we created new children of cardinal organ part, from '''terms that had no is_a parent'''. We can deal with definitions and relationships of each term later, but for now we simply need to approve moving them to cardinal organ part.
+
==Terms from last week==
 +
 
 +
 
 +
 
 +
'''1. fruit''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972169&group_id=76834&atid=835555/ fruit])
 +
 
 +
Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.
 +
 
 +
 
 +
Proposed new def'n:  A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it.''
 +
(Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.
 +
 
 +
Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it).
 +
Dbx ref to parthenogenesis: Medical subject heading Ontology D010312
 +
 
 +
 
 +
''Barry suggested that we reword the second half of the definition, because the final word 'it' was ambiguous about what it was referring to, and the use of the word 'other' was unclear. We agreed that the second part of the definition about other floral structures should go into the comments section. Started to discuss whether or not the seed should be included as part of the definition (fruit contains seed), but ran out of time. To be continued next meeting.''
 +
 
 +
 
 +
 
 +
 
 +
'''2.  Embryo''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555/ embryo])
 +
 
 +
 
 +
'''Current def'n:''' A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]
 +
 
 +
Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).
 +
 
 +
We could mention the cotyledons in a comment- specific to flowering plants
 +
 
 +
 
 +
(2) See [http://plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0000010&session_id=3880b1272975931/ Cultured embryo PO:0000010] for definition of in vitro plant embryo
  
−
Some of them can be dealt with later, but the terms listed here are a higher priority and/or can be dealt with very quickly. Many of the definitions need to be worked on at a future meeting. See Source Forge items for additional comments.
+
(3) Adventitious embryos do not arise from zygotes -add a comment?
  
−
'''*receptacle:''' The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators].
+
Relationships:
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2975273&group_id=76834&atid=835555/ receptacle])
 
  
−
propose revised def'n: The region at the top of either the peduncle or pedicel where the floral appendages (for example, sepals, petals, stamens, and pistils) are attached.(Brooklyn Botanic Garden http://www.bbg.org/gar2/topics/botany/parts_flowers.html)
+
(1) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity
 +
(2) develops_from zygote (see comment above) Usually
 +
(3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)
  
−
Comments: If both pedicel and peduncle is_a stalk, and stalk is_a 'cardinal organ part', then both pedicel and peduncle must be part of some
 
−
organ for this to work.
 
−
 
−
'''*hypanthium'''- A cup- or tube-like structure bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary of a flower.
 
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972200&group_id=76834&atid=835555/ hypanthium])
 
  
−
made part_of receptacle instead of part_of flower
 
  
 +
===Other Items===
 +
AmiGO issues
  
−
'''*pulvinus:'''-A more or less abrupt swelling, especially at the apex or base of a petiole or leaf sheath, often glandular and/or being the place where a plant responds to touch, gravity or light, in panicoid grasses a swollen region
+
Cross products
−
in the stem above the intercalary meristem - such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc., cf. articulation. [source: APWeb:Glossary]
+
[[Media:PO-corv-2010.pdf]]
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972236&group_id=76834&atid=835555/ pulvinus])
 
  
−
-currently is_a (an) organ
+
===8. Next meeting scheduled for: Weds July 14th, 10am PDT===

Latest revision as of 17:52, 12 July 2010

POC meeting, Webex Conference Call; Date: June 30th, 2010 10am (PDT)

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Chris Mungall (Lawrence Berkeley National Lab), Alejandra Gandolfo, (Cornell University)

Absent: Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY).

Collaborators: none

Acceptance of the minutes from the 6-29-10 meeting? All in favor? There were no additions, deletions or changes to th minutes of yesterday's meeting.

Workshop page: [Corvallis Workshop June 29th and 30th, 2010] o

*Work on items from Tuesday morning:

-Ontology development

Updates of upper level terms

Reviewed changes from yesterday and will keep what we decided on at that meeting.

bud

Reviewed changes from yesterday and will keep what we decided on at that meeting.

Tuber

Decided that tuber is_a axillary shoot system. This changed during the course of the day's discussion. See additional notes below under stem, shoot, etc.

cortex- hypodermis and endodermis

Decided to put changes from yesterday's meeting into an obo file so we can look at them later.

Terms from open SourceForge Trackers

1. stem (PO:0009047)

stem

Problem: Stem has no is_a parent- should be a collective plant structure or a plant organ?

Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]


Synonyms: cane, culm, stalk, trunk

OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.

Stem proposed def'n: A shoot axis that has parts nodes and internodes

Comment: may bear leaves and buds.


Decided to make new parent term axis which is_a plant organ.

parentage:- plant organ >axis >shoot axis, sibling root axis >> stem, siblings branch, stolon, pedicel, etc.

branch is synonymous with secondary, tertiary axis, etc.

RW notes are somewhat different. Say that stem is the primary axis, branch is all second or higher order axes. Therefore, definition of stem is: A shoot axis that is the primary axis of a plant. If you define stem by having nodes and internodes, that does not exclude secondary axes.

2. Shoot (PO:0009006)

shoot

current def'n: Part of the sporophyte composed of the stems and leaves, and includes shoot apical meristems. [source: POC:curators]

Problem: Shoot has no is_a parent- should be a collective plant structure or a plant organ?

merges into shoot system (new term)

proposed def'n: The axial system of a plant that only includes shoot apical meristems and the structures that arise from them.

Comment: may bear leaves and buds.

parentage: plant system >shoot system >>vegetative shoot system (new term),

vegetative shoot system proposed def'n: A shoot system that only bears vegetative structures.

Note: the root system and shoot system have no parts in common.

plant system >shoot system >reproductive shoot system (new term): proposed def'n: A shoot system that bears reproductive structures.

3. Tuber terms(PO:0004543)

tuber

see comments from 6-29 meeting

new proposed def'n: A swollen or enlarged storage stem.

comment: may have with determinate growth.

We will look into whether or not tubers are determinate or not, vs rhizomes

proposed def'n: A swollen or enlarged storage axillary shoot system.


  • Subterranean tuber (PO:0004547)

is_a 'tuber' and part_of 'rhizome'

current def'n: A swollen rhizome or a part of the rhizome with determinate growth. [source: POC:curator]

proposed def'n: A tuber that is part of a rhizome.


  • aerial tuber (PO:0004548)

current def'n: An axillary shoot with a swollen stem.

proposed def'n: A tuber that is above ground

4. rhizome (PO:0004542)

(need to add link to SF tracker)- under 'stem'

Current def'n: Underground shoot. [source: POC:curators]'

proposed def'n: A stem that grows horizontally and produces shoots above and roots or rhizoids below.

Comment: Usually produces scale-like leaves, may produce rhizoids, especially in ferns or Pteridophytes.

5. Stolon (PO:0003024)

(need to add link to SF tracker)

current def'n: A slender, prostrate or trailing above-ground stem which produces roots and sometimes erect shoots at its nodes. [source: APWeb:Glossary]

but it is classified as a shoot.

6. stalk (PO:0025066)

(See SF Tracker: stalk)

This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.

current def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.

Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.

-made it a child of cardinal organ part (as per its definition) rather than an organ.


Proposed children of stalk: (Test: do all of these fit the definition?)

  • filament: The stalk of a stamen.(stamen:organ)
  • petiole: The stalk of a leaf. (leaf:organ)
  • petiolule: The stalk of a leaflet (leaflet:cardinal organ part)
  • funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)
  • gynophore: The stalk at the base of the ovary.

(ovary: cardinal organ part)


current def'n: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ)


current def'n: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves.

proposed def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).


current def'n: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]

proposed def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).


Note: We also have the term 'stem'. We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.



Terms from last week

1. fruit (See SF Tracker: fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.


Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it). Dbx ref to parthenogenesis: Medical subject heading Ontology D010312


Barry suggested that we reword the second half of the definition, because the final word 'it' was ambiguous about what it was referring to, and the use of the word 'other' was unclear. We agreed that the second part of the definition about other floral structures should go into the comments section. Started to discuss whether or not the seed should be included as part of the definition (fruit contains seed), but ran out of time. To be continued next meeting.



2. Embryo (See SF Tracker: embryo)


Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants


(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes -add a comment?

Relationships:

(1) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity (2) develops_from zygote (see comment above) Usually (3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)


Other Items

AmiGO issues

Cross products Media:PO-corv-2010.pdf

8. Next meeting scheduled for: Weds July 14th, 10am PDT

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