Difference between revisions of "POC Conf. Call 5-11-10"

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Acceptance of the minutes from last weeks meeting? All in favor?
 
Acceptance of the minutes from last weeks meeting? All in favor?
 +
  
 
== Agenda: ==
 
== Agenda: ==
 +
 +
 +
'''1.  Discussion of plant cell child terms:'''
 +
 +
* '''Cell Type Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME. '''
 +
Laurel and Ramona will attend and will give a 10-15 minute presentation.
 +
 +
Scientific agenda will include:
 +
 +
1) Review and discussion of the ongoing work on specific areas of the Cell Ontology
 +
 +
2) Resolution of issues regarding the high level structure of the Cell Ontology
 +
 +
3) Relations to be employed and external ontologies to utilize in construction of logical definitions for cross-product terms
 +
 +
4) Organization of outreach efforts to import cell type terms from other ontologies and resources
 +
 +
5) Discussion about software enhancements to the AmiGO tool to enable and search of GO annotations that involve coannotation to CL terms
 +
 +
6) Applications of the CL (Cell Ontology)
 +
 +
 +
'''Questions to consider/Discuss:'''
 +
 +
 +
-Plant cell child terms: organization, completeness, definitions. Are we happy with them, or do we plan on a major overhaul?
 +
 +
-- [http://plantontology.org/amigo/go.cgi?action=minus_node&search_constraint=terms&query=PO:0000423&session_id=5918b1272559194 PO browser with all cell types expanded]
 +
 +
- List of PO plant cell types that are not in the Cell.obo file (thanks Rex!). Do we want to request that these terms be included in the CL?
 +
 +
- Need to think about tissues and organs that we and CL might want to use for cross-product definitions.
 +
 +
- Should we aim for complete redundancy between cells in PO and plant cells in CL?
 +
 +
 +
 +
* Laurel, Ramona and Rex had a brief discussion about plant cells at the end of the meeting.  Rex said he made the list of terms that were in the PO but not the CL by going through the two ontologies term by term. Ramona said there do not appear to be any terms that are in the CL but not the PO, but we need to check systematically.''
 +
 +
* The two ontologies have similar structure, with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.''
 +
 +
* In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.''
 +
 +
 +
 +
 +
 +
 +
 +
Items carried over from last week's agenda:
 +
 +
 +
'''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
 +
 +
 +
 +
'''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
 +
 +
(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)
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
'
 +
 +
* '''Cell Ontology Workshop''' on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME. Laurel and Ramona will attend.
 +
 +
Scientific agenda will include:
 +
 +
1) Review and discussion of the ongoing work on specific areas of the Cell Ontology
 +
 +
2) Resolution of issues regarding the high level structure of the Cell Ontology
 +
 +
3) Relations to be employed and external ontologies to utilize in construction of logical definitions for cross-product terms
 +
 +
4) Organization of outreach efforts to import cell type terms from other ontologies and resources
 +
 +
5) Discussion about software enhancements to the AmiGO tool to enable and search of GO annotations that involve coannotation to CL terms
 +
 +
6) Applications of the CL (Cell Ontology)
 +
 +
 +
 +
 +
 +
''4. Upcoming Conferences and Meetings: Updates'''
 +
 +
 +
  
 
'''New (older) items for discussion:'''  
 
'''New (older) items for discussion:'''  
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Items carried over from last week's agenda:
 
Items carried over from last week's agenda:
−
 
−
'''4. 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.
 
−
 
−
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.
 
−
 
−
'''*receptacle:''' The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators].
 
−
(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)
 
−
 
−
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
 
−
 
−
 
−
'''*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
 
−
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]
 
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972236&group_id=76834&atid=835555/ pulvinus])
 
−
 
−
-currently is_a (an) organ
 

Revision as of 23:40, 4 May 2010

POC meeting, Webex Conference Call; Date: May 11th, 2010 10am (PDT)


Acceptance of the minutes from last weeks meeting? All in favor?


Agenda:

1. Discussion of plant cell child terms:

  • Cell Type Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME.

Laurel and Ramona will attend and will give a 10-15 minute presentation.

Scientific agenda will include:

1) Review and discussion of the ongoing work on specific areas of the Cell Ontology

2) Resolution of issues regarding the high level structure of the Cell Ontology

3) Relations to be employed and external ontologies to utilize in construction of logical definitions for cross-product terms

4) Organization of outreach efforts to import cell type terms from other ontologies and resources

5) Discussion about software enhancements to the AmiGO tool to enable and search of GO annotations that involve coannotation to CL terms

6) Applications of the CL (Cell Ontology)


Questions to consider/Discuss:


-Plant cell child terms: organization, completeness, definitions. Are we happy with them, or do we plan on a major overhaul?

-- PO browser with all cell types expanded

- List of PO plant cell types that are not in the Cell.obo file (thanks Rex!). Do we want to request that these terms be included in the CL?

- Need to think about tissues and organs that we and CL might want to use for cross-product definitions.

- Should we aim for complete redundancy between cells in PO and plant cells in CL?


  • Laurel, Ramona and Rex had a brief discussion about plant cells at the end of the meeting. Rex said he made the list of terms that were in the PO but not the CL by going through the two ontologies term by term. Ramona said there do not appear to be any terms that are in the CL but not the PO, but we need to check systematically.
  • The two ontologies have similar structure, with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.
  • In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.




Items carried over from last week's agenda:


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


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)





'

  • Cell Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME. Laurel and Ramona will attend.

Scientific agenda will include:

1) Review and discussion of the ongoing work on specific areas of the Cell Ontology

2) Resolution of issues regarding the high level structure of the Cell Ontology

3) Relations to be employed and external ontologies to utilize in construction of logical definitions for cross-product terms

4) Organization of outreach efforts to import cell type terms from other ontologies and resources

5) Discussion about software enhancements to the AmiGO tool to enable and search of GO annotations that involve coannotation to CL terms

6) Applications of the CL (Cell Ontology)



4. Upcoming Conferences and Meetings: Updates'



New (older) items for discussion:

4. stem (See SF Tracker stem)

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

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.


5. stalk (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.

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 a 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)
  • 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: leaf rachis)
  • 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: peduncle)

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

  • pedicel: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]

(See SF Tracker: 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.


Items carried over from last week's agenda:

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