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

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POC meeting, Webex Conference Call; Date: May 11th, 2010 10am (PDT)
 
POC meeting, Webex Conference Call; Date: May 11th, 2010 10am (PDT)
 +
 +
''Minutes are in italics below each agenda item.''
 +
 +
''In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)''
 +
 +
Collaborators: Rex Nelson-SOYbase, USDA-ARS, Ames, Iowa
 +
 +
''Absent: Chris Mungall (Lawrence Berkeley National Lab), Alejandra Gandolfo, (Cornell University)''
  
  
 
Acceptance of the minutes from last weeks meeting? All in favor?
 
Acceptance of the minutes from last weeks meeting? All in favor?
 +
 +
''There were no additions, deletions or changes to last weeks minutes.''
  
 
== Agenda: ==
 
== Agenda: ==
 +
 +
 +
'''1.  Discussion of the Cell Type Ontology and our plant cell terms in preparation for the workshop in Bar Harbor.'''
 +
 +
(Cell Type Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME)
 +
 +
 +
'''Questions to Consider/Discuss:'''
 +
 +
*Introduction to the Cell Type Ontology- what is it and what are their goals? 
 +
[http://bioportal.bioontology.org/visualize/42165 Browse Cell Type Ontology on BioPortal]
 +
 +
Based on the 2005 Genome Biology paper [http://genomebiology.com/2005/6/2/R21 Cell Type Ontology, Genome Biology, 2005], the goals of the Cell Type Ontology are to:
 +
*Describe the cell types of the major model organisms, both animal and plant
 +
*Facilitate cross-organism queries in a single database
 +
*explicitly sets out to include cell types from all the major model organisms within a common framework
 +
*incorporate phenotypic information about these cell types and is thus far more comprehensive in its cellular detail than these other resources
 +
*provide organism-independent knowledge as well as cell-type unique identifiers (ID) that can be incorporated into any database holding cell-type-associated knowledge
 +
*expected use cataloging phenotypes and gene expression patterns
 +
 +
[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010#Agenda Cell Type Ontology Workshop]
 +
 +
 +
*Laurel and Ramona will attend and will give a 10-15 minute presentation
 +
Points:
 +
Basic goals of PO:
 +
 +
*to encompass all plants
 +
 +
*is_a completeness
 +
 +
*machine-readable definitions
 +
 +
*separation of ''in vitro'' and ''in vivo'' plant cell terms
 +
 +
*Re-organization of the plant cell terms:
 +
 +
*plant cell organization mirrors organization of plant structure with cell types that are specific to sporophytes, gametophytes and whole plant (can occur in gametophyte or sporophyte):
 +
 +
sporophytic cell is_a plant cell that is part_of sporophyte; example: apical cell (part of embryo)
 +
 +
gametophytic cell is_a plant cell that is part_of gametophyte; example: antipodal (part of megagametophyte)
 +
 +
whole plant cell is_a plant cell that can occur in a gametophyte or sporophyte; example: axial cell
 +
 +
 +
-- [http://plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:0000274&session_id=5918b1272559194 current PO browser with all cell types expanded]
 +
 +
-- [http://dev.plantontology.org:8080/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:0025029&session_id=7712b1273499903 dev PO browser with possible new organization for plant cell types]
 +
 +
*Should we aim for complete '''redundancy between cells in PO and plant cells in CL'''?
 +
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?
 +
 +
*If CL is going to use PO terms, definitions, and structures, should they use our ID numbers (see below:)?
 +
 +
*Should there be hyper links to the PO browser from the CL?
 +
 +
- [http://www.obofoundry.org/wiki/index.php/Identifiers From OBO foundry Identifiers wiki page]:
 +
 +
'''Reuse'''
 +
Entries that are re-used in a second, derivative ontology should NOT make copies and give the copied entities new IDs. Connection to the original term via an xref is firmly discouraged. One primary reason is that xrefs are used for many purposes, and do not imply that the terms are equivalent. The original ids must be used directly in the derivative ontology.
 +
 +
 +
 +
General Comments:
 +
 +
* The two ontologies have similar structure (at least under 'plant cell'), 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.''
 +
 +
 +
''Barry gave some background on what the CL is trying to accomplish. Said that the Bard et al. 2005 paper is largely out of date. They are currently aiming to have an ontology where each term has a single parent, based on structural properties of cells. Shared a paper that describes an ontology for dendritic cells (http://www.biomedcentral.com/1471-2105/10/70/abstract/) and provides an example of how the CL is trying to structure their entire ontology. Suggested that the PO should try to find cell types that are very general, based on their structure, and submit those to CL. We discussed parenchymatic cells as a cell type that is unique to plants and epidermal cells as a cell type that is shared by plants and animals (at least in name), but actually represents two different types of cells.''
 +
 +
 +
''There was general agreement that plant cell types should be defined and curated by, and annotated in, the PO, but it was not clear if upper level terms that appear in the CL would have CL or PO id's. We will need to discuss this at the meeting.''
 +
 +
  
 
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.
+
'''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])
 +
 
 +
''Discussion of embryo was postponed until next meeting.''
 +
 
 +
 
 +
'''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)
 +
 
 +
 
 +
 
 +
 
 +
'''4. Upcoming Conferences and Meetings:''' Updates
 +
 
 +
''There was no discussion of upcoming conferences and meeting (other than the CL meeting).''
 +
 
 +
 
 +
 
 +
'''* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.'''
 +
 
 +
Pankaj suggested we plan on meeting for two days. Dennis can make June 30th, but has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th.
 +
 
 +
Alejandra cannot travel that day -- can attend via conference call.
 +
 
 +
Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th.
 +
''Ramona has sent a request to schedule her talk on the 27th or 28th.''
 +
Barry will be in France this week and can't attend.
 +
What about Chris?
 +
 
 +
Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).
 +
 
 +
 
 +
'''* Bio-Ontologies 2010: Semantic Applications in Life Sciences.''' July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona are registered.
 +
 
 +
Our one page write up has been selected for a 'flash update talk' along with the poster.  Final revisions need to be submitted by Friday May 14th. 
 +
 
 +
'''* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada.''' Laurel, Pankaj going,
 +
PO Poster presentation and Annotation Workshop with Gramene.
 +
 
 +
Laurel is looking into the possibility of hosting a booth with other database groups. SGN and maizeGDB are interested and she will check with TAIR and Gramene. The estimated costs are $1600 for the plain booth (no carpet, electricity or tables). This could be shared or PJ said POC could host it.
 +
 
 +
We should prepare a brochure to distribute, similar to the one Gramene has.
 +
 
 +
Annotation workshop with Gramene is scheduled for '''Saturday July 31, 8am-12pm'''. more details TBA
 +
 
 +
 
 +
'''* International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia'''. Important dates (http://www.ibc2011.com/Dates.htm):
 +
 
 +
Dennis and Alejandra are already planning to attend IBC2011 and speak in other symposia.
 +
 
 +
Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities.
 +
 
 +
Pankaj will be co-organizer with Ramona.  Laurel and Ramona are interested in going and speaking if funds are available.
  
−
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.
+
Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if the proposal is accepted.
  
−
'''*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)
+
* '''Latin American Congress of Botany''' (http://www.botanica-alb.org/X_Congreso/index.php). La Serena, Chile, October 4-10; MAG: "I am not sure about due dates for this one due to the earthquake".
  
−
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
+
from 3-23-10: Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.
−
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
 
  
 +
* Annotation workshops to be held at NYBG in fall 2010. Date TBD. Will invite outside experts, scientists, students and postdocs.
  
−
'''*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
+
'''8. Next meeting scheduled for '''Tuesday May 25th at 10am PDT'''.'''

Latest revision as of 11:35, 12 May 2010

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

Minutes are in italics below each agenda item.

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)

Collaborators: Rex Nelson-SOYbase, USDA-ARS, Ames, Iowa

Absent: Chris Mungall (Lawrence Berkeley National Lab), Alejandra Gandolfo, (Cornell University)


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

There were no additions, deletions or changes to last weeks minutes.

Agenda:

1. Discussion of the Cell Type Ontology and our plant cell terms in preparation for the workshop in Bar Harbor.

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


Questions to Consider/Discuss:

  • Introduction to the Cell Type Ontology- what is it and what are their goals?

Browse Cell Type Ontology on BioPortal

Based on the 2005 Genome Biology paper Cell Type Ontology, Genome Biology, 2005, the goals of the Cell Type Ontology are to:

  • Describe the cell types of the major model organisms, both animal and plant
  • Facilitate cross-organism queries in a single database
  • explicitly sets out to include cell types from all the major model organisms within a common framework
  • incorporate phenotypic information about these cell types and is thus far more comprehensive in its cellular detail than these other resources
  • provide organism-independent knowledge as well as cell-type unique identifiers (ID) that can be incorporated into any database holding cell-type-associated knowledge
  • expected use cataloging phenotypes and gene expression patterns

Cell Type Ontology Workshop


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

Points: Basic goals of PO:

  • to encompass all plants
  • is_a completeness
  • machine-readable definitions
  • separation of in vitro and in vivo plant cell terms
  • Re-organization of the plant cell terms:
  • plant cell organization mirrors organization of plant structure with cell types that are specific to sporophytes, gametophytes and whole plant (can occur in gametophyte or sporophyte):

sporophytic cell is_a plant cell that is part_of sporophyte; example: apical cell (part of embryo)

gametophytic cell is_a plant cell that is part_of gametophyte; example: antipodal (part of megagametophyte)

whole plant cell is_a plant cell that can occur in a gametophyte or sporophyte; example: axial cell


-- current PO browser with all cell types expanded

-- dev PO browser with possible new organization for plant cell types

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

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?

  • If CL is going to use PO terms, definitions, and structures, should they use our ID numbers (see below:)?
  • Should there be hyper links to the PO browser from the CL?

- From OBO foundry Identifiers wiki page:

Reuse Entries that are re-used in a second, derivative ontology should NOT make copies and give the copied entities new IDs. Connection to the original term via an xref is firmly discouraged. One primary reason is that xrefs are used for many purposes, and do not imply that the terms are equivalent. The original ids must be used directly in the derivative ontology.


General Comments:

  • The two ontologies have similar structure (at least under 'plant cell'), 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.


Barry gave some background on what the CL is trying to accomplish. Said that the Bard et al. 2005 paper is largely out of date. They are currently aiming to have an ontology where each term has a single parent, based on structural properties of cells. Shared a paper that describes an ontology for dendritic cells (http://www.biomedcentral.com/1471-2105/10/70/abstract/) and provides an example of how the CL is trying to structure their entire ontology. Suggested that the PO should try to find cell types that are very general, based on their structure, and submit those to CL. We discussed parenchymatic cells as a cell type that is unique to plants and epidermal cells as a cell type that is shared by plants and animals (at least in name), but actually represents two different types of cells.


There was general agreement that plant cell types should be defined and curated by, and annotated in, the PO, but it was not clear if upper level terms that appear in the CL would have CL or PO id's. We will need to discuss this at the meeting.


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


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)

Discussion of embryo was postponed until next meeting.


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)



4. Upcoming Conferences and Meetings: Updates

There was no discussion of upcoming conferences and meeting (other than the CL meeting).


* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.

Pankaj suggested we plan on meeting for two days. Dennis can make June 30th, but has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th.

Alejandra cannot travel that day -- can attend via conference call.

Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th. Ramona has sent a request to schedule her talk on the 27th or 28th. Barry will be in France this week and can't attend. What about Chris?

Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).


* Bio-Ontologies 2010: Semantic Applications in Life Sciences. July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona are registered.

Our one page write up has been selected for a 'flash update talk' along with the poster. Final revisions need to be submitted by Friday May 14th.

* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation and Annotation Workshop with Gramene.

Laurel is looking into the possibility of hosting a booth with other database groups. SGN and maizeGDB are interested and she will check with TAIR and Gramene. The estimated costs are $1600 for the plain booth (no carpet, electricity or tables). This could be shared or PJ said POC could host it.

We should prepare a brochure to distribute, similar to the one Gramene has.

Annotation workshop with Gramene is scheduled for Saturday July 31, 8am-12pm. more details TBA


* International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm):

Dennis and Alejandra are already planning to attend IBC2011 and speak in other symposia.

Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities.

Pankaj will be co-organizer with Ramona. Laurel and Ramona are interested in going and speaking if funds are available.

Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if the proposal is accepted.


from 3-23-10: Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.


  • Annotation workshops to be held at NYBG in fall 2010. Date TBD. Will invite outside experts, scientists, students and postdocs.


8. Next meeting scheduled for Tuesday May 25th at 10am PDT.

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