Difference between revisions of "POC Conf. Call 5-24-11"

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* Reviews of the new version for release and the associated webinar: [[Plant_Ontology_Webinar-_May_2011_release]]  In progress...
 
* Reviews of the new version for release and the associated webinar: [[Plant_Ontology_Webinar-_May_2011_release]]  In progress...
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=Upcoming meetings 2011:=
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'''[http://www.phenotypercn.org/?page_id=458 Phenotype RCN Meeting]: June 1-3rd, Boulder CO'''
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'''Overall goals for this plant working group meeting (from preliminary agenda):'''
 +
 +
Discuss how PO (Plant Ontology) can serve as the reference ontology for all plants and come up with a list of specific changes that will be needed.  Explore how links can be made to taxanomic databases like RegNum to define the taxonomic scope of terms. Clarify the role of TO (trait ontology) - should it be used as a set of pre-composed EQ terms for all plant taxa and all areas of plant biology including systematics?
 +
 +
PJ, LC and RW will attend
 +
 +
 +
Tasks:
 +
1.  Examine the children of ‘leaf’ in PO (PO:0025034), looking at terms, definitions and relationships to determine what’s missing or in need of updating, generate a list of changes needed for this subsection of PO to serve as a reference anatomy ontology for all plants, look for terms with homology relationships and examine how these terms are related within PO. 
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2.  Within ‘leaf’ subsection of PO, find terms where database cross-references to taxonomic nodes within RegNum would be useful for delimiting which taxa the term applies to.  Find appropriate IDs within RegNum that could be used as dbxrefs for these PO terms.
 +
 +
3.  Examine a list of leaf-related characters (from RegNum or other sources), determine whether entity and attribute terms exist in PO and PATO that could be used to construct these characters, discuss whether the precomposed character terms should be housed in TO or elsewhere (review TO ‘leaf anatomy and morphology trait’ as needed), set up a character matrix and determine whether the value terms needed to populate the matrix exist in PATO.
 +
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4. Using the character matrix, discuss what ontology terms and other resources will be needed for annotation of quantitative traits (e.g. leaf length, width, area, dry weight, specific leaf area)
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 +
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'''[http://www.iplantcollaborative.org/2011/02/09/2011-semantic-web-workshop-june-6-7-santa-fe-nm 2011 Semantic Web Workshop] June 6th and 7th, Santa Fe, NM.
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'''
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Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
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-JE and JP will be attending
 +
 +
-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.
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For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
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'''Botany 2011 Meeting [[http://www.botanyconference.org/ Botany 2011]]'''  St. Louis, MO at the Chase Park Plaza, July 9-13.
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Societies participating:
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Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).
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Anybody going??
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'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
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July 26-30,  2011
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Buffalo, New York
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[http://icbo.buffalo.edu ICBO]
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LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability"
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along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
 +
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'''Full-Day Workshops Schedule:'''
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'''July 26 9am-6pm'''  The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
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'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
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'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
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'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
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- LC will attend and represent the PO.  Invite other plant people?
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'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
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[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
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For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
 +
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Gramene will be putting together a workshop again, focusing on pathways.  LC and PJ will present a PO poster.
 +
 +
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
 +
 +
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'''* International Botanical Congress (IBC2011)'''
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July 23rd-30th 2011, Melbourne, Australia'''
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Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
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Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.
 +
 +
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
 +
 +
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details

Revision as of 14:12, 23 May 2011

POC meeting, Webex Conference Call; Date: Tuesday May 24th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:


Acceptance of the minutes from the POC_Conf._Call_5-17-11?

Items arising from previous meetings:

Details for the Upcoming Release:

Upcoming meetings 2011:

Phenotype RCN Meeting: June 1-3rd, Boulder CO

Overall goals for this plant working group meeting (from preliminary agenda):

Discuss how PO (Plant Ontology) can serve as the reference ontology for all plants and come up with a list of specific changes that will be needed. Explore how links can be made to taxanomic databases like RegNum to define the taxonomic scope of terms. Clarify the role of TO (trait ontology) - should it be used as a set of pre-composed EQ terms for all plant taxa and all areas of plant biology including systematics?

PJ, LC and RW will attend


Tasks: 1. Examine the children of ‘leaf’ in PO (PO:0025034), looking at terms, definitions and relationships to determine what’s missing or in need of updating, generate a list of changes needed for this subsection of PO to serve as a reference anatomy ontology for all plants, look for terms with homology relationships and examine how these terms are related within PO.

2. Within ‘leaf’ subsection of PO, find terms where database cross-references to taxonomic nodes within RegNum would be useful for delimiting which taxa the term applies to. Find appropriate IDs within RegNum that could be used as dbxrefs for these PO terms.

3. Examine a list of leaf-related characters (from RegNum or other sources), determine whether entity and attribute terms exist in PO and PATO that could be used to construct these characters, discuss whether the precomposed character terms should be housed in TO or elsewhere (review TO ‘leaf anatomy and morphology trait’ as needed), set up a character matrix and determine whether the value terms needed to populate the matrix exist in PATO.

4. Using the character matrix, discuss what ontology terms and other resources will be needed for annotation of quantitative traits (e.g. leaf length, width, area, dry weight, specific leaf area)



2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.


Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.

Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).

Anybody going??


* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?


*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011


For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

Gramene will be putting together a workshop again, focusing on pathways. LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.



* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

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