Difference between revisions of "POC Conf. Call 4-16-13"

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POC meeting, Webex Conference Call; Date: Tuesday April 16th, 2013 10am PST/1pm EST
 
POC meeting, Webex Conference Call; Date: Tuesday April 16th, 2013 10am PST/1pm EST
  
−
In attendance:'  
+
In attendance:''Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Marie Alejandra Gandolfo (Cornell)''  
  
−
Absent:
+
Absent: ''Dennis W Stevenson (NYBG)''
  
−
=Items for discussion=
 
−
- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting
 
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3609161&group_id=76834&atid=835555 accessory branch]==
+
==[https://sourceforge.net/tracker/?func=detail&aid=3609161&group_id=76834&atid=835555 accessory branch or accessaory paraclade]==
 
Request from JL for the Plant Phenotype project for the term 'accessory branch' or accessory paraclade:
 
Request from JL for the Plant Phenotype project for the term 'accessory branch' or accessory paraclade:
  
−
The term 'accessory branch' is used in the description of the different types of phytomers (pg. 2724, top of left column):
+
Suggested term and def'n: accessory branch (new PO:ID): A shoot axis (PO:00025029) that develops from a shoot node (PO:0005004) that has produced at least one axillary branch (PO:0006343)
  
−
"...In both of these phytomer types, a second branch (accessory branch) may later develop between the axillary branch and its subtending leaf (Fig. 1A)."  [http://dev.biologists.org/content/121/9/2723.long  Talbert et al, 1995]
+
Literature citation: The term 'accessory branch' is used in the description of the different types of phytomers (pg. 2724, top of left column):
  
 +
"...In both of these phytomer types, a second branch (accessory branch) may later develop '''between the axillary branch and its subtending leaf''' (Fig. 1A)."  [http://dev.biologists.org/content/121/9/2723.long  Talbert et al, 1995]
 +
 +
This figure is actually referring to an accessory paraclade, not simply an accessory branch.
  
 
[[File:Talbert 1995, Fig 1.png]]
 
[[File:Talbert 1995, Fig 1.png]]
  
  
−
Comments: DWS: Accessory bud is the term used when more than one axillary bud occurs at a node as in many cacti and legumes.
+
We have the term paraclade, but it needs to be refined:
 +
 
 +
Current def'n: '''paraclade (PO:0004720)'''- An inflorescence branch (PO:0009081) that ends in an inflorescence that repeats the main inflorescence.
 +
 
 +
''Question: are they both from the same axillary bud meristem (PO:0000232)or is there more than one bud?''
  
−
We currently do not use the term "accessory", but we do have paraclade:
+
Comments: from SF: DWS:  Accessory bud is the term used when more than one axillary bud occurs at a node as in many cacti and legumes.
  
−
paraclade (PO:0004720)- An inflorescence branch that ends in an inflorescence that repeats the main inflorescence.
+
''Need to differentiate between the accessory paraclade in the rosette and cauline positions''
  
 +
''The term paraclade will be made obsolete and made an exact synonym of inflorescence branch (PO:0009081), since they mean the same thing. 
  
−
This figure is actually referring to an accessory paraclade, not simply an accessory branch.
+
inflorescence branch (PO:0009081): An inflorescence axis (PO:0020122) that is a branch forming from a primary or higher order inflorescence axis.
  
 
see this paper for additional information
 
see this paper for additional information
Line 32: Line 38:
 
http://aob.oxfordjournals.org/content/early/2011/03/01/aob.mcr039.full
 
http://aob.oxfordjournals.org/content/early/2011/03/01/aob.mcr039.full
  
−
== [https://sourceforge.net/tracker/index.php?func=detail&aid=3028442&group_id=76834&atid=835555 branch]==
 
−
branch (PO:0025073):  revised definition:  A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).
 
  
−
revised comment: In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3609161&group_id=76834&atid=835555 accessary paraclade] etc==
 +
Request from JL for the Plant Phenotype project for the term 'accessory branch' or accessory paraclade:
  
 +
Suggested term and def'n: accessory branch (new PO:ID): A shoot axis (PO:00025029) that develops from a shoot node (PO:0005004) that has produced at least one axillary branch (PO:0006343)
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3610120&group_id=76834&atid=835555 trichome tip]==
+
Literature citation: The term 'accessory branch' is used in the description of the different types of phytomers (pg. 2724, top of left column):
−
The problem with this is that sometimes a trichome is unicellular and sometimes it is multicellular. Direct child of plant structure.  
 
−
Part of a trichome is  not a cardinal organ part.
 
  
−
multicellular trichome (PO:0025162) A portion of plant tissue that forms a non-sclerified outgrowth from the epidermis. [source: POC:curators]  
+
"...In both of these phytomer types, a second branch (accessory branch) may later develop '''between the axillary branch and its subtending leaf''' (Fig. 1A)."  [http://dev.biologists.org/content/121/9/2723.long  Talbert et al, 1995]
  
 +
This figure is actually referring to an accessory paraclade, not simply an accessory branch.
  
−
So the tip would be a portion of plant tissue
+
We had an extensive discussion last week, so to help clarify things I took the figure from last week and labelled it with the new terms
  
−
multicellular trichome tip (new): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162).
+
Annotated figure:
  
−
part_of multicellular trichome
+
[[File:Talbert-paraclade terms.jpg]]
  
 +
== [https://sourceforge.net/tracker/index.php?func=detail&aid=3028442&group_id=76834&atid=835555 branch]==
 +
branch (PO:0025073):  revised definition:  A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).
  
−
==[http://sourceforge.net/tracker/?func=detail&aid=3609180&group_id=76834&atid=835555 petal nanoridges]==
+
revised comment: In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.
  
−
Suggested Definition: Microscopic, often parallel, ridges composed of cutin occurring on the surface of petals.
 
−
Parent/relationship: part_of petal epidermis (PO:0006041)
 
  
−
Reference: PMID 19959665
+
==Changes that were made to the [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3150504&group_id=76834 inflorescence branch] terms==
  
−
These are composed of cutin.
+
[[File:Inflorescence branches.jpg]]
  
 +
'''* primary inflorescence branch (PO:0006321):''' An inflorescence branch (PO:0009081) arising from a first order inflorescence axis (PO:0025104).
 +
was 'second order inflorescence axis' - swapped name and exact synonym and removed the related synonym: second order inflorescence branch as it was inconsistent.
  
−
plant cuticle ridge A portion of plant cuticle (PO:000022) that forms a ridge, may be overlayed with epicuticluar wax (PO:0025388).
+
'''* second order inflorescence branch (PO:0006322)'''- An inflorescence branch (PO:0009081) arising from a primary inflorescence branch (PO:0006321). (was third order inflorescence axis).
 +
Added exact synonyms: second order paraclade, secondary inflorescence branch, third order inflorescence axis, Removed the related synonym:  second order  inflorescence branch as it was inconsistent.
  
 +
'''* third order inflorescence branch (PO:0025105):''' An inflorescence branch (PO:0009081) arising from a secondary inflorescence branch (PO:0006322). (was fourth order third order inflorescence axis (PO:0025105).
  
−
epicuticular wax PO:0025388 
+
Added exact synonyms: third order paraclade, third order inflorescence branch, fourth order inflorescence axis, tertiary inflorescence branch
  
−
A portion of cuticular wax that forms crystalloids or a smooth film on the exterior of a cuticle. [source: PMID:12467640, PO_Ref:00010]
+
Please see https://sourceforge.net/tracker/index.php?func=detail&aid=3609161&group_id=76834&atid=835555
 +
for details about the paraclade terms
  
−
Comment: Epicuticular waxes may take a variety of forms, such as plates, ribbons, tubes, and rods.
+
see this paper for additional information http://aob.oxfordjournals.org/content/early/2011/03/01/aob.mcr039.full
  
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3610120&group_id=76834&atid=835555 trichome tip]==
 +
The problem with this is that sometimes a trichome is unicellular and sometimes it is multicellular. Direct child of plant structure.
 +
Part of a trichome is  not a cardinal organ part.
  
−
=Image annotations=
+
multicellular trichome (PO:0025162)  A portion of plant tissue that forms a non-sclerified outgrowth from the epidermis. [source: POC:curators]
−
Update on the progress on the image annotations:
 
  
−
- AISO to segment and label images with PO terms
 
  
−
- Sample images from DWS, NYBG (~2 dozen) can be used as a test set for segmenting and labeling with PO terms
+
So the tip would be a portion of plant tissue
  
−
- Data submission template for bulk uploads for whole images with keywords
+
multicellular trichome tip (new): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162).
  
−
- import script for whole images, can be used for any images with keyword associations, pull in stuff from Plantsystematics.org
+
part_of multicellular trichome
  
−
- first whole images, then segmented ones
+
''Decided to make new term: unicellular trichome, rather than having it a synonym of trichome cell.  The we will make  general terms trichome tip and trichome apex to be the parents of the parts of the multicellular trichome. Will request the parts of the unicellular trichome from GO.''
  
−
- image annotation tool, keywords, uses tab delimited file
+
Made new term:
 +
* trichome apex (new PO:0025550): A plant structure (PO:0009011) that is the apical most portion of a trichome (PO:0000282).
 +
comment: An apex of a unicellular trichome is a GO sub-cellular component GO:xxxxxxx. Will be requested from GO. Added dbxref to OBO_SF_PO:3610120 is_a plant structure, part_of trichome
 +
* multicellular trichome apex (new PO:0025551): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162). added exact synonym: apex of a multicellular trichome; Added dbxref to OBO_SF_PO:3610120
 +
is_a trichome apex, part_of multicellular trichome (PO:0025551)
  
−
- database and schema has been built to hold the whole images and the parts, along with the keyword annotations
+
* trichome tip (new PO:0025549): A plant structure (PO:0009011) that is the apical most portion of trichome apex (PO:0025550).
 +
is_a plant structure, part of trichome apex.  Comment: A tip of a unicellular trichome is a GO cellular component GO:xxxxxxx. Will be requested from GO. Added dbxref to OBO_SF_PO:3610120, added exact synonym: tip of a multicellular trichome
  
−
- DWS is providing the data for ~3 dozen images (tab delimited file), will be incorporated into the new database
+
* Made multicellular trichome tip (PO:0025535) is_a trichome tip and is_a A portion of plant tissue (PO:0009007). part_of multicellular trichome (PO:0025551), Added dbxref to OBO_SF_PO:3610120
  
−
- DWS has original images (higher res), sending 2 copies, labelled and unlabelled (lower res versions), needs help converting the pdfs into tab-delimited files
+
'''New GO terms:'''
 +
* unicellular trichome apex GO:0090552: "A cell projection part that is the apical most portion of a unicellular trichome." [GOC:PO_curators, PO:0025537]; is_a: GO:0044463 ! cell projection part
  
−
- Need to prioritize which terms need images: PJ: Physco terms, grass florets, root anatomy, SAM (fern and flowering plant), different kinds of veins in leaves, part of ATOL project
+
* unicellular trichome tip GO:0090553: "A cell projection part that is the apical most portion of a unicellular trichome apex." [GOC:PO_curators]; relationship: part_of GO:0090552 ! unicellular trichome apex
  
−
- DWS has images of thorns and prickles, septum, locule, pericarp,
+
See the [https://sourceforge.net/p/geneontology/ontology-requests/10138/ GO tracker] for these terms.
  
−
- New dropbox has  been set up for the Po-Images
+
[[File:Screen Shot 2013-05-24 at 10.15.07 AM.png]]
−
 
 
−
-DWS wants LC to look at the spreadsheet
 
−
 
 
−
=Other Items=
 
−
Chelsea Specht (http://spechtlab.berkeley.edu/) will be visiting OSU to give the Templeton Lecture. Her talk is entitled Petaloidy,  polarity, and pollination: the evolution and diversification of floral form in the Zingiberales.  
 
−
 
 
−
She will be on campus all day Thursday(4/25) and Friday morning (4/26). Should we plan to meet with her?
 
  
 +
''Done, This results in adding two new terms as direct children of plant structure; plus muticellular trichome (is_a portion of plant tissue) and unicellular trichome have dual parentage. Not ideal. see tracker for details''
  
 
=Upcoming meetings and Presentations 2013:=
 
=Upcoming meetings and Presentations 2013:=
Line 129: Line 140:
  
 
*1. To inform members of the Protein, Plant, Gene Ontology communities of  developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies. Specifically:  
 
*1. To inform members of the Protein, Plant, Gene Ontology communities of  developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies. Specifically:  
−
:a. To enhance the PO treatment of plant-related proteins  
+
**a. To enhance the PO treatment of plant-related proteins  
−
:b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages
+
**b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages
 
*2. To contribute to the [http://wiki.plantontology.org/index.php/The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative cROP] (Common Reference Ontologies for Plants) initiative
 
*2. To contribute to the [http://wiki.plantontology.org/index.php/The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative cROP] (Common Reference Ontologies for Plants) initiative
 
*3. To contribute to the ontological understanding of phenotype and disease in all model organisms.
 
*3. To contribute to the ontological understanding of phenotype and disease in all model organisms.
−
*4. To identify potentially fruitful applications which enhanced ontology coordination might bring.  
+
*4. To identify potentially fruitful applications which enhanced ontology coordination might bring.
−
 
 
−
 
 
−
Tentative participant list:
 
−
 
 
−
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?
 
−
 
 
−
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?
 
−
 
 
−
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)
 
−
 
 
−
''Need to share the PO with representatives from the ontologies and resources such as PRO, PIR (Claire O'Donovan), Uniprot. Annotations to newly sequenced plant genomes are going into Plant Ensemble, Uniprot etc.  Want to build early relationship with them to develop quality measures for plant-based ontology annotations.  Section on annotations is needed.''
 
−
 
 
−
''JB wanted to explore genotype and phenotype connections, can only stay for part of the day on Thursday''
 
−
 
 
−
''Need to know who will speak about what. Looking for volunteers.''
 
−
 
 
−
''Separate the sessions on disease and phenotype, include TO discussion to there?''
 
−
 
 
−
''RW presentation on Plant-IDO?, interest in new Plant DO, existing DO is no good (?),  Split phenotype  and diseases into separate sessions.''
 
−
 
 
−
''Reference ontologies need to know how to deal with terms that are used by both plants and animals, e.g. senesence.''
 
−
 
 
−
''Alert attendees to bring applications for the users, biological examples''
 
−
 
 
−
''Notices could be posted in advance of the meeting, send out on PO-announce, will do IBC article later.  Idea for future meeting- plants, human nutrition, toxicity, to include more NIH type people''
 
−
 
 
−
''Travel to Amherst: Need to book our rooms, plan to fly out Thursday afternoon. ''
 
  
 
==1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013==
 
==1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013==

Latest revision as of 01:41, 18 June 2013

POC meeting, Webex Conference Call; Date: Tuesday April 16th, 2013 10am PST/1pm EST

In attendance:Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Marie Alejandra Gandolfo (Cornell)

Absent: Dennis W Stevenson (NYBG)


accessory branch or accessaory paraclade

Request from JL for the Plant Phenotype project for the term 'accessory branch' or accessory paraclade:

Suggested term and def'n: accessory branch (new PO:ID): A shoot axis (PO:00025029) that develops from a shoot node (PO:0005004) that has produced at least one axillary branch (PO:0006343)

Literature citation: The term 'accessory branch' is used in the description of the different types of phytomers (pg. 2724, top of left column):

"...In both of these phytomer types, a second branch (accessory branch) may later develop between the axillary branch and its subtending leaf (Fig. 1A)." Talbert et al, 1995

This figure is actually referring to an accessory paraclade, not simply an accessory branch.

Talbert 1995, Fig 1.png


We have the term paraclade, but it needs to be refined:

Current def'n: paraclade (PO:0004720)- An inflorescence branch (PO:0009081) that ends in an inflorescence that repeats the main inflorescence.

Question: are they both from the same axillary bud meristem (PO:0000232)or is there more than one bud?

Comments: from SF: DWS: Accessory bud is the term used when more than one axillary bud occurs at a node as in many cacti and legumes.

Need to differentiate between the accessory paraclade in the rosette and cauline positions

The term paraclade will be made obsolete and made an exact synonym of inflorescence branch (PO:0009081), since they mean the same thing.

inflorescence branch (PO:0009081): An inflorescence axis (PO:0020122) that is a branch forming from a primary or higher order inflorescence axis.

see this paper for additional information

http://aob.oxfordjournals.org/content/early/2011/03/01/aob.mcr039.full


accessary paraclade etc

Request from JL for the Plant Phenotype project for the term 'accessory branch' or accessory paraclade:

Suggested term and def'n: accessory branch (new PO:ID): A shoot axis (PO:00025029) that develops from a shoot node (PO:0005004) that has produced at least one axillary branch (PO:0006343)

Literature citation: The term 'accessory branch' is used in the description of the different types of phytomers (pg. 2724, top of left column):

"...In both of these phytomer types, a second branch (accessory branch) may later develop between the axillary branch and its subtending leaf (Fig. 1A)." Talbert et al, 1995

This figure is actually referring to an accessory paraclade, not simply an accessory branch.

We had an extensive discussion last week, so to help clarify things I took the figure from last week and labelled it with the new terms

Annotated figure:

Talbert-paraclade terms.jpg

branch

branch (PO:0025073): revised definition: A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).

revised comment: In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.


Changes that were made to the inflorescence branch terms

Inflorescence branches.jpg

* primary inflorescence branch (PO:0006321): An inflorescence branch (PO:0009081) arising from a first order inflorescence axis (PO:0025104). was 'second order inflorescence axis' - swapped name and exact synonym and removed the related synonym: second order inflorescence branch as it was inconsistent.

* second order inflorescence branch (PO:0006322)- An inflorescence branch (PO:0009081) arising from a primary inflorescence branch (PO:0006321). (was third order inflorescence axis). Added exact synonyms: second order paraclade, secondary inflorescence branch, third order inflorescence axis, Removed the related synonym: second order inflorescence branch as it was inconsistent.

* third order inflorescence branch (PO:0025105): An inflorescence branch (PO:0009081) arising from a secondary inflorescence branch (PO:0006322). (was fourth order third order inflorescence axis (PO:0025105).

Added exact synonyms: third order paraclade, third order inflorescence branch, fourth order inflorescence axis, tertiary inflorescence branch

Please see https://sourceforge.net/tracker/index.php?func=detail&aid=3609161&group_id=76834&atid=835555 for details about the paraclade terms

see this paper for additional information http://aob.oxfordjournals.org/content/early/2011/03/01/aob.mcr039.full

trichome tip

The problem with this is that sometimes a trichome is unicellular and sometimes it is multicellular. Direct child of plant structure. Part of a trichome is not a cardinal organ part.

multicellular trichome (PO:0025162) A portion of plant tissue that forms a non-sclerified outgrowth from the epidermis. [source: POC:curators]


So the tip would be a portion of plant tissue

multicellular trichome tip (new): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162).

part_of multicellular trichome

Decided to make new term: unicellular trichome, rather than having it a synonym of trichome cell. The we will make general terms trichome tip and trichome apex to be the parents of the parts of the multicellular trichome. Will request the parts of the unicellular trichome from GO.

Made new term:

  • trichome apex (new PO:0025550): A plant structure (PO:0009011) that is the apical most portion of a trichome (PO:0000282).

comment: An apex of a unicellular trichome is a GO sub-cellular component GO:xxxxxxx. Will be requested from GO. Added dbxref to OBO_SF_PO:3610120 is_a plant structure, part_of trichome

  • multicellular trichome apex (new PO:0025551): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162). added exact synonym: apex of a multicellular trichome; Added dbxref to OBO_SF_PO:3610120

is_a trichome apex, part_of multicellular trichome (PO:0025551)

  • trichome tip (new PO:0025549): A plant structure (PO:0009011) that is the apical most portion of trichome apex (PO:0025550).

is_a plant structure, part of trichome apex. Comment: A tip of a unicellular trichome is a GO cellular component GO:xxxxxxx. Will be requested from GO. Added dbxref to OBO_SF_PO:3610120, added exact synonym: tip of a multicellular trichome

  • Made multicellular trichome tip (PO:0025535) is_a trichome tip and is_a A portion of plant tissue (PO:0009007). part_of multicellular trichome (PO:0025551), Added dbxref to OBO_SF_PO:3610120

New GO terms:

  • unicellular trichome apex GO:0090552: "A cell projection part that is the apical most portion of a unicellular trichome." [GOC:PO_curators, PO:0025537]; is_a: GO:0044463 ! cell projection part
  • unicellular trichome tip GO:0090553: "A cell projection part that is the apical most portion of a unicellular trichome apex." [GOC:PO_curators]; relationship: part_of GO:0090552 ! unicellular trichome apex

See the GO tracker for these terms.

Screen Shot 2013-05-24 at 10.15.07 AM.png

Done, This results in adding two new terms as direct children of plant structure; plus muticellular trichome (is_a portion of plant tissue) and unicellular trichome have dual parentage. Not ideal. see tracker for details

Upcoming meetings and Presentations 2013:

NCBO Hackathon April 29-30, 2013

The NCBO Hackathon will take place at Stanford University on April 29-30, 2013. This event will focus on projects in biomedical or clinical informatics that can benefit from use of ontology-based technology.

The entire NCBO Team will be available to brainstorm application ideas and to answer development questions. We will also have separate sessions to provide training on the NCBO Web services, the BioPortal SPARQL endpoint, and other topics of interest requested by participants.

If you are thinking of incorporating semantics into your software application, the Hackathon will provide a great opportunity to get a head start on your project.

Phenotype RCN Plant Group Meeting- Ames, Iowa April 30th-May 3rd

We will be meeting to work on the Plant Phenotype Pilot Project, LC is going

PR-PO-GO meeting, May 15-16th 2013

Please see this page for more information: PRO-PO-GO_Meeting

Location: Buffalo, NY

Dates: May 15-16th, 2013.

  • 1. To inform members of the Protein, Plant, Gene Ontology communities of developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies. Specifically:
    • a. To enhance the PO treatment of plant-related proteins
    • b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages
  • 2. To contribute to the cROP (Common Reference Ontologies for Plants) initiative
  • 3. To contribute to the ontological understanding of phenotype and disease in all model organisms.
  • 4. To identify potentially fruitful applications which enhanced ontology coordination might bring.

1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013

S4BIODIV

Registration Information ESWC 2013

Early Registration deadline March 17th

Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.

Held in parallel with the 10th Extended Semantic Web Conference (ESWC 2013)

Workshop date: May 27, 2013

IMPORTANT DATES:

  • Pre-submission inquiry deadline: February 24, 2013 (Abstract up to 500 words)
  • Submission Deadline: March 4, 2013
  • Notification: April 1, 2013
  • Camera ready: April 15, 2013


Note: May be able to send abstract on March 11th and then the final paper by April 15th


TOPICS:

Scientific themes of interest (include but are not limited to):

  • sustainable agriculture
  • plant
  • health and habitat
  • relationship between plant-pests/pathogens
  • usages of plants by community
  • biodiversity conservation
  • ecosystems services
  • quality of biodiversity data


Informatics technologies of interest (include but are not limited to):

  • ontology applications
  • knowledge engineering
  • linked biodiversity data
  • remote sensors
  • mobile devices
  • vizualization tools
  • data mining

MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)

The New York Botanical Garden & Fordham University


ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013

4th International Conference on Biomedical Ontologies 2013 (ICBO2013)

Concordia University, Montreal, Quebec, July 7th - 9th 2013 call for papers

The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.

The event is part of the Semantic Trilogy 2013 featuring:

  • International Conference on Biomedical Ontologies (ICBO 2013)
  • Canadian Semantic Web Symposium (CSWS 2013)
  • Data Integration in the Life Sciences (DILS 2013)

Workshop on Semantic Systems Biology 2013 (SSB2013) will be held as part of the International Conference on Biomedical Ontologies (ICBO2013) at Concordia University, Montreal, Quebec, on July 7th, 2013. The event is part of the Semantic Trilogy 2013 (above)

Topics of interest include, but are not limited to:

  • ontologies & terminologies for modeling computational biology
  • ontologies & terminologies for simulation (and result data) in computational biology/medicine/neuroscience
  • semantic web technologies for description, integration, query and discovery of models, simulations and result data
  • semantic web technologies for biological data and analysis
  • semantic annotations of bio-models
  • applications of ontologies in computational systems biology/medicine/neuroscience
  • semantic platforms for undertaking and visualizing simulation results


We welcome four types of submissions:

  • short papers, up to 4 pages.
  • long papers, up to 7 pages.
  • position papers, up to 1 page.
  • late breaking reports, up to 1 page.

See the ICBO website for further information on the submission types.

All submission are due on Monday, April 15 2013. Notification of acceptance: May 6th, 2013

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract

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