Tuesday Jan 6th, 2015: Difference between revisions

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== Planteome- cROP Meeting: Tuesday Jan 6th, 2015 ==
== Planteome- cROP Meeting: Tuesday Jan 6th, 2015 ==
Who: PJ, LC, JE, DWS, CM, ST, GG, JD
Who: PJ, LC, JE, DWS, CM, ST, GG, JD
Not available: EA, EZ, BS
Not available: EA, EZ, BS
Link to audio recording:  [[File: Planteome 1-6-2015.m4a|thumbnail|Planteome_1-6-2015.m4a]]


{| class="wikitable"
{| class="wikitable"
Line 15: Line 18:
|Elizabeth Arnaud, Bioversity International/CGIAR, France  || CO-PI || Lead on Crop Ontology- crop-specific trait and germplasm ontologies for agronomic databases of crops
|Elizabeth Arnaud, Bioversity International/CGIAR, France  || CO-PI || Lead on Crop Ontology- crop-specific trait and germplasm ontologies for agronomic databases of crops
|-
|-
|Sinisa Todorovic, Oregon State University  || CO-PI || Computer vision, machine learning, and artificial intelligence
|Sinisa Todorovic, School of Electrical Engineering and Computer Science, Oregon State University  || CO-PI || Computer vision, machine learning, and artificial intelligence
|-
|-
|Eugene Zhang, Oregon State University || CO-PI || omputer graphics, scientific visualization, and geometric modeling
|Eugene Zhang, School of Electrical Engineering and Computer Science, Oregon State University || CO-PI || Computer graphics, scientific visualization, and geometric modeling; genome sequence visualization
|-
|-
|Christopher Mungall, Lawrence Berkeley National Laboratory  || CO-PI || Functional Genomics, Gene Ontology, Disease Phenotype Informatics, Logic-based modeling and programming
|Christopher Mungall, Lawrence Berkeley National Laboratory  || CO-PI || Functional Genomics, Gene Ontology, Disease Phenotype Informatics, Logic-based modeling and programming
Line 23: Line 26:
|Barry Smith, University at Buffalo || Ontology consultant || Ontology and its applications, especially in biomedical informatics  
|Barry Smith, University at Buffalo || Ontology consultant || Ontology and its applications, especially in biomedical informatics  
|-
|-
|Georgios V. Gkoutos, University of Aberystwyth, UK ||Senior Personnel, collaborator||Molecular informatics and bioinformatics, association of genotype to phenotype  
|Georgios V. Gkoutos, University of Birmingham, UK ||Senior Personnel, collaborator||Molecular informatics and bioinformatics, association of genotype to phenotype  
|-
|-
|John Doonan, University of Aberystwyth, UK || Senior Personnel, collaborator, Director National Plant Phenomics Centre,|| High throughput phenotyping - gene discovery and plant breeding. Integration of  phenomic and genomic data
|John Doonan, University of Aberystwyth, UK || Senior Personnel, collaborator, Director National Plant Phenomics Centre,|| High throughput phenotyping - gene discovery and plant breeding. Integration of  phenomic and genomic data
|-
|Justin Elser, Oregon State University || Bioinformatics Researcher || Data analysis, System Administration
|-
|-


|Justin Elser, Oregon State University || Bioinformatics Researcher || Data analysis, System Administration
|Justin Preece, Oregon State University || Developer, programmer || AISO, visualization
|-
|}
|}


== Agenda: ==
== Agenda: ==
'''1. Introductions again, since we have not all met for about a year.'''
=== A. Introductions again, since we have not all met for about a year.===
''See Above''
''See Above''


'''B. Questions about grant, hiring  etc'''
===B. Questions about grant, hiring  etc ===
* GG, CM, have not received the subcontract paperwork, PJ will follow up on
* GG, CM, have not received the subcontract paperwork, PJ will follow up on
* DWS just received his 12-29  
* DWS just received his 12-29  
* Can start billing the grant back dated to Dec 1st
* Can start billing the grant back dated to Dec 1st


=== C. Setting some initial priorities:===
* The NSF agreed to fund the cROP proposal for an initial three year period.  After the first two years are completed, we will have a reverse site visit, at which time they may fund an additional (4th) year.
* PJ will circulate revised timeline


=== Three major components: ===
==== Reference Ontologies- PO, TO, PSO, EO, GO, PATO, ChEBI ====
* Continued and new development
* Training users and curators
* Cross linkings to the crop-specific ontologies at the CO
* moving repositories to centralized platform at GitHub
* Transition to AmiGO 2- new functionalities
* Who: Laurel, Elizabeth, new curator to be hired, Chris, Dennis, George, with Barry’s advice, others?


==== Accumulating annotations and large datasets, data warehouse- IT group ====
* Collaboration with data generating projects such as CO/IBP
* Annotations to sequenced plant genomes- approximately 100 done now
* Who: Eugene?, JE, new programmer, others?


C. Setting some initial priorities:
==== Image annotations with ontologies, ====
The NSF agreed to fund the cROP proposal for an initial three year period.  After the first two years are completed, we will have a reverse site visit, at which time they may fund an additional (4th) year.
* Collaboration with iplant Bisque (from UCSD) developers
PJ will circulate revised timeline
* Building on AISO, machine learning approaches
 
* integration of annotations and images
Three major components:
* Who: Sinisa, grad student, iPlant contacts: Nirav + ?, others?
Reference Ontologies- PO, TO, PSO, EO, GO, PATO, ChEBI
Continued and new development
Training users and curators
Cross linkings to the crop-specific ontologies at the CO
moving repositories to centralized platform at GitHub
Transition to AmiGO 2- new functionalities
Who: Laurel, Elizabeth, new curator to be hired, Chris, Dennis with Barry’s advice, others?
 
Accumulating annotations and large datasets, data warehouse- IT group
Collaboration with data generating projects such as CO/IBP
Annotations to sequenced plant genomes- approximately 100 done now
Who: Eugene?, JE, new programmer, others?
 
Image annotations with ontologies,  
Collaboration with iplant Bisque (from UCSD) developers
Building on AISO, machine learning approaches
integration of annotations and images
Who: Sinisia, grad student, iPlant contacts: Nirav + ?, others?
 


Potential hires joining the project:
===D. Potential hires joining the project: ===
Ez, ST will have grad students
* EZ, ST will have grad students
DWS- will start advertising, may have opssible candidtate
* DWS- will start advertising, may have possible candidate
CM- Seth is already present
* CM- Seth is already present
PJ: programmer and curator
* PJ: programmer and curator
EA???
* EA- Marie Angelique
Can help advertising through FB, mailing lists
* Can help advertising through FB, mailing lists


Other Project info:
===E. Other Project info: ===
New planteome wiki to be set up
* New planteome wiki to be set up- ''done''
tracker for issues
* tracker for issues
Need new Logo or modify cROP one?  
* Need new Logo or modify cROP one? -''done''
Will look into other web conf calling tools- Google hangouts, Go to Meetings, others?
* Will look into other web conf calling tools- Google hangouts, Go to Meetings, others?


Potential members for Project Advisory Board:
=== F. Potential members for Project Advisory Board: ===
Sandra Knapp
* Sandra Knapp  
Melissa Haendel
* Melissa Haendel  
Alejandra Gandolfo
* Alejandra Gandolfo  
Ruth Bastow
* Ruth Bastow  
other suggestions?  
* other suggestions?  
Someone more from the computer sciences field?
- Someone more from the computer sciences field?


''Suggest: Cyril Pommier''


D.  Planning for monthly all-hands meetings and group meetings
=== G.  Planning for monthly all-hands meetings and group meetings ===
LC will send out a doodle poll to find a good day/time for the monthly all-hands meetings
* LC will send out a doodle poll to find a good day/time for the monthly all-hands meetings  
Group meeting will be set up with the interested people on each part of the project.  
* Group meeting will be set up with the interested people on each part of the project.


E. Other items?  
=== H. Other items? ===


DWS: Is redoing the Glossary for the textbook he has authored and will include link to PO terms and definitions.
DWS: Is redoing the Glossary for the textbook he has authored and will include link to PO terms and definitions.

Latest revision as of 23:56, 27 April 2016

Planteome- cROP Meeting: Tuesday Jan 6th, 2015

Who: PJ, LC, JE, DWS, CM, ST, GG, JD

Not available: EA, EZ, BS

Link to audio recording: File:Planteome 1-6-2015.m4a

Name Role Major Focus
Pankaj Jaiswal, Oregon State University Lead PI plant systems biology and bioinformatics
Laurel Cooper, Oregon State University Senior Personnel, Project Coordinator, Bioinformatic Scientist Curation, data analysis, gene expression, genomics, project coordination
Dennis W. Stevenson, New York Botanical Garden CO-PI Plant anatomy and development, evolution and classification, genomics, taxonomy
Elizabeth Arnaud, Bioversity International/CGIAR, France CO-PI Lead on Crop Ontology- crop-specific trait and germplasm ontologies for agronomic databases of crops
Sinisa Todorovic, School of Electrical Engineering and Computer Science, Oregon State University CO-PI Computer vision, machine learning, and artificial intelligence
Eugene Zhang, School of Electrical Engineering and Computer Science, Oregon State University CO-PI Computer graphics, scientific visualization, and geometric modeling; genome sequence visualization
Christopher Mungall, Lawrence Berkeley National Laboratory CO-PI Functional Genomics, Gene Ontology, Disease Phenotype Informatics, Logic-based modeling and programming
Barry Smith, University at Buffalo Ontology consultant Ontology and its applications, especially in biomedical informatics
Georgios V. Gkoutos, University of Birmingham, UK Senior Personnel, collaborator Molecular informatics and bioinformatics, association of genotype to phenotype
John Doonan, University of Aberystwyth, UK Senior Personnel, collaborator, Director National Plant Phenomics Centre, High throughput phenotyping - gene discovery and plant breeding. Integration of phenomic and genomic data
Justin Elser, Oregon State University Bioinformatics Researcher Data analysis, System Administration
Justin Preece, Oregon State University Developer, programmer AISO, visualization

Agenda:

A. Introductions again, since we have not all met for about a year.

See Above

B. Questions about grant, hiring etc

  • GG, CM, have not received the subcontract paperwork, PJ will follow up on
  • DWS just received his 12-29
  • Can start billing the grant back dated to Dec 1st

C. Setting some initial priorities:

  • The NSF agreed to fund the cROP proposal for an initial three year period. After the first two years are completed, we will have a reverse site visit, at which time they may fund an additional (4th) year.
  • PJ will circulate revised timeline

Three major components:

Reference Ontologies- PO, TO, PSO, EO, GO, PATO, ChEBI

  • Continued and new development
  • Training users and curators
  • Cross linkings to the crop-specific ontologies at the CO
  • moving repositories to centralized platform at GitHub
  • Transition to AmiGO 2- new functionalities
  • Who: Laurel, Elizabeth, new curator to be hired, Chris, Dennis, George, with Barry’s advice, others?

Accumulating annotations and large datasets, data warehouse- IT group

  • Collaboration with data generating projects such as CO/IBP
  • Annotations to sequenced plant genomes- approximately 100 done now
  • Who: Eugene?, JE, new programmer, others?

Image annotations with ontologies,

  • Collaboration with iplant Bisque (from UCSD) developers
  • Building on AISO, machine learning approaches
  • integration of annotations and images
  • Who: Sinisa, grad student, iPlant contacts: Nirav + ?, others?

D. Potential hires joining the project:

  • EZ, ST will have grad students
  • DWS- will start advertising, may have possible candidate
  • CM- Seth is already present
  • PJ: programmer and curator
  • EA- Marie Angelique
  • Can help advertising through FB, mailing lists

E. Other Project info:

  • New planteome wiki to be set up- done
  • tracker for issues
  • Need new Logo or modify cROP one? -done
  • Will look into other web conf calling tools- Google hangouts, Go to Meetings, others?

F. Potential members for Project Advisory Board:

  • Sandra Knapp
  • Melissa Haendel
  • Alejandra Gandolfo
  • Ruth Bastow
  • other suggestions?

- Someone more from the computer sciences field?

Suggest: Cyril Pommier

G. Planning for monthly all-hands meetings and group meetings

  • LC will send out a doodle poll to find a good day/time for the monthly all-hands meetings
  • Group meeting will be set up with the interested people on each part of the project.

H. Other items?

DWS: Is redoing the Glossary for the textbook he has authored and will include link to PO terms and definitions.

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