Thursday May 21st, 2015: Difference between revisions

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* Who:  
* Who: GG, PJ, LC, MAL, JE, JP, LC
* Not available:
* Not available: DWS, EZ, ST, BS, CM


'''Zoom Connection Details:  Join from PC, Mac, iOS or Android: https://zoom.us/j/331293888'''


* Link to recording- Video: [[File:Planteome All Hands Meeting-5-21-15-video.mp4|thumbnail|Planteome All Hands Meeting-5-21-15-video.mp4]]


* Link to recording- Video: TBA
* Link to recording- Audio: [[File:Planteome All Hands Meeting-5-21-15 audio.m4a|thumbnail|Planteome All Hands Meeting-5-21-15 audio.m4a]]
* Link to recording- Audio: TBA




== A. General Comments and Updates:==
== A. General Comments and Updates:==
=== Introductions: ===
=== Introductions: ===
* Georgios V. Gkoutos, University of Aberystwyth, UK :
* Marie-Angelique LaPorte (Bioversity International):
===Updates on new hires===
- Post-doc position at OSU- Six candidates were interviewed and an offer has been made, new person should join in late June or early July.
- Post-doc position at Aberystwyth University, UK- GG will send the advertisement to LC, and we can help circulate it- post on Planteome social media sites (blog post, FB, Twitter) and send out on mailing lists: PO discuss, OBO-discuss?, etc. ''- done''
* PJ suggested that we could forward to a couple of the candidates who applied for the OSU position- recent PhD's from India with bioinformatics backgrounds. ''- done''
- Post-doc position at NYBG- No news on this yet
===Plan for ontology workshop===
- Involvement of Agmips, Agrovoc collaborators
===Discussion about the Advisory Board===
Suggestions:
* Ruth Bastow
* Sandy Knapp
* From BS: Suggest: Lynn Schriml, just named President of the [http://gensc.org/Genomic Standards Consortium] , (but I am not pressing on her behalf).


== B. Update from IT group- Data Store, AmiGO2- Justin Elser==
== B. Update from IT group- Data Store, AmiGO2- Justin Elser==
===AmiGO 2 progress===
* Working on creating an planteome importer owl file to simplify the loading of the ontologies via the golr Makefile.  Working on a catalog xml file to redirect URI in the importer OWL.
* Troubleshooting issue with loading both the environment and trait ontologies where loading both causes the EO to disappear from AmiGO.
===Git migration===
* Trait ontology has been moved to [https://github.com/Planteome GitHub].  Will move the rest after some more testing.


== C. Update from AISO/BisQue group- Justin Preece:==
== C. Update from AISO/BisQue group- Justin Preece:==
===[http://wiki.planteome.org/index.php/Planteome_Image_Annotation_Working_Group Working Group Summary Page: Meetings and activities]===
'''New member'''
*Ryan Kitchen (CS Undergrad, Sinisa Todorovic's group)
** will be working with Xu Xu on PIA development over the summer
'''Software Development'''
* XX and RK are actively developing Phase I
** using a local Bisque dev engine provided by KK
* [https://docs.google.com/document/d/14i3ED8cAX6-qwdpko8eV8aQrwplLRfLHZ93dZYpjZu8/edit Specification]
* [https://docs.google.com/spreadsheets/d/12Ue35yruoazIOH6OSp_eF2R8YJtJGaqDfyIF8u3JtW4/edit#gid=0 Phase I timeline]
'''Big Data + Bio-image Informatics Workshop: May 14-15, UC-Santa Barbara'''
* Attended this workshop as collaborators with the iPlant Bisque group
* JP gave an AISO software demo and talked about the Planteome project and our efforts to port AISO to iPlant Bisque
* [https://pods.iplantcollaborative.org/wiki/pages/viewpage.action?pageId=14588579 Meeting Agenda]
* [https://pods.iplantcollaborative.org/wiki/pages/viewpage.action?pageId=18186904 Report]


== D. Update from Ontologies Working Group:==
== D. Update from Ontologies Working Group:==
==E. Other Comments:==
==Next meeting Wednesday June 24th, 2015==

Latest revision as of 04:10, 23 June 2015

  • Who: GG, PJ, LC, MAL, JE, JP, LC
  • Not available: DWS, EZ, ST, BS, CM



A. General Comments and Updates:

Introductions:

  • Georgios V. Gkoutos, University of Aberystwyth, UK :
  • Marie-Angelique LaPorte (Bioversity International):

Updates on new hires

- Post-doc position at OSU- Six candidates were interviewed and an offer has been made, new person should join in late June or early July.

- Post-doc position at Aberystwyth University, UK- GG will send the advertisement to LC, and we can help circulate it- post on Planteome social media sites (blog post, FB, Twitter) and send out on mailing lists: PO discuss, OBO-discuss?, etc. - done

  • PJ suggested that we could forward to a couple of the candidates who applied for the OSU position- recent PhD's from India with bioinformatics backgrounds. - done

- Post-doc position at NYBG- No news on this yet

Plan for ontology workshop

- Involvement of Agmips, Agrovoc collaborators

Discussion about the Advisory Board

Suggestions:

  • Ruth Bastow
  • Sandy Knapp
  • From BS: Suggest: Lynn Schriml, just named President of the Standards Consortium , (but I am not pressing on her behalf).

B. Update from IT group- Data Store, AmiGO2- Justin Elser

AmiGO 2 progress

  • Working on creating an planteome importer owl file to simplify the loading of the ontologies via the golr Makefile. Working on a catalog xml file to redirect URI in the importer OWL.
  • Troubleshooting issue with loading both the environment and trait ontologies where loading both causes the EO to disappear from AmiGO.

Git migration

  • Trait ontology has been moved to GitHub. Will move the rest after some more testing.

C. Update from AISO/BisQue group- Justin Preece:

Working Group Summary Page: Meetings and activities

New member

  • Ryan Kitchen (CS Undergrad, Sinisa Todorovic's group)
    • will be working with Xu Xu on PIA development over the summer

Software Development

Big Data + Bio-image Informatics Workshop: May 14-15, UC-Santa Barbara

  • Attended this workshop as collaborators with the iPlant Bisque group
  • JP gave an AISO software demo and talked about the Planteome project and our efforts to port AISO to iPlant Bisque
  • Meeting Agenda
  • Report

D. Update from Ontologies Working Group:

E. Other Comments:

Next meeting Wednesday June 24th, 2015

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