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 | ||
* 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- | * Link to recording- Audio: [[File:Planteome All Hands Meeting-5-21-15 audio.m4a|thumbnail|Planteome All Hands Meeting-5-21-15 audio.m4a]] | ||
== 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=== | ===Updates on new hires=== | ||
- OSU | - 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=== | ===Plan for ontology workshop=== | ||
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===AmiGO 2 progress=== | ===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. | * 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. | ||
| Line 38: | Line 42: | ||
===Git migration=== | ===Git migration=== | ||
* Trait ontology has been moved to | * 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:== | ||
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==Next meeting | ==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
- Link to recording- Video: File:Planteome All Hands Meeting-5-21-15-video.mp4
- Link to recording- Audio: File:Planteome All Hands Meeting-5-21-15 audio.m4a
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
- XX and RK are actively developing Phase I
- using a local Bisque dev engine provided by KK
- Specification
- 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
- Meeting Agenda
- Report