May 2nd, 2017 Ontology Working Group Meeting: Difference between revisions

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=Planteome Ontology WG Zoom Meeting=
=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday April 25th, 2017
* Date: Tuesday May 2nd, 2017
* Time: 8:15am PDT (GMT-7)
* Time: 8:15am PDT (GMT-7)


* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/417836474
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/417836474
* Meeting Recordings:
** [[File:Ontology WG Meeting audio 5-2-17.m4a|thumb|Ontology WG Meeting audio 5-2-17]]
** [[File:Ontology WG Meeting video 5-2-17.mp4|thumb|Ontology WG Meeting video 5-2-17]]


=Agenda=
=Agenda=
TBA....
==Planteome Noctua==
== Plant Stress Ontology==
* In preparation for the Noctua workshop on June 4th, we will review the current version of the Planteome Noctua and test out features and functionalities.
* Demo and test of Planteome Noctua instance: '''http://noctua-dev.planteome.org/'''
** Link to [https://docs.google.com/document/d/1KYi1f53KCmPsLDBnz8fIosg4htkPoEHjeXZtj-QedgM/edit?usp=sharing Planteome Noctua SOP] (In progress)


* Items mentioned during call:
** Need list of people attending as they need to be added to the users.yaml file?
** CM will give an overview and intro
** Will use the Planteome version for demo, and annotate example from plants
** Need to include agro and EO
** Attendees should be given a couple of papers before hand to read- specifc pathways
** Justin will work on creating an OBO file with gene names for rice and Arabidopsis


==Update from AgBioData Workshop, Salt Lake City, April 18-19th, 2017==
==Updates==
* The purpose of this meeting is to bring together personnel from agricultural scientific databases to plan common projects, establish proof of principle for data sharing, and to establish standards and guidelines for agricultural genomic, genetic and breeding databases. 
* Luke and George:
** Development of AberOwl: http://aber-owl.net
*** [[https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0090-0| Slater et al, Journal of Biomedical Semantics (2016)]]
** provides automated reasoning-based access to all accessible and consistent ontologies in BioPortal


Link to folder on Google drive: [https://drive.google.com/drive/folders/0B1a8eLRiK74ARnF0eXdnWmd0OHM?usp=sharing AgBioData Ontology Working Group Notes]
 
* Ontology of Plant Stress (AM)- tabled for next meeting
 
== Current work going on in PO==
Link to pedicel document: https://docs.google.com/document/d/1GeMKf0s-M58355hakqeN7Aaf72kHvGaTubfwOh9Pf9o/edit?usp=sharing


= Upcoming Meetings and Workshops=
= Upcoming Meetings and Workshops=
== 2017 Gene Ontology Consortium Meeting, June 1-5th, 2017, Corvallis ==
== 2017 Gene Ontology Consortium Meeting, June 1-5th, 2017, Corvallis ==
* [https://sites.google.com/s/0BxnW-HvvUL8iMkM5VmxxWTBsYzg/p/0BxnW-HvvUL8iRnB0S1dtYUJXYUE/edit GO Meeting Corvallis]
* [https://sites.google.com/view/goc2017 GO Meeting Corvallis]
* [https://docs.google.com/forms/d/1cJWCL0mL3X3rXrNsIcmLtkAf9et6TfhyYbHX9ouLwZs/edit Registration]
* [https://docs.google.com/forms/d/1cJWCL0mL3X3rXrNsIcmLtkAf9et6TfhyYbHX9ouLwZs/edit Registration]
* [https://docs.google.com/forms/d/1F9BUTwzPqeyYQW81BXY1Qfj63OwCwWj9e0zC6sTt2jk/edit Travel plans]
* [https://docs.google.com/forms/d/1F9BUTwzPqeyYQW81BXY1Qfj63OwCwWj9e0zC6sTt2jk/edit Travel plans]
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==Plant Biology 2017, June 24th-28th, Honolulu, Hawaii==
==Plant Biology 2017, June 24th-28th, Honolulu, Hawaii==
* Links: http://plantbiology.aspb.org/
* Important deadlines:
* Important deadlines:
** April 30, 2017: Deadline for early-bird registration rates for Plant Biology 2017 and iMOSS 2017.
** May 24, 2017: Deadline for submission of abstracts to be included in the online program book and to receive a poster number.
** May 24, 2017: Deadline for submission of abstracts to be included in the online program book and to receive a poster number.
** May 27, 2017: Deadline for discount hotel rates. (Please note: Our discounted room block may fill up long before this deadline.)
** May 27, 2017: Deadline for discount hotel rates. (Please note: Our discounted room block may fill up long before this deadline.)

Latest revision as of 18:54, 9 May 2017

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday May 2nd, 2017
  • Time: 8:15am PDT (GMT-7)

Agenda

Planteome Noctua

  • In preparation for the Noctua workshop on June 4th, we will review the current version of the Planteome Noctua and test out features and functionalities.
  • Demo and test of Planteome Noctua instance: http://noctua-dev.planteome.org/
  • Items mentioned during call:
    • Need list of people attending as they need to be added to the users.yaml file?
    • CM will give an overview and intro
    • Will use the Planteome version for demo, and annotate example from plants
    • Need to include agro and EO
    • Attendees should be given a couple of papers before hand to read- specifc pathways
    • Justin will work on creating an OBO file with gene names for rice and Arabidopsis

Updates


  • Ontology of Plant Stress (AM)- tabled for next meeting

Current work going on in PO

Link to pedicel document: https://docs.google.com/document/d/1GeMKf0s-M58355hakqeN7Aaf72kHvGaTubfwOh9Pf9o/edit?usp=sharing

Upcoming Meetings and Workshops

2017 Gene Ontology Consortium Meeting, June 1-5th, 2017, Corvallis

  • Dates: June 1-5, 2017 (Details)
    • Arrive (May 31) View travel directions
    • GOC meeting (June 1-3)
    • Noctua gene annotation jamboree (June 4)
    • Reactome Pathway curation jamboree (June 5)
    • Depart (June 5 late evening / June 6 anytime)

Plant Biology 2017, June 24th-28th, Honolulu, Hawaii

  • Important deadlines:
    • May 24, 2017: Deadline for submission of abstracts to be included in the online program book and to receive a poster number.
    • May 27, 2017: Deadline for discount hotel rates. (Please note: Our discounted room block may fill up long before this deadline.)
    • June 12, 2017: Final deadline for Plant Biology 2017 abstract submissions.
    • June 12, 2017: Deadline for standard registration rates for Plant Biology 2017 and iMOSS 2017.
    • June 24–28, 2017: Onsite registration during Plant Biology 2017!

XIX International Botanical Congress, July 23-29, 2017, Shenzhen, China

  • Workshop proposal accepted-
  • T5-06:Ontologizing botanical knowledge (two sessions)
    • Organizer: Hong Cui (University of Arizona, USA)
    • James Macklin (Agriculture Agri-Food Canada, Canada)
    • Pankaj Jaiswal (Oregon State University, USA)
  • T5-18: Bioinformatics resources for comparative functional and phylogenetic analysis of plant genomes, pathways and diversity
    • Organizer: Pankaj Jaiswal (Oregon State University, USA)
    • Sushma Naithani (Oregon State University, USA)
  • Deadline for the abstract submission for oral presentations has been extended for 39 of the 212 general symposia where one or a few speaker slots are available
  • New deadline: February 15, 2017 for those 39 symposia and for posters only
  • Abstract submitted?

ICBO 2017, Sept 12th-15th, 2017

  • Newcastle, GB
  • http://icbo.buffalo.edu/
  • Important dates:
    • Mar 29, 2017: Workshops and tutorials proposals submission deadline
    • Apr 19, 2017: Notification of acceptance of workshops and tutorials
    • Jun 02, 2017: Paper and Poster Deadline
    • Jun 16, 2017: Paper Reviews Due
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