ASPB 2010 Workshop
Plant Ontology and Gramene's Gene Annotation Workshop Plant Biology 2010 LINK
Saturday July 31, 8:00 am - 12:00 pm
Contents
Workshop Agenda
Venue
Room 512 a,b,e,f
Palais des congrès (the Montrèal convention centre)
Schedule (Tentative)
July 31, 2010 8:00 - 8.10 am -- Workshop goals and introduction [Pankaj Jaiswal] 8.10 - 8.30 am -- What is annotation and why we need it. [Pankaj Jaiswal] 8.30 - 8.50*am -- TAIR by Kate Dreher 8.50 - 9.20#am -- Annotation Part-1: Phenote use and practice 9.20 - 9.30 am -- Break 9.30 - 10.00#am -- Annotation Part-2 Three papers. Everyone annotates all three 10.00 - 10.20 am -- MaizeGDB by Jack Gardiner 10.20 - 10.40*am -- Gramene 10.40 - 11.20#am -- Annotation Part-3: Gene/Library annotation set (TBA) -- Annotate your own data 11.20 - 11.40*am -- BAR 11.40 - 12.00 pm -- DISCUSSION and collect the annotations IMPORTANT: PLEASE READ * Talks : (15 min talk 5 min Q&A) $ Arrive 15 min early # Actual hands on training sessions. # Bring your own notebook/laptop computers # Wireless internet access will be provided
About the workshop
More and more plant species are getting sequenced and large-scale phenotyping screens are being setup, we see a diversity of annotation types and descriptors being used for these experiments. Having a new genome and large data sets are an excellent way forward to find novel ways to learn about plant development and behavior. However, in doing so we also realize that many of the descriptors are either very species specific may not meet the community standards of functional characterization by use of various controlled vocabularies (ontologies) such as Gene Ontology and Plant Ontologies. In addition to that not, every plant community has sufficient personnel, computational and monetary resources to manage the annotation of its genome. Therefore, these communities depend heavily on the high-quality annotations of the of model and reference plants.
Therefore, to create gold-standard data sets that can be used in annotations, we want to train the current and future plant biologists with emphasis on young investigators, students, postdocs and especially those representing the minority and underrepresented institutions to help us foster good practices and build a community of curators that will undertake the task of creating a gold-standard data set for plant biologists.
Workshop material
Please read these important instructions
Computers | Internet | software
COMPUTERS
Since this is a hands on training workshop with lectures. We will provide few on-site computers. However for you to help learn the process and work with the software we will use, we expect you to BRING YOUR LAPTOP/NOTEBOOK. We will mostlikely provide the ones with Windows OS. However, we will be able to teh exercises on Mac, Linux and other platforms as well. See more details about the software requirements
INTERNET ACCESS
We will provide FREE INTERNET for the duration of the workshop to first 100 connection. If you already have access to internet through another arrangement, please feel free to use. However, we will not reimburse you for buying access to the internet.
SOFTWARE
For the actual hands on training sessions #1, 2 and 3, we will use the software called PHENOTE.
Phenote
- Customized version of Phenote: Download from here
- Configuration file [Download]
- Frequently Asked Questions FAQ
- Phenote Download/Installation instructions
Annotation Exercise
Exercise #1
TBA
Exercise #2
TBA
Exercise #3
TBA
Participants
There are about 70 registered participants in this workshop. We will provide the list later.
Travel Awards
A limited number of travel award were announced on July 23 to support US residents affiliated with a US institution.
Awardees Institution name Andreas Madlung -- University of Puget Sound Arijit Mukherjee -- University of Wisconsin, Madison Dazhong Zhao -- University of Wisconsin-Milwaukee Fuyu Xu -- University of Maine Jeonghwa Lee -- University of Massachusetts-Amherst Jian Zhao -- The Samuel Roberts Noble Foundation Lei Zhu -- University of California, Riverside Michelle Facette -- University of California, San Diego Peter Lundquist -- Cornell University Manoj Kumar -- University of Louisiana at Lafayette Surinder Chopra -- Pennsylvania State University Tanya Falbel -- University of Wisconsin - Madison Veronica Justen * -- University of Wisconsin-River Falls Songqing Ye -- University of Minnesota * DECLINED
Questions?
Contact Us
Acknowledgements
Sponsored by
NSF Plant Genome Program funded projects on the Plant Ontology and the Gramene database projects on comparative plant genomics and genetics.
Phenote
Phenote is developed by the Berkeley Bioinformatics Open-Source Projects [1]. We greatly acknowledge the contribution made by the BBOP developers Nomi Harris and Chris Mungall for their help in customizing the Phenote tool for use in this workshop.
Ontologies/datasets
Several projects contributed data sets that are linked to the auto complete features in the Plant specific Phenote configuration. They include
