ASPB 2011 Workshop

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Plant Ontology and Gramene's Community Curation and Resources Workshop
Event Info Plant Biology 2011
Monday August 8, 2011, 7:30-10:pm
Auditorium 1, Minneapolis Convention Center

Workshop Agenda

7.30-7.45 Gramene Database Workshop Introduction: Ken Clark
7.45-8.15 Exploring the Plant Genomes (browse, search, upload personal data, analysis tools): Doreen Ware
8.15-8.30 Phylogenetic analysis tools and targeted query tools using Biomart: Doreen Ware
8:30-8.45 Exploring the Plant's Genetic Diversity: Doreen Ware 
8.45-9.05 Comparative Pathways Networks and future directions: Pankaj Jaiswal 
9:05-9:25 Plant Ontology (Pankaj Jaiswal/Laurel Cooper)
9.25-10.30 Exercises and Q/A 

About the workshop

As more plant species are sequenced and large-scale phenotyping screens are created, we see a diversity of annotation types and descriptors being used in these experiments. Having a new genome and large data sets is an excellent way to learn about plant development and behavior; however, in doing so we also realize that many of the descriptors are very species-specific may not meet the community standards of functional characterization as they fail to employ various controlled vocabularies (ontologies) such as Gene Ontology and Plant Ontologies. In addition to that, not every plant community has sufficient personnel, computational, or monetary resources to manage the annotation of its genome. Therefore, these communities depend heavily on the high-quality annotations of the model and reference plants.

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 who will undertake the task of creating accurate and reliable data sets for plant biologists.

At the workshop a set of talks and hands on training will introduce you to genome searches, analysis, ontologies and gene annotations.

Workshop material

Please read these important instructions:


There will be a hands-on portion of the workshop as the network connection allows. You are encouraged to bring your laptop to follow along.

Internet Access

We will provide FREE WIRELESS INTERNET for the duration of the workshop to first 100 connections. If you already have access to Internet through another arrangement, please feel free to use that; however, we will not reimburse you for buying access to the Internet.

  • RECOMMENDATION: Make sure the computer you are bringing has a wireless network card



Annotation Exercises

Exercise #1

File:Gramene gene exercise 1.doc

Exercise #2

File:Gramene gene exercise 2.doc

Exercise #3

File:Gramene adding data track exercise 3.doc

Exercise Data


NSF Plant Genome Program funded projects on the Plant Ontology and the Gramene database projects on comparative plant genomics and genetics.