ASPB 2010 Workshop

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Plant Ontology and Gramene's Gene Annotation Workshop Plant Biology 2010 LINK

Saturday July 31, 8:00 am - 12:00 pm

Workshop Agenda


Room 512 a,b,e,f

Palais des congrès (the Montrèal convention centre)


  July 31, 2010
   8:00 -  8.10 am --  Workshop goals and introduction [Pankaj Jaiswal]  Media:Workshop_introduction-1.pdf
   8.10 -  8.30 am --  What is annotation and why we need it. [Pankaj Jaiswal] Media:Why_we_need_annotations_ASPB2010_jaiswal.ppt
   8.30 -  8.50*am --  TAIR by Kate Dreher Media:TAIR_ASPB2010_dreher.ppt
   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 Media:MaizeGDB_ASPB2010_gardiner.ppt
  10.20 - 10.40*am --  Gramene-->not presented due to lack of time
  10.40 - 11.20#am --  Annotation Part-3: continue curating papers
                   --  Annotate your own data
  11.20 - 11.40*am --  ASPB by Crispin Taylor 
  11.20 - 11.40*am --  BAR by Rohan Patel Media:BAR_ASPB2010_patel.ppt
  11.40 - 12.00 pm --  DISCUSSION and collect the annotations
  * 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

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.

Workshop material

Please read these important instructions:


This is a hands on training workshop with lectures. We will provide few on-site computers, however, it is necessary for you to BRING YOUR LAPTOP/NOTEBOOK in order to learn the process and work with the software we will use. Those computers we provide will most likely run Windows OS, but you will be able to perform the exercises on Mac, Linux and other platforms as well. See more details about the software requirements.

    • OS: Windows, Mac, Linux
    • You should have administrative rights and/or access to the ROOT for installing the software
    • INSTALL the Phenote software available from the links provided in the "Software" section below

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


For the actual hands on training sessions #1, 2 and 3, we will use the Annotation Software called: Phenote.

Please see Installation Tutorial.

  • Customized version of Phenote from any of these sites:
  1. Download from Phenote site
  2. Download from Gramene FTP
  3. Download from SourceForge

Annotation Exercises

Exercise #1

  • start with installing the Phenote tool.
  • Practice doing annotations using Phenote
  • example paper to use

Exercise #2

Everyone annotates the following three papers

Exercise #3

  • Continue with annotating papers from exercise #3
  • Do annotations from other papers [just look at the ABSTRACTS]
  1. MicroRNA156-Targeted SPL Genes in Arabidopsis thaliana PubMed: 20622149
  2. OsSPO11-1 is essential for both homologous chromosome pairing PubMed: 20625906
  3. OsPIE1, the rice ortholog of Arabidopsis PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 PubMed: 20585576
  4. BLADE-ON-PETIOLE1 and 2 Control Arabidopsis Leaf Morphogenesis PubMed: 20610407
  5. OsCOL4 is a constitutive flowering repressor PubMed: 20409004


  • Perform annotation of your favorite gene(s).


Contact Us


There are about 70 registered participants in this workshop.

Attendees Low.JPG

Workshop Low.jpg

Travel Awards

A limited number of travel fellowships were awarded 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
  Surinder Chopra    --  Pennsylvania State University
  Tanya Falbel       --  University of Wisconsin - Madison
  Songqing Ye        --  University of Minnesota
  Veronica Justen*   --  University of Wisconsin-River Falls 
  Manoj Kumar^       --  University of Louisiana at Lafayette
  ^ Did not show up

Awardees Low.JPG

Other Pictures

ASPB workshop1 .jpg ASPB workshop2 .jpg

ASPB workshop3 .jpg

ASPB workshop5 .jpg ASPB workshop4 .jpg


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


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.


Several projects contributed data sets that are linked to the auto complete features in the Plant specific Phenote configuration. They include