Latest revision as of 23:50, 5 October 2010

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

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

Workshop Agenda

Venue

Room 512 a,b,e,f

Palais des congrès (the Montrèal convention centre)

Schedule

  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
  
  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

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:

Computers

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.

RECOMMENDATIONS
- 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

Software

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:

Configuration file [Download]
Frequently Asked Questions FAQ
Phenote Download/Installation instructions

Annotation Exercises

Exercise #1

start with installing the Phenote tool.
Practice doing annotations using Phenote
example paper to use
- File:Rice-LOG1.pdf

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]

MicroRNA156-Targeted SPL Genes in Arabidopsis thaliana PubMed: 20622149
OsSPO11-1 is essential for both homologous chromosome pairing PubMed: 20625906
OsPIE1, the rice ortholog of Arabidopsis PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 PubMed: 20585576
BLADE-ON-PETIOLE1 and 2 Control Arabidopsis Leaf Morphogenesis PubMed: 20610407
OsCOL4 is a constitutive flowering repressor PubMed: 20409004

OR

Perform annotation of your favorite gene(s).

Questions?

Contact Us

Have Workshop question?

Have Phenote questions?

Have travel award question?

Have annotation question?

Participants

There are about 70 registered participants in this workshop.

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
  
  * DECLINED
  ^ Did not show up

Other Pictures

Acknowledgments

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

@@ Line 5: / Line 5: @@
 =Workshop Agenda=
 ==Venue==
+Room 512 a,b,e,f
+Palais des congrès (the Montrèal convention centre)
 ==Schedule==
+   '''July 31, 2010'''
+:00 -  8.10 am --  Workshop goals and introduction [Pankaj Jaiswal]  [[Media:Workshop_introduction-1.pdf]]
+.10 -  8.30 am --  What is annotation and why we need it. [Pankaj Jaiswal] [[Media:Why_we_need_annotations_ASPB2010_jaiswal.ppt]]
+.30 -  8.50*am --  [http://www.arabidopsis.org TAIR] by Kate Dreher [[Media:TAIR_ASPB2010_dreher.ppt]]
+.50 -  9.20#am --  Annotation Part-1: Phenote use and practice
+.20 -  9.30 am --  Break
+.30 - 10.00#am --  Annotation Part-2  Three papers. Everyone annotates all three
+.00 - 10.20 am --  [http://www.MaizeGDB.org MaizeGDB] by Jack Gardiner [[Media:MaizeGDB_ASPB2010_gardiner.ppt]]
+.20 - 10.40*am --  [http://www.gramene.org Gramene]-->not presented due to lack of time
+.40 - 11.20#am --  Annotation Part-3: continue curating papers
+                    --  Annotate your own data
+.20 - 11.40*am --  [http://www.aspb.org ASPB] by Crispin Taylor
+.20 - 11.40*am --  [http://bar.utoronto.ca/ BAR] by Rohan Patel [[Media:BAR_ASPB2010_patel.ppt]]
+.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==
+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 [http://www.geneontology.org Gene Ontology] and [http://www.plantontology.org 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=
-=Participants=
-=Travel Awards=
-A limited number of travel award were made to US residents affiliated with a US institution. For more information, please see [http://plantontology.org/workshop/pb2010.html here]
-=Questions. Contact Us=
+Please read these important instructions:
-=Sponsored by=
+==Computers==
+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.
+* RECOMMENDATIONS
+** 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
+==Software==
+For the actual hands on training sessions #1, 2 and 3, we will use the Annotation Software called: [http://www.phenote.org/ '''Phenote'''].
+Please see [http://dev.gramene.org/tutorials/phenote/phenote_demo.htm Installation Tutorial].
+* Customized version of Phenote from any of these sites:
+# [http://www.phenote.org/phenote/1.8/ Download from Phenote site]
+# [ftp://ftp.gramene.org/pub/gramene/outreach/phenote/ Download from Gramene FTP]
+# [http://sourceforge.net/projects/obo/files/ Download from SourceForge]
+* Configuration file [Download]
+* Frequently Asked Questions [http://phenote.org/faq.shtml FAQ]
+* Phenote [http://phenote.org/download.shtml Download/Installation instructions]
+==Annotation Exercises==
+===Exercise #1===
+* start with installing the Phenote tool.
+* Practice doing annotations using Phenote
+* example paper to use
+** [[File:Rice-LOG1.pdf]]
+===Exercise #2===
+Everyone annotates the following three papers
+* [[Image:OsEIL1.pdf]]
+* [[Image:Os-at-LOG.pdf]]
+* [[Image:At-FLS2.pdf]]
+===Exercise #3===
+* Continue with annotating papers from exercise #3
+* Do annotations from other papers [just look at the ABSTRACTS]
+# MicroRNA156-Targeted SPL Genes in Arabidopsis thaliana [http://www.ncbi.nlm.nih.gov/pubmed/20622149 PubMed: 20622149]
+# OsSPO11-1 is essential for both homologous chromosome pairing [http://www.ncbi.nlm.nih.gov/pubmed/20625906 PubMed: 20625906]
+# OsPIE1, the rice ortholog of Arabidopsis PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 [http://www.ncbi.nlm.nih.gov/pubmed/20585576 PubMed: 20585576]
+# BLADE-ON-PETIOLE1 and 2 Control Arabidopsis Leaf Morphogenesis [http://www.ncbi.nlm.nih.gov/pubmed/20610407 PubMed: 20610407]
+# OsCOL4 is a constitutive flowering repressor [http://www.ncbi.nlm.nih.gov/pubmed/20409004 PubMed: 20409004]
+OR
+* Perform annotation of your favorite gene(s).
+=Questions?=
+==Contact Us==
+*[mailto:gramene@gramene.org,po-workshop@plantontology.org?subject=PB2010_Workshop_questions_workshop Have Workshop question?]
+*[mailto:gramene@gramene.org,po-workshop@plantontology.org?subject=Phenote_questions Have Phenote questions?]
+*[mailto:gramene@gramene.org,po-workshop@plantontology.org?subject=Trave_award_question Have travel award question?]
+*[mailto:gramene@gramene.org,po-workshop@plantontology.org?subject=annotation_question Have annotation question?]
+===Participants===
+There are about 70 registered participants in this workshop.
+[[File:Attendees_Low.JPG]]
+[[File: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
+   * DECLINED
+   ^ Did not show up
+[[File:Awardees_Low.JPG]]
+===Other Pictures===
+[[File:ASPB workshop1 .jpg]]   [[File:ASPB workshop2 .jpg]]
+[[File:ASPB workshop3 .jpg]]
+[[File:ASPB workshop5 .jpg]] [[File:ASPB workshop4 .jpg]]
+=Acknowledgments=
+==Sponsored by==
+NSF Plant Genome Program funded projects on the [http://www.plantontology.org/ Plant Ontology] and the [http://www.gramene.org/ Gramene database] projects on comparative plant genomics and genetics.
+==Phenote==
+Phenote is developed by the Berkeley Bioinformatics Open-Source Projects [http://www.berkeleybop.org/(BBOP)]. 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
+* [http://www.brachybase.org Brachybase]
+* [http://rapdb.dna.affrc.go.jp/ Rice Genome project in Japan]
+* [http://rice.plantbiology.msu.edu/ MSU rice Genome project]
+* [http://www.arabidopsis.org/ TAIR]
+* [http://www.gramene.org/ Gramene]
+* [http://www.geneontology.org/ Gene Ontology]
+* [http://www.plantontology.org/ Plant Ontology]
+* [http://www.obofoundry.org/ OBO foundry]

Difference between revisions of "ASPB 2010 Workshop"