Difference between revisions of "ASPB 2010 Workshop"
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Palais des congrès (the Montrèal convention centre) | Palais des congrès (the Montrèal convention centre) | ||
| − | ==Schedule | + | ==Schedule== |
'''July 31, 2010''' | '''July 31, 2010''' | ||
| − | 8:00 - 8.10 am -- Workshop goals and introduction [Pankaj Jaiswal] | + | 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] | + | 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 -- [http://www.arabidopsis.org TAIR] by Kate Dreher | + | 8.30 - 8.50*am -- [http://www.arabidopsis.org TAIR] by Kate Dreher [[Media:TAIR_ASPB2010_dreher.ppt]] |
8.50 - 9.20#am -- Annotation Part-1: Phenote use and practice | 8.50 - 9.20#am -- Annotation Part-1: Phenote use and practice | ||
9.20 - 9.30 am -- Break | 9.20 - 9.30 am -- Break | ||
9.30 - 10.00#am -- Annotation Part-2 Three papers. Everyone annotates all three | 9.30 - 10.00#am -- Annotation Part-2 Three papers. Everyone annotates all three | ||
| − | 10.00 - 10.20 am -- [http://www.MaizeGDB.org MaizeGDB] by Jack Gardiner | + | 10.00 - 10.20 am -- [http://www.MaizeGDB.org MaizeGDB] by Jack Gardiner [[Media:MaizeGDB_ASPB2010_gardiner.ppt]] |
| − | 10.20 - 10.40*am -- [http://www.gramene.org Gramene] | + | 10.20 - 10.40*am -- [http://www.gramene.org Gramene]-->not presented due to lack of time |
| − | 10.40 - 11.20#am -- Annotation Part-3: | + | 10.40 - 11.20#am -- Annotation Part-3: continue curating papers |
-- Annotate your own data | -- Annotate your own data | ||
| − | 11.20 - 11.40*am -- [http://bar.utoronto.ca/ BAR] | + | 11.20 - 11.40*am -- [http://www.aspb.org ASPB] by Crispin Taylor |
| + | 11.20 - 11.40*am -- [http://bar.utoronto.ca/ BAR] by Rohan Patel [[Media:BAR_ASPB2010_patel.ppt]] | ||
11.40 - 12.00 pm -- DISCUSSION and collect the annotations | 11.40 - 12.00 pm -- DISCUSSION and collect the annotations | ||
| Line 32: | Line 33: | ||
# Actual hands on training sessions. | # Actual hands on training sessions. | ||
# Bring your own notebook/laptop computers | # Bring your own notebook/laptop computers | ||
| − | # Wireless internet access will be provided | + | # Wireless internet access will be provided. |
==About the workshop== | ==About the workshop== | ||
| − | |||
| − | Therefore, | + | 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= | =Workshop material= | ||
| − | Please read these important instructions | + | Please read these important instructions: |
| − | ==Computers | + | ==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 | + | ==Annotation Exercises== |
===Exercise #1=== | ===Exercise #1=== | ||
| − | + | * start with installing the Phenote tool. | |
| − | + | * Practice doing annotations using Phenote | |
| + | * example paper to use | ||
| + | ** [[File:Rice-LOG1.pdf]] | ||
===Exercise #2=== | ===Exercise #2=== | ||
| + | Everyone annotates the following three papers | ||
| − | + | * [[Image:OsEIL1.pdf]] | |
| + | * [[Image:Os-at-LOG.pdf]] | ||
| + | * [[Image:At-FLS2.pdf]] | ||
===Exercise #3=== | ===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?] | |
| − | =Travel Awards= | + | *[mailto:gramene@gramene.org,po-workshop@plantontology.org?subject=annotation_question Have annotation question?] |
| − | A limited number of travel | + | |
| + | ===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''' | '''Awardees Institution name''' | ||
| Line 97: | Line 138: | ||
Michelle Facette -- University of California, San Diego | Michelle Facette -- University of California, San Diego | ||
Peter Lundquist -- Cornell University | Peter Lundquist -- Cornell University | ||
| − | |||
Surinder Chopra -- Pennsylvania State University | Surinder Chopra -- Pennsylvania State University | ||
Tanya Falbel -- University of Wisconsin - Madison | Tanya Falbel -- University of Wisconsin - Madison | ||
| − | |||
Songqing Ye -- University of Minnesota | Songqing Ye -- University of Minnesota | ||
| + | |||
| + | Veronica Justen* -- University of Wisconsin-River Falls | ||
| + | Manoj Kumar^ -- University of Louisiana at Lafayette | ||
* DECLINED | * 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== | ==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== | ||
| − | 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. | + | |
| + | 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== | ==Ontologies/datasets== | ||
| − | Several | + | 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://www.brachybase.org Brachybase] | ||
* [http://rapdb.dna.affrc.go.jp/ Rice Genome project in Japan] | * [http://rapdb.dna.affrc.go.jp/ Rice Genome project in Japan] | ||
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
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
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
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
