ASPB 2011 Workshop
Plant Ontology and Gramene's Community Curation and Resources Workshop Plant Biology 2011 LINK
Monday August 8, 2011, 7:30-10:pm
Contents
Workshop Agenda
Venue
Minneapolis Convention Center Auditorium 3
Schedule
August 8, 2011 7:30-10:pm
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).