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GENEBOREE
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Title: Title goes here Author: Cheryl Ventimiglia Last modified by: joe infinity Created Date: 4/28/2005 9:01:06 PM Document presentation format: On-screen Show – PowerPoint PPT presentation
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Title: GENEBOREE
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- GENEBOREE
- A Tool for Collaborative Gene Annotation
- DOE Joint Genome Institute
- Integrated Microbial Genomes
- Annette Greiner
- Anya Kartavenko
- Rowena Luk
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A Genetics Primer
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Geneboree
- Collaborative gene annotation
- Geographically distributed
- Open to all bioscientists
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Goals
- Credibility
- Security
- Standards
- Ease of use
- Seamless integration
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Developing Personas
- Interviews at JGI
- Professional annotators (3)
- Scientists (1)
- Interviews with field scientists
- UC Berkeley (2)
- LBL (3)
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Personas
- Bill Newman, PhD, 48
- Staff Scientist at Los Alamos National Lab
- Microbial bioterrorism
- Naïve computer user and recognized authority in
his field
- Martha Jane Gilbert, PhD, 30
- Postdoctoral fellow at University of Oxford, UK
- Metagenomics
- Intermediate computer user and fairly experienced
professional
- Phil Dupont, 24 (Primary User)
- Third year PhD student at Rutgers University
- Fungi studies in evolutionary biology
- Expert computer user and least experienced
professional
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Fourth Persona
- Bill Newman, PhD, 48
- Staff Scientist at Los Alamos National Lab
- Microbial bioterrorism
- Naïve computer user and recognized authority in
his field
- Martha Jane Gilbert, PhD, 30
- Postdoctoral fellow at University of Oxford, UK
- Metagenomics
- Experienced computer user and fairly experienced
professional
- Phil Dupont, 24 (Primary User)
- Third year PhD student at Rutgers University
- Fungi studies in evolutionary biology
- Expert computer user and least experienced
professional
- Ann Taylor, 35
- Professional annotator at Sanger Institute, UK
- Updates automatic annotations
- Intermediate computer user and expert annotator
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Scenario Bill
- Compares gene sequences from Chernobyl and finds
an oddball - Verifies annotators credibility
- Updates annotation
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Scenario Martha Jane
- Searches IMG for genes involved in carbon
fixation - Notices that most results were automatically
annotated and not reliable - Makes a comment on all of the genes in her set
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Scenario Phil
- Decides to transfer annotation from one homolog
to his gene of interest - Just to be sure, he checks his assumptions
against a phylogenetic tree and finds that the
annotation he wanted to transfer was inaccurate - Corrects annotation of the homolog and annotates
his gene of interest
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First Interactive Prototype
- Built with Dreamweaver/PHP/MySQL
- Dreamweaver templates control navigation, headers
- PHP and MySQL make pages dynamic
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First Interactive Prototype
- Prototype uses the existing IMG site for existing
IMG functions - IMG (http//img.jgi.doe.gov)
- Gene searches
- Comparative tools
- Geneboree (http//groups.sims.berkeley.edu/annotat
ion) - Collaborative annotation
- Discussion about gene function
- Authentication
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First Interactive Prototype
- Differences from paper prototype
- No drafts
- Replies to batch discussion
- Automatic previews (can be turned off in prefs)
- Voting buttons on gene cart page
- Hyperlinks in discussions
- Flags to indicate genes recently annotated
- New method of comparing and transferring
annotations from other genes - Additional evidence fields (Pfam and UniProt)
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First Interactive Prototype
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First Interactive Prototype
- http//groups.sims.berkeley.edu/annotation/
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Lessons Learned
- Users are different!
- Manual checking vs automatic annotation
- Homology vs. phylogeny vs. experimental data
- More evidence
- Open question does voting work?
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- Questions?
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