Transcript Title goes here

Advancing Science with DNA Sequence
GENEBOREE
A Tool for Collaborative Gene Annotation
DOE Joint Genome Institute
Integrated Microbial Genomes
Annette Greiner
Anya Kartavenko
Rowena Luk
Advancing Science with DNA Sequence
A Genetics Primer
Advancing Science with DNA Sequence
Geneboree
• Collaborative gene
annotation
• Geographically
distributed
• Open to all
bioscientists
Advancing Science with DNA Sequence
Goals
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Credibility
Security
Standards
Ease of use
Seamless integration
Advancing Science with DNA Sequence
Developing Personas
• Interviews at JGI:
– Professional annotators (3)
– Scientists (1)
• Interviews with field scientists:
– UC Berkeley (2)
– LBL (3)
Advancing Science with DNA Sequence
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
Advancing Science with DNA Sequence
Fourth Persona
Bill Newman, PhD, 48
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Staff Scientist at Los Alamos National Lab
Microbial bioterrorism
Naïve computer user and recognized authority in his field
Martha Jane Gilbert, PhD, 30
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Postdoctoral fellow at University of Oxford, UK
Metagenomics
Experienced computer user and fairly experienced professional
Phil Dupont, 24 (Primary User)
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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
Advancing Science with DNA Sequence
Scenario: Bill
• Compares gene sequences from
Chernobyl and finds an oddball
• Verifies annotator’s credibility
• Updates annotation
Advancing Science with DNA Sequence
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
Advancing Science with DNA Sequence
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
Advancing Science with DNA Sequence
First Interactive Prototype
Built with Dreamweaver/PHP/MySQL
• Dreamweaver templates control navigation,
headers
• PHP and MySQL make pages dynamic
Advancing Science with DNA Sequence
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/annotation)
• Collaborative annotation
• Discussion about gene function
• Authentication
Advancing Science with DNA Sequence
First Interactive Prototype
Differences from paper prototype
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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)
Advancing Science with DNA Sequence
First Interactive Prototype
Advancing Science with DNA Sequence
First Interactive Prototype
http://groups.sims.berkeley.edu/annotation/
Advancing Science with DNA Sequence
Lessons Learned
• Users are different!
• Manual checking vs automatic
annotation
• Homology vs. phylogeny vs.
experimental data
• More evidence
• Open question: does voting work?
Advancing Science with DNA Sequence
Questions?