Transcript gonuts - AgBase

GONUTS
Community annotation and usage guides for
Gene Ontology
TAMU GO Workshop
17 May 2010
Why GONUTS?
• GONUTS = Gene Ontology Normal Usage Tracking
System
– Not an official GOC component
– But we are used by the GOC for a variety of purposes
• GONUTS = Community wiki for
– Recording usage notes at the level of GO terms
– Curating to the GO annotation of gene products
– Comparing annotations of sets of gene products
GO is only as useful as the quality and
coverage of the annotations
• Traditional models of centralized
curation don't scale well
– Too many genomes
• Bee, beetle, paramecium, platypus, sea
urchin, dog, cat, chicken, turkey, cow,
grape, truffle, zebrafinch, Neandertal ...
– Rise of clade-oriented and
metagenome databases
• Graminae, vertebrates, “Atlantic
Ocean,” “thermal vent”, "human
microbiome"
– Communities too small and fragmented
to support classic MODs
• not enough money or expertise to
support experiments and curators
• Need a mechanism to enlist expert
communities to contribute to GO and
GO annotation
"Wikifying" Genome Annotation
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The need for ongoing annotation and reannotation is accelerating
Expertise is distributed across broad communities of scientists
Plan for the demo
• Create accounts
• Browsing GO with GONUTS
– Usage notes
– Getting to and from Amigo/Sourceforge
• Gene pages
– Viewing annotations from GOC MOD examples
– Creating a gene page
• Annotation jamborees
– Reference Genomes Project
– CACAO - integrating GO annotation with undergraduate teaching
Accounts
• You don't need an account to browse GONUTS
• You do need an account to
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edit GONUTS
create watchlists
track your contributions
customize your views
• Registered users can create new registered users
– Unless they are student accounts
Create account
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http://gowiki.tamu.edu
Login link on upper right
User: XXXX
Password: XXXX
Create account
• The Demo user can
only create new
accounts
• Get back to the login
page to create your
own account
Create account
Create account
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Fill in your desired username
Fill in the password you want to use
Fill in your email
Fill in your real name
Click either "Create account" or "by email"
Plan for the demo
• Create accounts
• Browsing GO with GONUTS
– Usage notes
– Getting to and from Amigo/Sourceforge
• Gene pages
– Viewing annotations from GOC MOD examples
– Creating a gene page
• Annotation jamborees
– Reference Genomes Project
– CACAO - integrating GO annotation with undergraduate teaching
Search for a GO term
• Go tries to go directly to a
matching page
• Search shows you all
matching results
• G uses Google instead of
the built-in mediawiki search
GONUTs has a page for every GO term
• Upper box:
information from
the GO ontology
file
– updated
weekly
• Usage notes:
more extensive
explanation from
users
• References
GONUTs has a page for every GO term
• Child terms
– expand and
collapse
• Genes
annotated with
this term
– note that this
does not
include genes
annotated to
child terms
Adding to Usage Notes
• What we want
– When to use a term vs
alternatives
– Assays used to assess
whether a term should be
used
– Links to the literature about
what the term describes
– etc.
• You can add uploaded
figures
• Wiki philosophy: Let the user
community decide what to
add or delete
Usage notes are linked from AmiGO
• Others will use
them!
• A web service
from GONUTS
counts how
many times the
page has been
saved
– excludes
robots
Plan for the demo
• Create accounts
• Browsing GO with GONUTS
– Usage notes
– Getting to and from Amigo/Sourceforge
• Gene pages
– Viewing annotations from GOC MOD examples
– Creating a gene page
• Annotation jamborees
– Reference Genomes Project
– CACAO - integrating GO annotation with undergraduate teaching
MOD gene pages
• Search for a
gene
• Example "SIR3"
MOD gene pages
• Basic
information
• Editable table
with the GO
annotations for
that gene
– Sort
– Filter
• Helps us think of
properties to
check when
annotating
homologs
User-created gene pages
• Annotation pages
based on UniProt
IDs
• GONUTS creates a
page automatically
User-created gene pages
• Annotation pages
based on UniProt
IDs
• GONUTS creates a
page automatically
• We can also add
pages for you
– Example:
Chicken
Reactome targets
added for Carl
Schmidt (Univ. of
Delaware).
Editing annotation tables
• Tables of GO
annotations can be
edited via our
TableEdit interface
• Table structure tags
the entries for data
mining
Plan for the demo
• Create accounts
• Browsing GO with GONUTS
– Usage notes
– Getting to and from Amigo/Sourceforge
• Gene pages
– Viewing annotations from GOC MOD examples
– Creating a gene page
• Annotation jamborees
– Reference Genomes Project
– CACAO - integrating GO annotation with undergraduate teaching
Reference genomes project
• Goals
– Generate sets of high-quality literature-based annotations for
sets of orthologous genes from well-characterized organisms
• E. coli, yeast, Dictyostelium, C. elegans, Drosophila,
Arabidopsis, Zebrafish, Rat, Mouse, Chicken, Human
– Support annotation transfer by orthology
– Improve annotation consistency
• Monthly lists of ~30 ortholog sets are annotated by all
groups
• Every few months, an "Electronic jamboree" held to
focus on 2-3 ortholog sets
Annotation Jamborees in Cyberspace
• Groups of genes
are marked with a
category to put
them in a group to
compare
• Wiki tools mine
the annotations on
the individual
pages and make
summary tables
and figures
Annotation Jamborees in Cyberspace
• Groups of genes
are marked with a
category to put
them in a group to
compare
• Wiki tools mine
the annotations on
the individual
pages and make
summary tables
and figures
Annotation Jamborees in Cyberspace
• Each wiki page has an
associated discussion page
• Embed a chat room to record
discussion between remote
locations
• Or coordinate with
conference calls
Making your own Annotation Jamboree
• Not just for the RefGenome
project
• Make a category tag and tag
your genes of interest
• Create a jamboree page
using our template
Making your own Annotation Jamboree
• Not just for the RefGenome
project
• Make a category tag and tag
your genes of interest
• Create a jamboree page
using our template
• Example:
– Complement comparison
page
Participation is still the major challenge
• People are busy
• GO annotation is even more complicated than
entering information in EcoliWiki
• What's in it for community members?
– Does improving the wiki help your own research enough?
– Does it help with funding?
– Does it help with promotion?
CACAO
coupling annotation to teaching credit
Community
Assessment of
Community
Annotation with
Ontologies
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Teams of students curate
Faculty supervision
Support from our team
Intramural or Intercollegiate competition
Distributed annotation jamborees
Assessment via surveys and wiki datamining
Important features of wikis/GONUTS
• Content evolves. It's a large-scale, long-term
collaboration
• There is no overall gatekeeper
• Every revision is saved
• Every version has a permanent URL link
• You can set pages to be watched
• We welcome new uses
• We're funded to help ([email protected])
Acknowledgements
• EcoliWiki/GONUTS Team
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Dave Clements
Gwen Knapp
Nathan Liles
Brenley McIntosh
Debby Siegele
Daniel Renfro
Amanda Supak
Anand Venkatraman
Adrienne Zweifel
• EcoliHub
• GO consortium
• Chris Elsik
• Funding NIGMS