This is the talk I gave at the 7th Arthropod Genomics Symposium, hosted by the Eck Institute for Global Health at University of Notre Dame in South Bend, Indiana, USA. More efficient sequencing technologies mean a dramatic increase in our access to whole genome sequences, and annotation efforts must adapt to keep pace in converting these sequence data into knowledge. The growing number of genome sequencing projects also means there will be a larger reliance on contributions from domain specialists. This is indicative of a curation environment shifting from a traditional centralized model to a geographically dispersed community annotation model, which requires new tools to support collaborative annotation. WebApollo is a successor to the Apollo annotation editor; it provides a web-based environment that allows multiple distributed users to review, edit, and share manual annotations. The WebApollo client is designed as an extension to JBrowse, a genome browser that provides a fast, highly interactive interface for visualization of genomic data. WebApollo allows users to create and modify transcript and exon structures through intuitive gestures, and flags potential problems within these manual annotations.

1. {
Web Apollo
A Web-based Genomics Annotation Editing Platform
Eduardo Lee, Gregg Helt, Justin Reese, Monica Munoz-Torres*, Christopher
Childers, Rob Buels, Lincoln Stein, Ian Holmes, Christine Elsik, Suzanna Lewis
Arthropod Genomics Symposium 2013 | South Bend, IN | * @monimunozto
Lawrence Berkeley National Laboratory, Joint Genome Institute, for the US Department of Energy at UCB

2.  The first real-time, collaborative genomics
annotation editor on the Web
 Easy-to-use environment for multiple,
distributed users to review, update, and share
genome feature markups
Web Apollo is:

3. Working Concept
‘Gene Models’
Automated predictions,
assisted by some evidence
‘Evidence’
cDNA, HMM searches for
protein domains, alignments
of assemblies, curated genes
or other species
‘Manual annotation’:
Correct coordinates for
genes of interest.

4. The need for annotation tools
Assembly
Manual
annotation
Experimental
validation
Automated
Annotation
Requires optimized genome
visualization and editing tools
The need for genome visualization and editing tools prompted the
development of the genome browsers we commonly use.
Annotation editing tools then became necessary.

5.  Gather and evaluate all available evidence using quality-
control metrics, to corroborate/modify automated predictions
 Use literature and public databases to infer gene function
from experimental data
 Run sequence-similarity searches within a phylogenetic
framework (e.g. alignment trees)
 To predict protein functional assignments
 Distinguish orthologs from paralogs, classify genes as members
of a family
 Otherwise, incorrect and incomplete genome annotations will
poison every experiment that uses them
Manual curation is necessary!

6.  Access to computational analysis
& experimental evidence
 Manual annotation & curation
 Compatibility with GMOD
 Saved annotations directly to
database (not via email)*
 Widely used (initially designed
for centralized, resource-rich
projects).
Apollo: Desktop and Java Web Start*

7.  BUT…
 Must load all data for a region (range) at once
 No [automated]* support for sharing
 Possible update conflicts due to stale annotation data
 One annotator at a time
 Edits from other users not visible without reloading
 Require Apollo Download, Chado Install, Java Installation*
Apollo: Desktop and Java Web Start*

8. The need for updated tools
The democratization of genome-scale sequencing
calls for a new kind of annotation editing tool.
• more assembly errors
• lack of gold standard gene
structure training data

9.  No installation required (for users).
 User interface is a browser-based
Javascript client communicating with an
annotation editing server.
Apollo: on the Web
 Is a plug-in for JBrowse, a successor to
the GBrowse genome browser. (GMOD)
 Plug-in offers a ‚User-created
Annotations‛ track.
 Real Time annotation updates;
annotations saved to centralized
database.
 Uses dynamic (lazy) data loading:
only the region of interest
 Customizable: rules, appearance.
 Supports user authentication:
 read, edit, review, complete, publish (export).
 Automatically promote tracks (script).

10. Navigation tools:
pan and zoom
Search box: go
to a scaffold or a
gene model.
Grey bar of coordinates
indicates location. You can
also select here in order to
zoom to a sub-region.
‘Options’:
change color by
CDS, toggle
strands
‘File’:
Upload your
own evidence:
GFF3, BAM,
BigWig, VCF*
‘Tools’:
Use BLAT to query the
genome with a protein
or DNA sequence.
Available Tracks
Evidence Tracks Area
‘User-created Annotations’ Track
‘Share’: a stable link
shares your view and
shows exactly what
you are seeing (keeps a
record of your
annotation process)
Login
Web Apollo
Graphical User Interface (GUI) for editing annotations

11. Flags non-canonical
splice sites.
Selection of features and
sub-features
Edge-matching
Evidence Tracks Area
‘User-created Annotations’ Track
Web Apollo
 The editing logic is on the server:
 selects longest ORF as CDS
 flags non-canonical splice sites

12. DNA Track
‘User-created Annotations’ Track
 Two new kinds of tracks:
 annotation editing
 sequence alteration editing
Web Apollo

13. Web Apollo
 Annotations, annotation edits and History are stored in centralized
database

14. Web Apollo
 Annotation Information Editor

15. - BAM
- BigWig
- GFF3
- VCF*
Trellis
Data Broker
(Java)
Static JSON
Generation Pipeline
(Perl)
Server-side Data Service Annotation Editing Engine (Java)
Berkeley DB
realtime store
User
Management
Data Sources
Analysis Pipelines
- BAM
- BED
- BigWig
- GFF3
- MAKER
output
Data Repositories
Chado
MySQL
DAS servers
e.g. Ensembl
Annotation Exports
Local DB.
e.g. Chado
- GFF3
- FASTA
Annotators
Web
Apollo
JBrowse
Apollo Edit Operations
& User Management
User Interface (JavaScript)
JSON
Web Apollo
Architecture

16. DEMO

17.  Ability to annotate regulatory regions & features
 Collapsing and expanding tracks
 Sticky ‘User Annotations’ track
 Genome slicing: annotating across contigs
 Folding of intronic space
 Web Apollo at GMOD in the cloud
[Near] Future Enhancements

18.  Release
 http://genomearchitect.org/webapollo/releases
 Demo Site
 http://genomearchitect.org/WebApolloDemo
 User Guide
 http://genomearchitect.org/webapollo/docs/webapollo_user_guide.pdf
 At GMOD
 http://gmod.org/wiki/WebApollo
Releases & Demo

19.  To all our users & contributors! Especially:
 Code: Mitch Skinner, Nomi Harris, Thomas Down, Carson Holt.
 Feedback: Sue Brown, Sanjay Chellapilla, Daniel Ence, Juergen
Gadau, Nicolae Herndon, Elisabeth Huguet, Carolyn Lawrence,
Sasha Mikheyev, Barry Moore, Jan Oettler, Xiang Qin, Lukas
Schrader, Kim Worley, Mark Yandell, Jing-Jiang Zhou.
Formatting: Anna Bennett.
 To our funding agencies:
 NIH: NIGMS and NHGRI.
 DOE: Office of the Director, Office of Science, Office of Basic
Energy Sciences.
Thanks

20. Thanks
 VectorBase
 AgriPest Base
 FlyBase
 Hymenoptera Genome Database
 Apis mellifera
 Tribolium castaneum
 Pogonomyrmex barbatus
 Manduca sexta
 Bombus terrestris
 Helicoverpa armigera
 Nasonia vitripennis
 Acyrthosiphon pisum
 Mayetiola destructor
 Atta cephalotes
 Linepithema humile
 Camponotus floridanus
 Solenopsis invicta
 Acromyrmex echinatior