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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
 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:
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.
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.
 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!
 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*
 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*
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
 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).
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
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
DNA Track
‘User-created Annotations’ Track
 Two new kinds of tracks:
 annotation editing
 sequence alteration editing
Web Apollo
Web Apollo
 Annotations, annotation edits and History are stored in centralized
database
Web Apollo
 Annotation Information Editor
- 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
DEMO
 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
 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
 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
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

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Web Apollo: A Web-based Genomics Annotation Editing Platform. 13ArthGen

  • 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

Editor's Notes

  1. - Thank the organizers, specially the scientific committee- Introduce the team, collaboration between three labs.
  2. - The need for genome visualization and editing tools prompted the development of the genome browsers we commonly use. - It was further necessary to create editing tools.
  3. Before I explain to you about the tools we have been working on, I will first explain why I think Manual curation is necessary.
  4. A series of changes have introduced both positive and negative elements into the process of genome sequencing and annotation- Cheaper sequencingMore researchers getting involvedMore genomes being sequencedHigh throughput RNAseq and improved automated annotationMore assembly errors & lack of gold standards are more reasons for manual annotation.All of these factors are part of a process we call ‘the democratization of genome-scale sequencing’, which calls for a new kind of tool.
  5. - Apollo API, using Javascript. - No installation required.- JBrowse plugin with “User-created Annotations” track.- Uses dynamic (lazy) data loading- Real Time annotation updates to centralized database.- Customizable: rules, appearance, user authentication.- Auto-promote (script)
  6. File: GFF3, BAM, BigWig, VCF (soon).Tools: The plug-in architecture of the annotation editing engine allows for sequence alignment searches using BLAT
  7. The editing logic is on the server:It selects the longest ORF as CDSAnd flags non-canonical splice sitesThe server is a Java servlet- it uses the GMOD biological object layer (gbol) data model: object model & API, based on the Chado schema
  8. A BerkeleyDB stores annotations, annotation edits, and their History
  9. Take Home Message:Annotators can upload their own data. Data Sources: Analysis Pipelines can process BAM, BED, BigWig, GFF3, and MAKER output without “much” massaging.Data Repositories: INNOVATION: Trellis A data broker with plug-in architecture for both output formats and back-end data stores.On the back-end we implemented 3 plug-ins for:- UCSC MySQL genome database- Chado- DAS servers (e.g.: Ensembl)