An introduction to Web Apollo for i5K Pilot Species Projects - Hemiptera

An introduction to Web Apollo.
A webinar for the i5K Pilot Species Projects - Hemiptera
Monica Munoz-Torres, PhD
Biocurator & Bioinformatics Analyst | @monimunozto
Genomics Division, Lawrence Berkeley National Laboratory
12+1 May, 2014
UNIVERSITY OF
CALIFORNIA

Outline
1. What is Web Apollo?:
• Definition & working concept.
2. Community based curation from our
experience. Lessons Learned.
3. Manual Annotation at i5K: how do we
get there?
4. Becoming acquainted with Web
Apollo.
An introduction to
Web Apollo.
A webinar for the i5K
Pilot Species Projects -
Hemiptera.
Outline 2

What is Web Apollo?
• Web Apollo is a web-based, collaborative genomic
annotation editing platform.
We need annotation editing tools to modify and refine the
precise location and structure of the genome elements that
predictive algorithms cannot yet resolve automatically.
31. What is Web Apollo?
Find more about Web Apollo at
http://GenomeArchitect.org
and
Genome Biol 14:R93. (2013).

Brief history of Apollo*:
a. Desktop:
one person at a time editing a
specific region, annotations
saved in local files; slowed down
collaboration.
b. Java Web Start:
users saved annotations directly
to a centralized database;
potential issues with stale
annotation data remained.
1. What is Web Apollo? 4
Biologists could finally visualize computational analyses and
experimental evidence from genomic features and build
manually-curated consensus gene structures. Apollo became a
very popular, open source tool (insects, fish, mammals, birds, etc.).
*

Web Apollo
• Browser-based; plugin for JBrowse.
• Allows for intuitive annotation creation and editing,
with gestures and pull-down menus to create
transcripts, add/delete/resize exons, merge/split
exons or transcripts, insert comments
(CV, freeform text), etc.
• Customizable rules and
appearance.
• Edits in one client are
instantly pushed to all other
clients: Collaborative!
1. What is Web Apollo? 5

Working
Concept
In the context of gene manual annotation,
curation tries to find the best examples
and/or eliminate (most) errors.
To conduct manual annotation efforts:
Gather and evaluate all available evidence
using quality-control metrics to
corroborate or modify automated
annotation predictions.
Perform sequence similarity searches
(phylogenetic framework) and use
literature and public databases to:
• Predict functional assignments from
experimental data.
• Distinguish orthologs from paralogs,
and classify gene membership in
families and networks.
2. In our experience. 6
Automated gene models
Evidence:
cDNAs, HMM domain searches,
alignments with assemblies or
genes from other species.
Manual annotation & curation

Dispersed, community-based gene
manual annotation efforts.
Using Web Apollo, we* have trained
geographically dispersed scientific
communities to perform biologically
supported manual annotations, and
monitored their findings: ~80 institutions,
14 countries, hundreds of scientists, and
gate keepers.
– Training workshops and geneborees.
– Tutorials with detailed instructions.
– Personalized user support.
2. In our experience. 7
*Collaboration with Elsik Lab,
Hymenoptera Genome
Database.

What have we learned?
Harvesting expertise from dispersed researchers who
assigned functions to predicted and curated peptides,
we have developed more interactive and responsive
tools, as well as better visualization, editing, and
analysis capabilities.
82. In our experience.

It is helpful to work together.
Scientific community efforts bring together domain-
specific and natural history expertise that would have
otherwise remain disconnected.

Improved Automated Annotations*
In many cases, automated annotations have been
improved (e.g: Apis mellifera. Elsik et al. BMC Genomics 2014, 15:86).
Also, learned of the challenges of newer sequencing
technologies, e.g.:
– Frameshifts and indel errors
– Split genes across scaffolds
– Highly repetitive sequences
To face these challenges, we train annotators in
recovering coding sequences in agreement with all
available biological evidence.

Understanding the evolution of sociality.
Comparison of the genomes of 7 species of
ants contributed to a better understanding
of the evolution and organization of insect
societies at the molecular level.
Insights drawn mainly from six core aspects of
ant biology:
1. Alternative morphological castes
2. Division of labor
3. Chemical Communication
4. Alternative social organization
5. Social immunity
6. Mutualism
11
… groups of
communities
have taught us a
lot!
Libbrecht et al. 2012. Genome Biology 2013, 14:212

A little training goes a long way!
With the right tools, wet lab scientists make exceptional
curators who can easily learn to maximize the
generation of accurate, biologically supported gene
models.

Manual annotation at i5K
How do we get there?
3. How do we get there? 13
Assembly
Manual
annotation
Experimental
validation
Automated
Annotation
In a genome sequencing project…

Gene Prediction
Gene Prediction:
Identification of protein-coding genes, tRNAs, rRNAs,
regulatory motifs, repetitive elements (masked), etc.
Ab initio or homology-based. E.g: fgenesh, Augustus,
geneid, SGP2
14
Nucleic Acids 2003 vol. 31 no. 13 3738-3741
3. How do we get there?

Gene Annotation
Gene Annotation:
Integration of data from prediction tools to generate a
consensus set of predictions (gene models).
• Models may be organized by:
- automatic integration of predicted sets; e.g: GLEAN
- packaging necessary tools into pipeline; e.g: MAKER
• Transcriptomes are used to further inform the annotation
process.

The Collaborative Curation Process at
i5K
1) A computationally predicted consensus gene set has
been generated using multiple lines of evidence; e.g.
CLEC_v0.5.3-Models.
2) i5K Projects will integrate consensus computational
predictions with manual annotations to produce an updated
Official Gene Set (OGS):
» If it’s not on either track, it won’t make the OGS!
» If it’s there and it shouldn’t, it will still make the OGS!

Consensus set: reference and start point
• In some cases algorithms and metrics used to generate
consensus sets may actually reduce the accuracy of the gene’s
representation; e.g. use Augustus model instead to create a new
annotation.
• Isoforms: drag original and alternatively spliced form to ‘User-
created Annotations’ area.
• If an annotation needs to be removed from the consensus set,
drag it to the ‘User-created Annotations’ area and label as
‘Delete’ on Information Editor.
• Overlapping interests? Collaborate to reach agreement.
• Follow guidelines for i5K Pilot Species Projects as shown at
http://goo.gl/LRu1VY

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.
‘View’: change
color by CDS,
toggle strands,
set highlight.
‘File’:
Upload your own
evidence: GFF3,
BAM, BigWig, VCF*.
Add combination
and sequence
search tracks.
‘Tools’:
Use BLAT to query the
genome with a protein
or DNA sequence.
Available Tracks
Evidence Tracks Area
‘User-created Annotations’ Track
Login
Web Apollo
Graphical User Interface (GUI) for editing annotations
4. Becoming Acquainted with Web Apollo.

Flags non-
canonical splice
sites.
Selection of features and
sub-features
Edge-matching
Evidence Tracks Area
 The editing logic (server):
 selects longest ORF as CDS
 flags non-canonical splice sites
Web Apollo

DNA Track
 Two new kinds of tracks:
 annotation editing
 sequence alteration editing
Web Apollo

Web Apollo
 Annotations, annotation edits, and History: stored in a centralized database.

Web Apollo
 Annotation Information Editor

[Some of the] Functionality:
 Protein-coding gene annotation (that you know and love)
 Sequence alterations (less coverage = more fragmentation)
 Visualization of stage and cell-type specific transcription data as
coverage plots, heat maps, and alignments

Example: ORCO
Live Demonstration using the Cimex lectularius genome
Footer 25

Arthropodcentric Thanks!
AgriPest Base
FlyBase
Hymenoptera Genome Database
VectorBase
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

Thanks!
• Berkeley Bioinformatics Open-source Projects
(BBOP), Berkeley Lab: Web Apollo and Gene
Ontology teams. Suzanna E. Lewis (PI).
• Elsik Lab. § University of Missouri. Christine G.
Elsik (PI).
• Ian Holmes (PI). * University of California Berkeley.
• Arthropod genomics community, i5K
http://www.arthropodgenomes.org/wiki/i5K Steering
Committee, USDA/NAL, HGSC-BCM, BGI, and
1KITE http://www.1kite.org/.
• Web Apollo is supported by NIH grants 5R01GM080203
from NIGMS, and 5R01HG004483 from NHGRI, and by the
Director, Office of Science, Office of Basic Energy
Sciences, of the U.S. Department of Energy under Contract
No. DE-AC02-05CH11231.
• Insect images used with permission:
http://AlexanderWild.com
• For your attention, thank you!
Thank you. 27
Web Apollo
Ed Lee
Gregg Helt
Colin Diesh §
Deepak Unni §
Rob Buels *
Gene Ontology
Chris Mungall
Seth Carbon
Heiko Dietze
BBOP
Web Apollo: http://GenomeArchitect.org
GO: http://GeneOntology.org
i5K: http://arthropodgenomes.org/wiki/i5K

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