Workshop held at PAG Asia 2015

1. PAG-ASIA Singapore
13th July 2015
Genomic Resources at the EMBL-EBI
Denise Carvalho-Silva (Ensembl and Ensembl Genomes)
Gary Saunders (European Variation Archive, EVA)
www.ebi.ac.uk
@emblebi

2. What is EMBL-EBI?
• Part of the European Molecular
Biology Laboratory
• European Bioinformatics Laboratory
• Based in Hinxton - Cambridge (UK)
EMBL-EBI staff:
> 500 people
> 50 nations
Europe’s hub for:
Bioinformatics Services (free)
User Training
Computational Research
Engagement with the Industry

3. EMBL-EBI users: a one-day snapshot
Hub in Europe à worldwide user community

4. www.ebi.ac.uk

5. 5
www.ebi.ac.uk/services

6. Our services

7. Archive
ClassifyShareAnalyse
Provide
tools
EMBL-EBI’s
data cycle

8. This workshop: 1:00-3:00 pm

9. www.ebi.ac.uk/training
@EBItraining

10. Training at EMBL-EBI, off-site and online

11. Register to EMBL-EBI train online
• www.ebi.ac.uk/training/online
• Take – record quizzes
• Get updates on new courses, features
Quarterly newsletter
• Get involved in usability testing

15. PAG-ASIA Singapore
13th July 2015
Ensembl and Ensembl Genomes:
Browser and toolkit
Denise Carvalho-Silva, PhD
www.ensembl.org
www.ensemblgenomes.org
@ensembl
@ensemblgenomes

16. EBI is an Outstation of the European Molecular Biology Laboratory.
Outline
• Introduction to Ensembl and Ensembl Genomes
• Some highlights of last year
• Live demos
1. Browser and custom data upload
2. Toolkit: BioMart and VEP
• How to cite and connect with us

17. EBI is an Outstation of the European Molecular Biology Laboratory.
Outline
• Introduction to Ensembl and Ensembl Genomes
• Some highlights of last year
• Live demos
1. Browser and custom data upload
2. Toolkit: BioMart and VEP
• How to cite and connect with us

18. EBI is an Outstation of the European Molecular Biology Laboratory.
Do We Need Genome Browsers?
q YES q NO

19. EBI is an Outstation of the European Molecular Biology Laboratory.

20. EBI is an Outstation of the European Molecular Biology Laboratory.
Annotation: Making sense

21. EBI is an Outstation of the European Molecular Biology Laboratory.
The Ensembl projects
www.ensembl.org
www.ensemblgenomes.org
• launched in 1999
• Ensembl gene annotation
• EBI and WTSI
• launched in 2009
• community gene annotation
• EBI

22. EBI is an Outstation of the European Molecular Biology Laboratory.
Vertebrate genomes
www.ensembl.org
pre.ensembl.org
>80 genomes*
D. melanogaster
C. elegans
S. cerevisae
*Release 80
May 2015

23. EBI is an Outstation of the European Molecular Biology Laboratory.
Extends the use of Ensembl to other species
Wider taxonomic range (v27, >25K genomes)
Non-vertebrate genomes
x 53
x 39
x 408
x 133
x 24,913
plants.ensembl.org

24. EBI is an Outstation of the European Molecular Biology Laboratory.
Dicotyledons
12 in 7 orders: Brassicales, Fabales, Malpighiales,
Malvales, Rosales, Solanales, Vitales

25. EBI is an Outstation of the European Molecular Biology Laboratory.
Monocotyledons
Poales
Zingiberales
21 in 2 orders
etc…

26. EBI is an Outstation of the European Molecular Biology Laboratory.
'Others': 6 in 5 Classes

27. EBI is an Outstation of the European Molecular Biology Laboratory.
Comparative GenomicsGene models
Custom data display
Programmatic access Free code and data
RegulationVariation Toolkit
Ensembl features

28. How to access our data

29. EBI is an Outstation of the European Molecular Biology Laboratory.
Outline
• Introduction to Ensembl and Ensembl Genomes
• Some highlights of last year
• Live demos
1. Browser and custom data upload
2. Toolkit: BioMart and VEP
• How to cite and connect with us

30. EBI is an Outstation of the European Molecular Biology Laboratory.
Highlights
• New assemblies
• Genotype data for Iranian and Moroccan sheep*
• Update SNP and phenotype data
http://appris.bioinfo.cnio.es
*http://projects.ensembl.org/nextgen/#fn1
http://www.ebi.ac.uk/gxa/home
• APPRIS
•

31. EBI is an Outstation of the European Molecular Biology Laboratory.
Highlights

32. EBI is an Outstation of the European Molecular Biology Laboratory.
Highlights

33. EBI is an Outstation of the European Molecular Biology Laboratory.
• New assemblies
Highlights
• New RNA-Seq data
• New whole genome alignments
• Toolkit: assembly converter v2.4 v25
• New variation data

34. EBI is an Outstation of the European Molecular Biology Laboratory.
Outline
• Introduction to Ensembl and Ensembl Genomes
• Some highlights of last year
• Live demos
1. Browser and custom data upload
2. Toolkit: BioMart and VEP
• How to cite and connect with us

35. EBI is an Outstation of the European Molecular Biology Laboratory.
Live demos
1. Browsers
• Viewing our annotation
• Attaching custom data
2. Toolkit
1.
2. v

36. The Arabidopsis floral homeotic gene APETALA1 (AP1)
encodes a putative TF that acts locally to specify the
identity of the floral meristem and to determine sepal and
petal development (https://www.wikigenes.org/e/gene/
e/843244.html).
Browser demo

37. EBI is an Outstation of the European Molecular Biology Laboratory.
Toolkit: BioMart
• Data export tool for easy retrieval of Ensembl/Ensembl Plants data
DATA FILTERS ATTRIBUTES RESULTS
e.g.
Gene IDs
e.g. Tables
FASTA
wheate.g. Gene
e.g. Homologs
Sequences
Domains

38. EBI is an Outstation of the European Molecular Biology Laboratory.
Live demo: exporting data with BioMart
I’ve got a list of affymetrix probeset IDs from my microarray
experiment that seem to map uniquely to genes in the chicken
genome. Here they are: Gga.1444.1.S1_at, Gga.12669.1.S1_at,
GgaAffx.7784.1.S1_at, GgaAffx.12530.1.S1_at
• What are the Ensembl IDs, names and locations of these genes
• Possible function according to the Gene Ontology (GO) names
• Export their protein sequences and get them emailed to me
Tip: include probeset IDs
in the results table

39. Toolkit: The Variant Effect Predictor
• Annotate your own SNPs and CNVs
• Different input formats
• SIFT/PolyPhen for missense variants
PMID: 20562413
Perl scriptWeb interface REST API
XML

40. EBI is an Outstation of the European Molecular Biology Laboratory.
CODING
Synonymous
INTRONIC5’ UTR
ATG AAAAAAA
Regulatory
Splice sites
CODING
Missense
3’ UTR5’ Upstream 3’ downstream
Mapping variants on transcripts
Identify transcripts that overlap variants and predict
their functional consequence using

41. EBI is an Outstation of the European Molecular Biology Laboratory.
Live demo: annotating my variants
My GWAS experiments in pigs have identified few variants associated
with meat quality:
chr 18, genomic coordinate 37452309, alleles A/T, forward strand
chr 10, genomic coordinate 17387779, alleles G/A, forward strand
chr X, genomic coordinate 120285089, alleles A/-, forward strand
Can I use VEP to annotate them and find out:
• in which genes and transcripts they map to
• what effect do these variants have on these transcripts?
• are these variants known in public databases?

42. EBI is an Outstation of the European Molecular Biology Laboratory.
Ensembl videos

43. EBI is an Outstation of the European Molecular Biology Laboratory.
Outline
• Introduction to Ensembl and Ensembl Genomes
• Some highlights of last year
• Live demos
1. Browser and custom data upload
2. Toolkit: BioMart and VEP
• How to cite and connect with us

44. Latest publication

45. EBI is an Outstation of the European Molecular Biology Laboratory.
Latest Publication

46. Acknowledgements
Funding
European Commission
Framework Programme 7

47. EBI is an Outstation of the European Molecular Biology Laboratory.
Acknowledgements
Our users and our funders
Ensembl Genome team

48. EBI is an Outstation of the European Molecular Biology Laboratory.
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PAG
PAG
Connect with us
helpdesk@ensemblgenomes.org
helpdesk@ensembl.org

49. Ensembl workshops at your institute
Activities
Countries
Continents
Trainers
Participants
~100
19
3
~30
2,087
Host our workshops! denise@ebi.ac.uk
2014