publications · introduction to the ensembl rest apis astrid gall emily perry. session structure...
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• If you wish to re-use these materials, please credit Ensembl for their creation
• If you use Ensembl for your work, please cite our papers
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Training materials
EBI is an Outstation of the European Molecular Biology Laboratory.
Custom data export with Ensembl BioMart
Erin Haskell
@ensembl /@mycoacia
Questions?○ We’ve muted all of your microphones
○ Join our Slack workspace and ask questions (link in your registration confirmation email)
○ My Ensembl colleagues will respond during the talk
○ Please reply @username to reply to a specific person
Emily Perry Astrid Gall
Course exercisesAll materials and exercises located here:
http://www.ebi.ac.uk/training/online/course/ensembl-browser-webinar-series-2016
A link to exercises and their solutions will appear in the
page hierarchy
This text will be replaced by a YouTube (link to YouKu too) video of the webinar
and a pdf of the slides.
The “next page” will be the exercises
Get help with the exercises
• Use the exercise solutions in the online course
• Join our Slack workspace and discuss the exercises with everybody in dedicated channels (register to get sent a link)
• Email us [email protected]
EBI is an Outstation of the European Molecular Biology Laboratory.
Custom data export with Ensembl BioMart
Erin Haskell
@ensembl /@mycoacia
This webinar courseDate Webinar topic Instructor
4th Sept Introduction to Ensembl ✔�
Ensembl genes ✔�
Astrid Gall
Emily Perry
6th Sept Variation data in Ensembl and the Ensembl VEP ✔�
Comparing genes and genomes with Ensembl Compara ✔�
Erin Haskell
Astrid Gall
11th Sept Finding features that regulate genes – the Ensembl Regulatory Build ✔�
Data export with BioMart
Emily Perry
Erin Haskell
13th Sept Uploading your data to Ensembl
Introduction to the Ensembl REST APIs
Astrid Gall
Emily Perry
Session structurePresentation:
- What is BioMart?- How to build a query
Exercises:Available on the train online site
Demo:Using BioMart
What is BioMart?
• An Ensembl tool available through the website
• Export varied data with no programming skills required
• Quickly build highly-customised queries using point-and-click
• View results online or download in variety of formats
For things that would be time consuming or difficult with the Ensembl browser
Why use BioMart?
● Query multiple things at once:○ Convert IDs from different databases○ Gene locations○ Download sequences
● Export large amounts of data
I want a sandwich!
Why use BioMart?
I want a sandwich!
Why use BioMart?
Why use BioMart?I want a sandwich!
Where to find BioMart www.ensembl.org/biomart/martview
grch37.ensembl.org/biomart/martview
In ensemblgenomes.org:division.ensembl.org/biomart/martview***Not available for Bacteria***
BioMart queries: The 4 step process
AttributesFiltersDataset Results
Choose database
and species
Narrow down the dataset
Column headers in
output table
Table or sequences
Building a BioMart query: Step 1 Dataset
AttributesFiltersDataset Results
● Choose the database:○ Genes, Variation, Regulation
● Choose your dataset:○ Define the species
Filters
Building a BioMart query: Step 2 Filters
AttributesDataset Results
Define a (large) set of genes/variants by combinations of filters, eg:
○ A region○ A list of IDs○ Function (GO term)○ Phenotypes Filter 1 Filter 2
Get attributes for these
Filters
Building a BioMart query: Step 3 Attributes
Dataset Results
Define your output variables you want for your dataset, eg:
○ IDs (from other databases)○ Features○ Sequences○ Orthologues/paralogues
Attributes
Filters
Building a BioMart query: Step 3 Attributes
Dataset ResultsAttributes
Filters
Building a BioMart query: Step 4 Results
Dataset
● Table: ○ HTML○ TSV○ CSV○ Excel (xls)
● Sequence:○ FASTA
Attributes Results
Building a BioMart query: filters vs attributes
AttributesFilters vs.
For each query…
- Your search terms
- The answers you want
Filters
Attributes
Building a BioMart query: filters vs attributes
AttributesFilters vs.
“Which of my human genes are also present in cat?”
Filter the output to only show me genes that have orthologues in cat
Show me all my genes and the matching gene ID in cat if it has one
Filters
Attributes
Building a BioMart query: filters vs attributes
AttributesFilters vs.
“Which of my human genes are also present in cat?”
Filters
Attributes
Building a BioMart query: help!
We want to find out the following information about these genes:
ESPN, MYH9, USH1C, CISD2, THRB, GIPC3.
1) Are there associated functions from the GO (Gene Ontology)
project that might help describe their function?
2) What are the NCBI IDs for these genes?
3) What are their cDNA sequences?
Hands on
Course exercisesAll materials and exercises located here:
http://www.ebi.ac.uk/training/online/course/ensembl-browser-webinar-series-2016
A link to exercises and their solutions will appear in the
page hierarchy
This text will be replaced by a YouTube (link to YouKu too) video of the webinar
and a pdf of the slides.
The “next page” will be the exercises
Get help with the exercises
• Use the exercise solutions in the online course
• Join our Slack workspace and discuss the exercises with everybody in dedicated channels (register to get sent a link)
• Email us [email protected]
This webinar courseDate Webinar topic Instructor
4th Sept Introduction to Ensembl ✔�
Ensembl genes ✔�
Astrid Gall
Emily Perry
6th Sept Variation data in Ensembl and the Ensembl VEP ✔�
Comparing genes and genomes with Ensembl Compara ✔�
Erin Haskell
Astrid Gall
11th Sept Finding features that regulate genes – the Ensembl Regulatory Build ✔�
Data export with BioMart ✔�
Emily Perry
Erin Haskell
13th Sept Uploading your data to Ensembl
Introduction to the Ensembl REST APIs
Astrid Gall
Emily Perry
Coming up!
Uploading your data to Ensembl
As well as exploring genomic data through the web interface, you are
also able to upload your own data to view within the browser.
This webinar will show you how you can view custom data, such as
BED or BAM files, in the Ensembl browser.
Introduction to the Ensembl REST APIs
This final webinar will introduce the Ensembl REST API, which can be used for language agnostic programmatic access to the Ensembl database.
Astrid Gall
Thursday 13th September, 15:00 BST
Emily Perry
Keep in touch!
facebook.com/ensembl.org
@ensembl@ensemblgenomes@mycoacia
www.ensembl.info
Email us [email protected]
Online courses: http://www.ebi.ac.uk/training/Tutorials www.ensembl.org/info/website/tutorials
Videos and demonstrations:
www.youtube.com/user/EnsemblHelpdesk
http://u.youku.com/Ensemblhelpdesk
Email us [email protected]
Ensembl public mailing lists:
Help and documentation
Zerbino D. et al
Ensembl 2018
Nucleic Acids Research (2017) gkx1098, doi.org/10.1093/nar/gkx1098
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkx1098/4634002
Xosé M. Fernández-Suárez and Michael K. SchusterUsing the Ensembl Genome Server to Browse Genomic Sequence Data.Current Protocols in Bioinformatics (2010) 30:1.15.1-1.15.48http://europepmc.org/abstract/MED/20521244
Giulietta M. Spudich and Xosé M. Fernández-SuárezTouring Ensembl: A practical guide to genome browsingBMC Genomics (2010) 11:295http://europepmc.org/articles/PMC2894802
...and topic-specific publications mentioned throughout the workshop
Publicationshttp://www.ensembl.org/info/about/publications.html
The Ensembl team
Acknowledgements - the Ensembl team
• Ensembl training materials are protected by a CC BY license
http://creativecommons.org/licenses/by/4.0/
• If you wish to re-use these materials, please credit Ensembl for their creation
• If you use Ensembl for your work, please cite our papers
http://www.ensembl.org/info/about/publications.html
Training materials