publications · introduction to the ensembl rest apis astrid gall emily perry. session structure...

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Training materials

EBI is an Outstation of the European Molecular Biology Laboratory.

Custom data export with Ensembl BioMart

Erin Haskell

helpdesk@ensembl.org

@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 helpdesk@ensembl.org

EBI is an Outstation of the European Molecular Biology Laboratory.

Custom data export with Ensembl BioMart

Erin Haskell

helpdesk@ensembl.org

@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 helpdesk@ensembl.org

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 helpdesk@ensembl.org

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 helpdesk@ensembl.org

Ensembl public mailing lists:

dev@ensembl.org

announce@ensembl.org

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