1. Programmatic access to EMBL-EBI resources
Web Services
Programmatic access to EMBL-EBI resources
Andrew Cowley

2. Web interfaces are great for several uses
Single jobs
Hypothesis testing
Publications
Training
But what if I want to examine every sequence in a proteome?
Or my data needs lots of repetitive analysis?

3. Solution 1 – local install
You could download programs/data to your own computer/server
Lots of control
Flexible
Add your own programs/data
But data is large
Storage cost
Maintenance/updating cost
Just how friendly are you with your local IT?!

4. Solution 2 – Script against websites
Literally automatic pasting data and clicking ‘run’??!
NO! (well, please don’t)
Instead, resources expose APIs (Application Programming Interface) via Web Services
Use EMBL-EBIs compute resources, and up-to-date programs and data

5. Web Services Well-established protocols: REST and SOAP
Built-in function help
Large range of example clients available to download and run as is
‘Easy’ to plug into existing workflow tools
Many third-party tools also exist that use our Web Services behind the scenes
(In fact they’re so nice, we use them a lot either behind our own web interface or to chain together bioinformatics services)

6. EBI Search WS usage: Results enrichment
Sequence similarity search tool results display referenced data, e.g. for BLAST/FASTA search:

7. Web Service examples
Client front end and results, WP engine (UniProt, InterProScan)

8. Web Service examples
External front end and results

9. EBI Search

10. EBI Search

11. How analysis tools are called
Jobs per month

12. Web Services
Synchronous & asynchronous

13. Web Services - synchronous

14. Web Services - synchronous

15. Web Services - asynchronous
JobID
“Is JobID done?”
“Still cooking”

16. Web Services - asynchronous
“Is JobID done?”
“It’s ready!”
Fetch JobID

17. Steps... Input parameters
Meta-Information
List parameters
Get parameter details → Name, description, values...
Submission
Run ( , title, values...) → Job Identifier
Check status → RUNNING, FINISHED, ERROR...
Results analysis
List results available → Name, description, media type...
Get result → Output, text, binaries (images)...
Input
parameters
Job identifier (e.g. iprscan-S pg)

18. Web Services role play…

19. Key resources Documentation/example clients
Pre-compiled clients available for a large variety of languages
SOAP
WSDL:
Most programming languages have SOAP client libraries
Generate stubs or dynamically call methods
REST
Basic HTTP requests
Web browser, HTTP client libraries, CURL…

20. Tools at EMBL-EBI http://www.ebi.ac.uk/services
Analyse your own data via ~100 tools:
Search across our databases for homologous sequences using a suite of tools from classics such as BLAST and FASTA to recent advances such as PSI-Search
Functionally annotate your sequence with protein domains and important sites using InterProScan
Align your sequences to discover conserved regions with Clustal Omega, MUSCLE etc.
Perform sequence translation, repeat analysis/masking, trans- membrane topology prediction etc. with EMBOSS and other tools
Results enriched with data from EBI resources
As well as providing data itself at EMBL-EBI, we also enable you to analyse your own data using our resources and data collections.
The wide-ranging tools are developed internally, externally and by collaboration with leading authors. They are incorporated into our web framework to allow a consistent user experience, access to the latest data and to leverage cross-resource information, for example automatically annotating aligned regions of a BLAST protein search with domain and motif information.
(and there are tools for things other than sequence! I’ve just concentrated on them for brevity)
Sequence similarity searching:
Central to genome annotation
Characterising protein families
Exploring distant evolutionary relationships

21. Tools at EMBL-EBI

22. Web Services exercise Linux command line help
Open terminal
cd =change directory/folder
cd .. =go up directory
mkdir =make directory
cp <file1> <file2> =copy
[tab] auto completes
ls =list files in current directory
./[program] run program in my current directory
cat =view contents of text file
[shift PgUp/PgDn] scroll up/down a page
[double click] select word
[right click] paste
chmod a+x <file> =make file executable

23. Workflows

24. Workflows
Galaxy
Taverna

25. Web Services workflow
$ncbiblast_lwp.pl -- --program blastp --database uniprotkb_human --stype protein P01174.fasta
$wsdbfetch_soaplite.pl fasta > P01174search2016_11_03.fasta
$kalign_soaplite.pl -- P01174search2016_11_03.fasta

26. Web Services workflow
$ncbiblast_lwp.pl -- --program blastp --database uniprotkb_human --stype protein P01174.fasta | wsdbfetch_soaplite.pl fasta | kalign_soaplite.pl -- -

27. How to get help/contact us
Most resources have Web Services or programmatic API links for more info
Central collection of links/example clients:
Step-by-step instructions and example command lines:
“Using EMBL-EBI Services via Web Interface and Programmatically via Web Services”
Lopez R , Cowley A , Li W , McWilliam H
Curr Protoc Bioinformatics Dec 12;48: doi: / bi0312s48
Helpdesk: