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European Life Sciences Infrastructure for Biological Information
www.elixir-europe.org
Rafael C Jimenez
ELIXIR CTO
EMBL-EBI workshop networks and pathways 2014, Friday 23June
An introduction to
programmatic access

Query interfaces
2
Graphical
User
Interface
(GUI)
FTP
access
Database
access
Application
Programmatic
Interface
(API)
Data
Web
Services
Biologist Bioinformaticians Developers
remote resource

Query interfaces
3
Graphical
User
Interface
(GUI)
FTP
access
Database
access
Application
Programmatic
Interface
(API)
Data
Web
Services
This introduction is intended for a non technical audience
with purposely simplified technical concepts.
remote resource

Web Services
Service on the server side providing functionality
It is accessible over a network (Internet)
It is meant for machine to machine communication
Independent from programming languages
It can be operated following specific rules (protocols: REST or
SOAP)
This introduction is intended for a non technical audience
with purposely simplified technical concepts.

Web Services
How should I invoke you?
Documentation
Make a request
Results
Web server
Application
Web Service
describes the methods and variables to query the service
11
22
33
44
22
User/Developer
Client

RESTWeb Services
Documentation
Make a request ( GET or POST)
Results (data + status)
Web server
Web Service
Sometimes a WADL file is available in the server to describe
the service
11
22
33
44
22
WADLor
Informal
Description
Formal
Description
Application
Developer
Client

SOAPWeb Services
Documentation (WSDL)
Make a SOAP request
Web server
Web Service
11
22
33
WSDL
Method /
Parameters
Data
44
33 44SOAP request SOAP response
and
Informal
Description
Formal
Description
Results (SOAP response)
Application
Developer

SOAP vs. REST
8
REST
• Geared to simplicity.
• A browser can be a client.
• Request as complex as a URL can be.
REST query: http://www.ebi.ac.uk/…/query/P99999?format=xml25
WADL: http://www.ebi.ac.uk/…/current?_wadl
SOAP
• Based on Standards.
• Only accessed by specialized software.
• Allow description of complex data structure in request and response.
SOAP REST
WSDL: http://www.ebi.ac.uk/…/psicquic?wsdl

PSICQUIC REST queries
Bruno Aranda (baranda@ebi.ac.uk)
http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/query/p53
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/p53
http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/p53
1
2
3

MIQL
Bruno Aranda (baranda@ebi.ac.uk)

MIQL
…/query/specie:rat
…/query/brca AND rpa1
• Terms
• Fields
• Operands

PSICQUIC SOAP service
species:trypanosoma AND detmethod:’two hybrid’

Workflows

Introduction to Web Services at EBI
Workflow
• Workflow
– Sequence of tasks that produces a
result of observable value
• Workflow management
system
– Computer system to compose and
execute workflows.
• Workflow components
– Input
– Service
– Output
– Shims
Service A
Service B

MatchMismatch
Shims: Connecting services
Shim
Service A
Service B
Service A
Service B
• Convert data formats and act as connectors

MyGrid

Create and run workflows
Share, discover and reuse workflows
Discover and reuse services
myGrid solutions

• A public centralised and curated registry of
Life ScienceWeb Services
• ‘Web 2.0’-style website and API
• Allow anyone to register, discover and curate
Web Services
• Community oriented with expert guidance
• Open content, open source, open platform
Paul Fisher, myGrid, University of Manchester
Biocatalogue
http://www.biocatalogue.org

BioCatalogue’s Mission
12/18/18 19

Workflow
diagram
Tree view of
workflow structure
Tree view of
workflow structure
Available
services
Taverna
• Workflow management system
• Java desktop application
• Open source and extensible
• Includes access to Biocatalogue and myExperiment
• http://www.taverna.org.uk/

Sharing Experiments
• You can share results/experiments/experiences with your
– Research group
– Collaborators
– Scientific community
A registry of workflows

myExperiment
http://www.myexperiment.org/

Recycling, Reuse, Repurposing
• Paul writes workflows for identifying biological pathways
implicated in resistance toTrypanosomiasis
• Paul meets Jo. Jo is investigating mouseWhipworm infection.
• Jo reuses one of Paul’s workflows.
• Jo identifies the biological pathways involved in sex dependence
in the mouse model, believed to be involved in the ability of
mice to expel the parasite.
• Previously a manual two year study by Jo had failed to do this.
Workflows are protocols

Examples from myExperiment
OLS
PICR
Biomart and
Microarray
analysis
ChEBI

Taverna

Workflow
Diagram
Services Panel
Workflow
Explorer
Run workflow

Input
list
Input description
Input example
Input value

Output
tab
Results
List of
results

Installing theWorkbench
• Download theTaverna 2.5 workbench from
http://www.taverna.org.uk/
• InstallTaverna
• OpenTaverna
• Start / All programs /Taverna /TavernaWorkbench 2.5
• You do not have to complete the registration now. Click on “Do no ask
me again”.

Tutorial
myExperiment &Taverna

1. Open one PSICQUIC workflow
1. OpenTaverna and click the “myExperiment” button.
myExperiment is a repository of workflows
2. In the “Query” field, type “psicquic”
3. Find the “Molecular Interactions from IntAct PSICQUIC service (REST)” workflow and
click on the “Open” button.
2. Run a PSICQUIC workflow
1. In the menu click on “File” and “Run workflow”
3. Define your query
1. Find and click the “Set value” button
2. Specify your MIQL query. i.e
1. species:trypanosoma AND detmethod:"two hybrid"
3. Click on the button “Run workflow”
4. Check your results
1. In the bottom left corner, in the “MITAB” tab, click on “Value1”
5. Save results
1. Click on the “Save value” button on the bottom right corner.
Simple PSICQUIC workflow withTaverna
to query IntAct

Make your own workflow,
reuse workflows
Look at the following workflows:
• Get a list of Protein Identification experiments from PRIDE by a Gene Ontology query
http://www.myexperiment.org/workflows/2746.html
• Get a list of proteins annotated with an Ontology term and use these proteins to query
BioModels
Create a similar workflow to retrieve molecular interactions from IntAct
using a GO term as input. Reuse one of the previous workflows and
connect it with one of the following workflows:
• Retrieve Molecular Interactions from PSICQUIC Services:

Thank you

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An introduction to programmatic access

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