European Life Sciences Infrastructure for Biological Information

www.elixir-europe.org

Rafael C JimenezELIXIR CTO

EMBL-EBI workshop networks and pathways 2014, Friday 23 June

An introduction to programmatic

access

Query interfaces

2

GraphicalUser

Interface(GUI)

FTPaccess

Databaseaccess

ApplicationProgrammatic

Interface(API)

Data

WebServices

Biologist Bioinformaticians Developers

remote resource

Query interfaces

3

GraphicalUser

Interface(GUI)

FTPaccess

Databaseaccess

ApplicationProgrammatic

Interface(API)

Data

WebServices

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

REST Web Services

How should I invoke you?

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

InformalDescription

FormalDescription

Application

Developer

Client

SOAP Web Services

How should I invoke you?

Documentation (WSDL)

Make a SOAP request

Web server

Web

Service

11

22

33

WSDL

Method / Parameters

Data

44

33 44SOAP request SOAP response

and

InformalDescription

FormalDescription

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=xml25WADL: 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 servicespecies:trypanosoma AND detmethod:’two hybrid’

European Life Sciences Infrastructure for Biological Information

www.elixir-europe.org

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

European Life Sciences Infrastructure for Biological Information

www.elixir-europe.org

MyGrid

Create and run workflows

Share, discover and reuse workflows

Discover and reuse services

myGrid solutions

• A public centralised and curated registry of Life Science Web 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

Biocataloguehttp://www.biocatalogue.org

BioCatalogue’s Mission

04/18/23 19

Service Search

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

Paul Fisher, myGrid, University of Manchester

myExperiment

http://www.myexperiment.org/

Recycling, Reuse, Repurposing

• Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis

• Paul meets Jo. Jo is investigating mouse Whipworm 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

Paul Fisher, myGrid, University of Manchester

Examples from myExperiment

OLS

PICR

Biomart and Microarray analysis

ChEBI

European Life Sciences Infrastructure for Biological Information

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Taverna

Workflow Diagram

Services Panel

Workflow Explorer

Run workflow

Input list

Input description

Input example

Input value

Output tab

Results display

List of results

Installing the Workbench

• Download the Taverna 2.5 workbench from http://www.taverna.org.uk/

• Install Taverna

• Open Taverna• Start / All programs / Taverna / Taverna Workbench 2.5

• You do not have to complete the registration now. Click on “Do no ask me again”.

European Life Sciences Infrastructure for Biological Information

www.elixir-europe.org

TutorialmyExperiment & Taverna

1. Open one PSICQUIC workflow1. Open Taverna 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” button2. Specify your MIQL query. i.e

• species:trypanosoma AND detmethod:"two hybrid"3. Click on the button “Run workflow”

4. Check your results1. In the bottom left corner, in the “MITAB” tab, click on “Value1”

5. Save results1. Click on the “Save value” button on the bottom right corner.

Simple PSICQUIC workflow with Tavernato query IntAct

Workflow results

Make your own workflow,reuse workflows

Look at the following workflows:• Get a list of Protein Identification experiments from PRIDE by a Gene

Ontology queryhttp://www.myexperiment.org/workflows/2746.html

• Get a list of proteins annotated with an Ontology term and use these proteins to query BioModelshttp://www.myexperiment.org/workflows/3113.html

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:http://www.myexperiment.org/workflows/2153.htmlhttp://www.myexperiment.org/workflows/1799.html http://www.myexperiment.org/workflows/2458.html

European Life Sciences Infrastructure for Biological Information

www.elixir-europe.org

Thank you