1. EBI is an Outstation of the European Molecular Biology Laboratory. Web Services Programmatic access to Life Sciences resources. Rodrigo Lopez

2. Web Services Course CBS, DK. February 20082 Outline 1.What are Web Services. 2.Types of Web Services. 3.Lists of Web Services. 4.Building workflows.

3. Web Services Course CBS, DK. February 20083 What are Web Services Network based tools that permit access to methods… In a programmatic fashion. Without using traditional browsers. Exposing more granularity and thus giving the user more control. Web Services models… SOAP/REST models SOAP is great for embedding methods into complex programs – PERL, Python, Ruby, Java, C/C++, etc. REST is simpler, easier and provides basic end-points. http://www.site.dom/param1/param2/data1/...

4. Web Services Course CBS, DK. February 20084 Web Services Paradigms Silo based approach Services (Tools such as blast, EB-eye, etc.) present methods for their use. Ideal for running from the command line using simple clients. Relieve the user from the tool maintenance overhead. The service provider is responsible for this. SOA – Service Oriented Architecture Combines SILO-based methods to generate a ‘workflow’. User decides which tool method to use thus establishing a business relationship with one or several service providers.

5. Web Services Course CBS, DK. February 200855 Web Services We have travelled in WS space since 2004. Tried, tested and put into production SOAP and REST services for more than 150 discrete applications. All using the SILO based approach to Web Services. Intend to migrate into a SOA based architecture during 2007-2008.

6. Web Services Course CBS, DK. February 20086 Web Services – our focus There has been far too much ‘hype’ about WS during the last years. WS are a just a packaging/messaging technology. WS are just that: services – and are not meant to be the centre of attention. Our definition: Bioinformatic WS are just transparent means of running bioinformatic tools that help integrate expensive computation and maintenance into remote analytical pipe-lines and workflows.

7. Web Services Course CBS, DK. February 20087 Web Services (1) Sequence Analysis Similarity searching. DNA & Protein sequence analysis. Genomes – Inquisitor (integr8). Protein Function prediction InterProScan Protein secondary and tertiary structure PDBSum, MSD-lite, MSD-pro, MSD-motif,… Proteomics IntAct PRIDE Literature & Ontology services CiteXplore Whatizit ChEBI, SBO,… Biological models and simulation BioModels Future services: Biological images EB-eye WS

8. Web Services Course CBS, DK. February 20088 Web Services (2) But there are Web Services from others to exploit, mix and match, complement… NCBI:http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help. htmlhttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help. html BioMoby: http://biomoby.org/http://biomoby.org/ KEGG: http://www.genome.jp/kegg/soap/http://www.genome.jp/kegg/soap/ DDBJ: http://xml.nig.ac.jp/wsdl/?lang=enhttp://xml.nig.ac.jp/wsdl/?lang=en EBI: http://www.ebi.ac.uk/Tools/webservices/http://www.ebi.ac.uk/Tools/webservices/

9. Web Services Course CBS, DK. February 20089 Building workflows Running ‘business transactions’ with Taverna and Triana