1. CATH Soap Web Services http://farmer2.biochem.ucl.ac.uk/cgi-bin/SWSScan.cgi SWSScan

2. Orengo Group, UCL What we want to offer Access to the CATH algorithms Access to CATH data “Programmable” access to our own resources for a new automated update protocol

3. Orengo Group, UCL Sequence Comparisons BLAST query sequences against complete CATH domain sequence database NW query sequences against complete CATH domain sequence database Scan query sequences against the CATH Sam HMM library Scan query sequences against the CATH HMMer HMM library

4. Orengo Group, UCL Structural Comparisons SSAP is a residue-based pairwise comparison algorithm that scores structural similarity between chains/domains in PDB format. Cathedral uses graphs to identify the fold of the query structure and then confirms fold assignment using SSAP Both algorithms require additional files that can be derived from the original PDB on the fly

5. Orengo Group, UCL Why SOAP? It’s Simple Allows management of our farms without changing the current configuration. A protocol being adopted by other FP6 projects such as BioSapiens

6. Orengo Group, UCL SWSScan SOAP HTTP Layer Perl Layer SGE Farm Manager Animal

7. Orengo Group, UCL SOAP Bits #!/usr/local/bin/perl –w use SOAP::Transport::HTTP; SOAP::Transport:HTTP::CGI ->dispatch_to(“/usr/local/bin/cath/perl/SWSScan.pm ->handle; #!/usr/local/bin/perl –w use SOAP::Lite; my $urn = “SWSScan”; my $proxy = “http://farmer2.biochem.ucl.ac.uk/cgi-bin/SWSScan.cgi”; my $URI = SOAP::Lite->uri(“urn:$urn”); my $hWebService = $URI->proxy($proxy); my $job_id = $hWebService->submit_scan($in, “blast”)->result;

8. Orengo Group, UCL Input formats Accept as many formats as possible to make the service as useable as possible Makes the web service responsible for parsing data rather than the user Ultimately parses all input data into a standard data structure

9. Orengo Group, UCL Input Formats Scalar –Single or multiple sequence FASTA –Full or chain/domain PDB –Single or list of CATH chain/domain ids –Single or list of PDB codes Array –As scalar in each element Object –Standard data structure only

10. Orengo Group, UCL SWSScan Output Job id is returned rather than the results because –Apache has a timeout –The farm could be busy –The job could be big Requires a monitoring call and a retrieval call

11. Orengo Group, UCL SWSScan Output A structured data object consisting of a results object that contains in a keyed hash query sequence objects which in turn contain an array of matching sequence objects All returned data is contained in the object including any requested files

12. Orengo Group, UCL Wrapper date e.g. ‘date’ source e.g. ‘CATH’ Sequencee.g. Sequence Object

13. Orengo Group, UCL Sequence date e.g. ‘set date’ source e.g. ‘source of data’ type e.g. ‘?’ Ide.g. ‘1cuk001’ length e.g. size of residue array sequence pdb_header/footer e.g. ‘raw text’ fasta_header e.g. ‘raw text’ wolf_file, sec_file, etc. e.g. ‘raw text’ matches-> an array of sequence objects

14. Orengo Group, UCL Residue sequence_number e.g. key to Residue array letter e.g. ‘residue single letter’ coords e.g. ‘ ATOM 1 N MET 1 -7.750 -4.498 -20.265 1.00 21.82 ATOM 2 CA MET 1 -7.178 -5.177 -19.122 1.00 18.39 ATOM 3 C MET 1 -7.857 -4.686 -17.798 1.00 20.00 ATOM 4 O MET 1 -8.202 -5.472 -16.932 1.00 18.10 ATOM 5 CB MET 1 -5.728 -4.808 -19.125 1.00 19.97 ATOM 6 CG MET 1 -4.838 -5.882 -18.694 1.00 29.38 ATOM 7 SD MET 1 -3.162 -5.241 -18.626 1.00 33.40 ATOM 8 CE MET 1 -3.477 -3.687 -19.473 1.00 39.23

15. Orengo Group, UCL Sequence - matches date e.g. 'Tue Nov 29 10:29:27 GMT 2005’ type e.g. 'BLAST', id e.g. '12asA0', source e.g. 'CATH', sequence_length e.g. '330', matched_length e.g. '22', query_start e.g. '1', query_stop e.g. '20', match_start e.g. '185' match_stop e.g. '206', raw_score e.g. '15.4' evalue e.g. '1.9' sequence_id e.g. '36.364'

16. Orengo Group, UCL Other Web Services Retrieval of CATH data –Accession codes –PDB definitions of domains –Derived CATH files Gene3D –CATH Uniprot mappings

17. Orengo Group, UCL Questions We are also offering our machines to be used, but is there some kind of quota system expected to be used? Is using a job id an acceptable protocol? If you only use a retrieval call how do you tell the difference between “no results” with “no results YET”? Will there be a central repository of code? What about BioPerl? How much more complex is the structured data model going to get?