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EBI is an Outstation of the European Molecular Biology Laboratory. Web Services Course CBS, DK.
EBI Web Services
Teresa Miyar EMBL-EBI
External Services Group
Web Services Course CBS, DK.
EBI web services (analysis tools)
jobid
getResults (jobid)
results available
checkStatus (jobid)
status
run(params, data)
poll (jobid, type)
result file
Web Services Course CBS, DK.
Perl Soap Client (synchronous)
• #!/usr/bin/env perl
• use SOAP::Lite;
• my $WSDL = 'http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl';
• my $fasta_client = SOAP::Lite->service($WSDL);
• my %params=(); • $params{'program'}='fasta3'; • $params{'database'}='uniprot';• $params{'email'}='youremail';• $data={type=>"sequence",• content=>“uniprot:slpi_human"};
• my $jobid = $fasta_client->runFasta(• SOAP::Data->name('params')->type(map=>\%params), • SOAP::Data->name( content => [$data]));
• print $fasta_client->poll($jobid);
Web Services Course CBS, DK.
Perl Soap Client (asynchronous)
• #!/usr/bin/env perl
• use SOAP::Lite; • my $WSDL =
'http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl'; • my $fasta_client = SOAP::Lite->service($WSDL); • my %params=(); • SOAP::Lite->import(+trace => debug);• $params{'program'}='fasta3'; • $params{'database'}='uniprot';• $params{'email'}='[email protected]';• $params{'async'}= 1;
• $data={type=>"sequence",• content=>"uniprot:slpi_human"};
• my $jobid = $fasta_client->runFasta(• SOAP::Data->name('params')->type(map=>\%params), • SOAP::Data->name( content => [$data]));
Web Services Course CBS, DK.
Perl Soap Client (asynchronous cont.)
• # set a loop for checking job submission status • # RUNNING, NOT_FOUND, ERROR, DONE
• my $status = $fasta_client ->checkStatus($jobid); • while ($status eq "RUNNING") {• sleep 10; $status = $fasta_client-checkStatus($jobid); • }
• # when job is done, poll for the results
• my $result = $fasta_client ->poll($jobid) if ($status eq "DONE") ;
• print $result;
Web Services Course CBS, DK.
Perl Rest Client
• #!/usr/bin/env perl
• use LWP::UserAgent;• use HTTP::Request;• use HTTP::Request::Common;
• $URL="http://www.ebi.ac.uk/Tools/webservices/rest/submit";
• my %params=();• $params{'tool'}="iprscan";• $params{'sequence'}="uniprot:slpi_human";• $params{'seqtype'}="P";• $params{'email'}=“youremail";• @args=%{\%params};
• $ua= LWP::UserAgent->new(); • $resp = $ua->request( POST $URL , 'Content' => \@args); • print $resp->content();
Web Services Course CBS, DK.
Python Soap Client
• #!/usr/bin/env python
• import sys• from SOAPpy import WSDL
• blast_wsdUrl='http://www.ebi.ac.uk/Tools/webservices/wsdl/WSWUBlast.wsdl'• server = WSDL.Proxy(blast_wsdUrl)• server.soapproxy.config.dumpSOAPOut = 1• server.soapproxy.config.dumpSOAPIn = 1
• seq = """>UniProt/TrEMBL|Q8E5Q5|Q8E5Q5_STRA3 Hypothetical protein gbs0925• MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFI• VAQIVQIVFPVIPGGVTTVAGFLIFGPTLGFIYNYIGIIIGSVILFWLVKFYGRKFVLLF• MDQKTFDKYESKLETSGYEKFFIFCMASPISPADIMVMITGLSNMSIKRFVTIIMITKPI• SIIGYSYLWIYGGDILKNFLN"""• blast_params = {'program':'blastp','database':'uniref90',• 'email':'[email protected]', 'async':0}• blast_data = [{'type':'sequence',• 'content':seq}]• jobid = server.runWUBlast(params=blast_params,content=blast_data)• print jobid• sys.stdout.flush()• result = server.poll(jobid,'tooloutput')• print result
Web Services Course CBS, DK.
Python Rest Client
• #!/usr/bin/env python
• import urllib
• url = 'http://www.ebi.ac.uk/Tools/webservices/rest/submit'
• params = {}
• params = urllib.urlencode({'tool':'iprscan',• 'sequence':'uniprot:slpi_human',• 'email':'[email protected]',• 'seqtype':'P'})• • jobid = urllib.urlopen(url, params).read()
• print jobid
Web Services Course CBS, DK.
Ensembl (Martservice)
Ensembl (Martservice)
Data Retrieval
(WSDbfetch)
Data Retrieval
(WSDbfetch)
Expression ProfilerExpression Profiler
Protein families, motifs and domains (WSInterProScan)
Protein families, motifs and domains (WSInterProScan)
Protein structure & function: (MSD API)
Protein structure & function: (MSD API)
Literature and text mining (Whatizit, CiteXplore)
Literature and text mining (Whatizit, CiteXplore)
Sequence homology WSWUBlast
WSFastaWSMPsrchWSScanPS
Wise, PromoterWise, ScanWise
Sequence homology WSWUBlast
WSFastaWSMPsrchWSScanPS
Wise, PromoterWise, ScanWise
Sequence alignment WSClustalWWSMuscleWSTCoffee
Sequence alignment WSClustalWWSMuscleWSTCoffee
Sequence analysis
(WSEmboss)
Sequence analysis
(WSEmboss)
Ontologies (OntologyLookup)Ontologies (OntologyLookup)
DaliLite, MaxsproutDaliLite, Maxsprout
Integr8 APIIntegr8 API
Uniprot APIUniprot API
Available Services
ID mapping (Picr, Martservice)ID mapping (Picr, Martservice)
Search (EB-Eye)Search (EB-Eye)
ChEBI APIChEBI API
Web Services Course CBS, DK.
Text output
Web Services Course CBS, DK.
XML results
Web Services Course CBS, DK.
Documentation
http://www.ebi.ac.uk/Tools/webservices
Web Services Course CBS, DK.
Exercise Proposal
• Stacey, G., Koh, S., Granger, C. & Becker, J. M. (2002). Peptide transport in plants. Trends Plant Sci 7, 257-263.
• Reproduce the philogenetic tree from Stacey’s article • Find in Uniprot an id for a PTR (Peptide Transporters) protein• Do a Blast using Uniprot • Download the sequences of the hits• Align These sequences using a MSA (Muscle, Mafft, TCoffee)• Generate ClustalW tree
Web Services Course CBS, DK.
Acknowledgements
