EBI PICR, find cross-references for protein accessions
Created: 2011-05-18 09:36:26
Last updated: 2011-05-29 17:35:20
Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.
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Authors (1)
Titles (3)
|
| Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status. |
| EBI PICR, find cross-references for protein accessions |
Descriptions (1)
| Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status. |
Dependencies (0)
Inputs (4)
| Name |
Description |
| accessions |
Input a list of protein accessions
|
| searchDatabases |
Which databases do you want the cross-references for? You can add more than one. You can get a list of databases available in PICR using the method "getMappedDatabaseNames" from the same PICR service or looking at this document http://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do
|
| onlyActive |
Do you just want accession that are active (no-deprecated)? … write down "true" or "false". If you do not specify this parameter the workflow will not work.
|
| taxonId |
Create a new value and leave it empty if you do not want to filter by specie. Chose a Taxa Id if you want to limit by specie … http://www.uniprot.org/taxonomy/?query=*
|
Processors (8)
| Name |
Type |
Description |
| getUPIForAccession |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/picr/service?wsdlWsdl OperationgetUPIForAccession |
| getUPIForAccession_input |
xmlsplitter |
|
| getUPIForAccession_output |
xmlsplitter |
|
| getUPIForAccession_getUPIForAccessionReturn |
xmlsplitter |
|
| getUPIForAccessionReturn_identicalCrossReferences |
xmlsplitter |
|
| remove_empty_values_1 |
beanshell |
ScriptList stringListOut = new ArrayList();
for(Object list:stringListIn){
for (Iterator i = list.iterator(); i.hasNext();) {
String text = (String)i.next();
if(text.length() != 0){
stringListOut.add(text);
}
}
} |
| remove_empty_values_2 |
beanshell |
ScriptList stringListOut = new ArrayList();
for(Object list:stringListIn){
for (Iterator i = list.iterator(); i.hasNext();) {
String text = (String)i.next();
if(text.length() != 0){
stringListOut.add(text);
}
}
} |
| remove_empty_values_3 |
beanshell |
ScriptList stringListOut = new ArrayList();
for(Object list:stringListIn){
for (Iterator i = list.iterator(); i.hasNext();) {
String text = (String)i.next();
if(text.length() != 0){
stringListOut.add(text);
}
}
} |
Beanshells (3)
| Name |
Description |
Inputs |
Outputs |
| remove_empty_values_1 |
|
stringListIn
|
stringListOut
|
| remove_empty_values_2 |
|
stringListIn
|
stringListOut
|
| remove_empty_values_3 |
|
stringListIn
|
stringListOut
|
Outputs (3)
| Name |
Description |
| acc |
|
| databaseName |
|
| taxonId |
|
Datalinks (14)
| Source |
Sink |
| getUPIForAccession_input:output |
getUPIForAccession:parameters |
| accessions |
getUPIForAccession_input:accession |
| searchDatabases |
getUPIForAccession_input:searchDatabases |
| onlyActive |
getUPIForAccession_input:onlyActive |
| taxonId |
getUPIForAccession_input:taxonId |
| getUPIForAccession:parameters |
getUPIForAccession_output:input |
| getUPIForAccession_output:getUPIForAccessionReturn |
getUPIForAccession_getUPIForAccessionReturn:input |
| getUPIForAccession_getUPIForAccessionReturn:identicalCrossReferences |
getUPIForAccessionReturn_identicalCrossReferences:input |
| getUPIForAccessionReturn_identicalCrossReferences:accession |
remove_empty_values_1:stringListIn |
| getUPIForAccessionReturn_identicalCrossReferences:databaseName |
remove_empty_values_2:stringListIn |
| getUPIForAccessionReturn_identicalCrossReferences:taxonId |
remove_empty_values_3:stringListIn |
| remove_empty_values_1:stringListOut |
acc |
| remove_empty_values_2:stringListOut |
databaseName |
| remove_empty_values_3:stringListOut |
taxonId |
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EBI_PICR_Sequence_to_ID
(1)
Map a protein sequence to the known identifiers of identical sequences.
Uses the EBI's PICR web service (see http://www.ebi.ac.uk/Tools/picr/) to perform the mapping.
Created: 2008-06-08
Credits:
Hamish McWilliam
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