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PINA

Finds the interacting proteins of query proteins for a list of query Uniprot ACs. Optionally also produces interactions between interactors.

Version 1.1
Bundle microarray
Categories Annotation
Authors Jianmin Wu (jianmin.wu@gmail.com), Marko Laakso (Marko.Laakso@Helsinki.FI)
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Requires commons-codec-1.3.jar (jar) ; commons-httpclient-3.0.1.jar (jar) ; commons-logging-1.1.1.jar (jar)
Source files component.xml Interactome.java
Usage Example with default values

Inputs

Name Type Mandatory Description
query CSV Mandatory If query partners of proteins, it must contain the column named by the parameter "column" that contains query Uniprot IDs. If query whether interactions existing, it must contain two columns named by parameters "column" and "column2".

Outputs

Name Type Description
interactions CSV There are two columns including queryProtein and interactingProtein. Each row corresponds to one protein interaction.
network GraphML Ouput interactions in graphML format with Gene Ontology annoation.

Parameters

Name Type Default Description
WS_URL string "http://cbg.garvan.unsw.edu.au/pina/batchDownload" URL for PINA web service.
column string "Uniprot" Column name in the input CSV file that contains Uniprot IDs.
column2 string "Uniprot" Column name in the input CSV file that contains Uniprot IDs.
extend boolean false If true, also query interactions between interactors of query proteins.
findPartners boolean true If true, fetch partners of query proteins, otherwise check whether query interactions are known in PINA.
outputCSV boolean true If true, produce content for interactions output.
outputGraphML boolean false If true, produce content for network output.

Test cases

Test case Parameters IN
query
OUT
interactions
OUT
network
case1 properties query interactions network

column=MyUniprotColumn,
findPartners=true,

case2 properties query interactions network

column=UniProtA,
column2=UniProtB,
findPartners=false

case3 properties query interactions network

column=MyUniprotColumn,
findPartners=true,

case4 properties query interactions network

column=MyUniprotColumn,
findPartners=true,
outputGraphML=true,

case5 properties query interactions network

column=MyUniprotColumn,
findPartners=true,
extend=true

case6 properties query (missing) (missing)

column=Uniprot/SWISSPROT


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