Workflow Entry: ProteinSynonymsToQuery

Created at: 03/10/07 @ 18:36:10 Last updated: 13/11/07 @ 23:47:41

Version 2 (latest) (of 2)

Version created on: 03/10/07 @ 18:36:10 by: Marco Roos | Revision comments Expand

Last edited on: 13/11/07 @ 23:47:41 by: Marco Roos

Title: ProteinSynonymsToQuery

Type: Taverna 1

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Description

This workflow uses Martijn Schuemie’s protein synonym service to produce synonyms and a new query string from the input query term. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost.

Workflow URL: _{marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml”>http://rdf.adaptivedisclosure.org/}marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

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Option 1:

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Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/30/download?version=2
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Workflow Components

Inputs (1)

Name	Description
query_term	Query term without quotes, only synonyms of proteins, enzymes and genes will be returned. Boolean queries will be processed, but the input boolean logic will be lost. E.g. 'EZH2'

Processors (5)

Name	Type	Description
Flatten_list	local
Flatten_list2	local
Concat_synonyms	beanshell
SplitQuery	workflow
getSynsets	arbitrarywsdl	Protein synonym service by Martijn Schuemie, Erasmus Medical Centre, University of Rotterdam, The Netherlands.

Outputs (2)

Name	Description
synonyms
new_query

Links (8)

Sink	Source
new_query	Concat_synonyms:new_query
Flatten_list2:inputlist	Flatten_list:outputlist
getSynsets:term	SplitQuery:queryList
synonyms	Flatten_list2:outputlist
Flatten_list:inputlist	getSynsets:getSynsetsReturn
Concat_synonyms:query_term	query_term
SplitQuery:queryString	query_term
Concat_synonyms:synonymlist	Flatten_list2:outputlist