ProteinSynonymsToQuery

Created: 2007-10-03 18:36:10 Last updated: 2007-11-13 23:47:41

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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: http://rdf.adaptivedisclosure.org/~marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

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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.

Beanshells (1)

Name	Description	Inputs	Outputs
Concat_synonyms		synonymlist query_term	new_query

Outputs (2)

Name	Description
synonyms
new_query

Links (8)

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

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Taverna 1

Information Uploader

Marco Roos

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3431 downloads

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ProteinSynonymsToQuery

Created by Marco Roos on Wednesday 03 October 2007 18:36:10 (UTC)
ProteinSynonymsToQuery

Created by Marco Roos on Wednesday 03 October 2007 18:36:10 (UTC)

Last edited by Marco Roos on Tuesday 13 November 2007 23:47:41 (UTC)

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Other workflows that use similar services (1)

Taverna 1

Uploader

Marco Roos

BioAID_Discover_proteins_from_text_plus_sy... (1)

This workflow discovers proteins from plain text and adds synonyms using Martijn Schuemie's proteins synonym service. Proteins are discovered with the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

Created: 2007-11-15

Credits: Marco Roos Martijn Schuemie AID