Workflow Entry: EBI_Whatizit

Created at: 09/07/08 @ 05:14:28 Last updated: 09/07/08 @ 05:14:29

Version 1 (of 1)

Version created on: 09/07/08 @ 05:14:28 by: Hamish McWilliam | Revision comments Expand

Title: EBI_Whatizit

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

Perform a text-mining analysis of an input text document using the EBI’s Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf).

Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

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/249/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
Analysis_pipeline	Name of the Whatizit text-mining pipeline to use. For example: whatizitSwissprot See the results of the getPipelinesStatus() method for a complete list of the available pipelines and their status.
Text	Input text to process. For example: NPY, BRCA1, Brca2 and Ca2

Processors (3)

Name	Type	Description
contact	arbitrarywsdl	Process an input text document using a Whatizit pipeline.
Input_params	local	Build the input parameters data structure. Wraps the Whatizit pipeline name and the text document.
Unwrap_result	local	Unwrap the XML result.

Outputs (1)

Name	Description
Whatizit_result	Whatizit analysis result.

Links (5)

Sink	Source
Input_params:pipelineName	Analysis_pipeline
contact:parameters	Input_params:output
Input_params:text	Text
Whatizit_result	Unwrap_result:return
Unwrap_result:input	contact:parameters