Workflow Entry: Extract_proteins

Created at: 10/12/07 @ 22:10:51 Last updated: 10/12/07 @ 22:30:53

Version 2 (latest) (of 2)

Version created on: 10/12/07 @ 22:10:51 by: Marco Roos | Revision comments Expand

Last edited on: 10/12/07 @ 22:30:53 by: Marco Roos

Title: Extract_proteins

Type: Taverna 1

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Description

This workflow filters protein_molecule-labeled terms from an input string(list). The result is a tagged list of proteins (disregarding false positives in the input).

Internal information:

This workflow is a copy of 'filter_protein_molecule_MR3' used for the NBIC poster (now in Archive).

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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/113/download?version=2
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Workflow Components

Inputs (1)

Name	Description
input_string	Example: <result_final><doc id="15208672"><other_name>Replicative</other_name><other_name>cell</other_name><cell_type>damaged</cell_type><other_name>tumor</other_name><protein_molecule>tumor</protein_molecule><protein_molecule>p53</protein_molecule><other_name>EZH2</other_name><protein_molecule>p53</protein_molecule><other_name>epigenetic</other_name><other_name>genetic</other_name><other_name>EZH2</other_name><tissue>tumors</tissue><protein_molecule>p53</protein_molecule><other_name>cancer</other_name></doc><doc id="15520282"><protein_molecule>Ezh2</protein_molecule><protein_molecule>Polycomb</protein_molecule><protein_complex>PRC3</protein_complex><other_organic_compound>histone</other_organic_compound><other_name>HKMT</other_name><protein_molecule>Ezh2</protein_molecule><protein_molecule>HDAC1</protein_molecule><protein_family_or_group>YY1</protein_family_or_group><other_organic_compound>H3</other_organic_compound><protein_molecule>MyoD</protein_molecule><protein_molecule>SRF</protein_molecule><DNA_family_or_group>chromatin</DNA_family_or_group><other_organic_compound>H3</other_organic_compound><protein_complex>Ezh2</protein_complex><protein_family_or_group>positive</protein_family_or_group><DNA_domain_or_region>genomic</DNA_domain_or_region><other_name>muscle</other_name><other_name>cell</other_name></doc></result_final>

Processors (11)

Name	Type	Description
splitOn_protein_molecule_regexp	stringconstant
Remove_duplicate_strings	local
Filter2	local
SplitOn_protein_molecule	local
filter_protein_molecule_regexp	stringconstant
UniProtOrNot	beanshell
Filter_protein_molecules	local
FilterTrueProteinByUniProtID	beanshell
getUniprotID	arbitrarywsdl
Filter1	local
Strip_xml	beanshell

Beanshells (3)

Name	Inputs	Outputs
UniProtOrNot	uniprotIDlist	uniprotID_or_False
FilterTrueProteinByUniProtID	protein uniprot	true_protein true_uniprot
Strip_xml	tagged_term	term

Outputs (2)

Name	Description
protein_molecule
uniprotID

Links (14)

Source	Sink
input_string	SplitOn_protein_molecule:string
Filter1:filteredlist	uniprotID
Filter2:filteredlist	protein_molecule
FilterTrueProteinByUniProtID:true_protein	Filter2:stringlist
FilterTrueProteinByUniProtID:true_uniprot	Filter1:stringlist
Filter_protein_molecules:filteredlist	Remove_duplicate_strings:stringlist
Remove_duplicate_strings:strippedlist	Strip_xml:tagged_term
SplitOn_protein_molecule:split	Filter_protein_molecules:stringlist
Strip_xml:term	FilterTrueProteinByUniProtID:protein
Strip_xml:term	getUniprotID:term
UniProtOrNot:uniprotID_or_False	FilterTrueProteinByUniProtID:uniprot
filter_protein_molecule_regexp:value	Filter_protein_molecules:regex
getUniprotID:getUniprotIDReturn	UniProtOrNot:uniprotIDlist
splitOn_protein_molecule_regexp:value	SplitOn_protein_molecule:regex