Extract_proteins
Created: 2007-12-10 22:10:51
Last updated: 2007-12-10 22:30:53
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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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 |
Description |
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 |
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Version 2 (latest)
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