Workflow Entry: Discover_proteins_from_text

Created at: 15/11/07 @ 08:58:00 Last updated: 15/11/07 @ 09:12:34

Version 2 (latest) (of 2)

Version created on: 15/11/07 @ 08:58:00 by: Marco Roos | Revision comments Expand

Last edited on: 15/11/07 @ 09:12:34 by: Marco Roos

Title: Discover_proteins_from_text

Type: Taverna 1

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Description

This workflow discovers proteins from plain text. It is built around 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.

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Option 1:

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Option 2:

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http://www.myexperiment.org/workflows/80/download?version=2
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Workflow Components

Inputs (1)

Name	Description
text	plain text, example: Polycomb-group (PcG) proteins form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. Components of PcG complexes and their mutual interactions have been identified and analysed through extensive genetic and biochemical analyses. Molecular mechanisms underlying PcG-mediated repression of gene activity, however, have remained largely unknown. Previously we reported the existence of two distinct human PcG protein complexes. The EED/EZH protein complex contains the embryonic ectoderm development (EED) and enhancer of zeste 2 (EZH2; refs 9,10) PcG proteins. The HPC/HPH PcG complex contains the human polycomb 2 (HPC2; ref. 11), human polyhomeotic (HPH), BMI1 (ref. 13 ) and RING1 (refs 14, 15) proteins. Here we show that EED (refs 4, 5, 6, 7, 8) interacts, both in vitro and in vivo, with histone deacetylase (HDAC) proteins. This interaction is highly specific because the HDAC proteins do not interact with other vertebrate PcG proteins. We further find that histone deacetylation activity co-immunoprecipitates with the EED protein. Finally, the histone deacetylase inhibitor trichostatin A (ref. 17) relieves transcriptional repression mediated by EED, but not by HPC2, a human homologue of polycomb. Our data indicate that PcG-mediated repression of gene activity involves histone deacetylation. This mechanistic link between two distinct, global gene repression systems is accomplished through the interaction of HDAC proteins with a particular PcG protein, EED.

Processors (3)

Name	Type	Description
prelearned_genomics_model	stringconstant
Extract_proteins	workflow	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).
Discover_entities	workflow	This workflow contains the 'Named Entity Recognize' web service from the AIDA toolbox, created by Sophia Katrenko. It can be used to discover entities of a certain type (determined by 'learned_model') in documents provided in a lucene output format.

Outputs (1)

Name	Description
discovered_proteins

Links (4)

Sink	Source
Extract_proteins:input_string	Discover_entities:discovered_entities
discovered_proteins	Extract_proteins:protein_molecule_list
Discover_entities:learned_model	prelearned_genomics_model:value
Discover_entities:text	text