Discover_entities

Created: 2007-12-10 21:48:33 Last updated: 2007-12-10 22:54:42

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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.

Known issues:

The output of NErecognize contains concepts with / characters, breaking the xml. For post-processing its results it is better to use string manipulation than xml manipulations. The output is per document, which means entities will be redundant if they occur in more than one document.

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Workflow Components

Inputs (2)

Name	Description
input_from_lucene	Example: <?xml version="1.0" encoding="UTF-8"?> <aid:result xmlns:aid="http://aid.vle.org" query="+content:ezh2 +(year:2007^10.0 year:2006^9.0 year:2005^8.0 year:2004^7.0 year:2004^6.0 year:2003^5.0 year:2002^4.0 year:2001^3.0 year:2000^2.0 year:1999)" total="78" time="2"> <doc rank="1" score="0.55880820751190185546875"> <field name="PMID"> <value>15208672</value> </field> <field name="year"> <value>2004</value> </field> <field name="PT"> <value>Journal Article</value> </field> <field name="title"> <value>Activated p53 suppresses the histone methyltransferase EZH2 gene.</value> </field> <field name="content"> <value>... Furthermore, the repression of EZH2 promoter by p53 is dependent on p53 transcriptional target p21(Waf1) inactivating RB/E2F pathways. In addition, the knockdown of EZH2 expression retards cell proliferation and induces G2/M arrest. We suggest that the p53-dependent suppression of EZH2 expression is a novel pathway that contributes to p53-mediated G2/M arrest. EZH2 associated complex possesses HMTase activity and is involved in epigenetic regulation. Activated p53 suppresses EZH2 expression, suggesting a further role for p53 in epigenetic regulation and in the maintenance of genetic stability. Suppression of EZH2 expression in tumors by p53 may lead to novel approaches to control cancer progression.</value> </field> <field name="LuceneDocID"> <value>14861224</value> </field> </doc> </aid:result>
learned_model	Model to discover a set of specific concepts; e.g. the prelearned model named 'MedLine' will make the service discover genomics concepts.

Processors (3)

Name	Type	Description
Default_output_type	stringconstant
Default_input_type	stringconstant
NErecognize	arbitrarywsdl

Beanshells (0)

Outputs (1)

Name	Description
discovered_entities	Entities discoverd in documents provided in lucene output format.

Links (5)

Source	Sink
input_from_lucene	NErecognize:input_data
learned_model	NErecognize:r_type
Default_input_type:value	NErecognize:input_type
Default_output_type:value	NErecognize:output_type
NErecognize:NErecognizeReturn	discovered_entities

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Taverna 1

Information Uploader

Marco Roos

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Information Statistics

3395 viewings

2726 downloads

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Version History

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Discover_entities

Created by Marco Roos on Monday 10 December 2007 21:48:33 (UTC)

Last edited by Marco Roos on Monday 10 December 2007 22:07:30 (UTC)
Discover_entities

Created by Marco Roos on Monday 10 December 2007 21:48:33 (UTC)

Last edited by Marco Roos on Monday 10 December 2007 22:54:42 (UTC)

Revision comment:

Added example input

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