Retrieve_bio_documents

Created: 2007-12-10 22:15:54 Last updated: 2007-12-10 22:45:49

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This workflow retrieves relevant documents, based on a query optimized by adding a string to the original query that will rank the search output according to the most recent years. The added string adds years with priorities (most recent is highest); it starts at 2007.

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Workflow Components

Inputs (4)

Name	Description
query_string	e.g. EZH2
document_index	e.g. MedLine_new
search_field	e.g. content
maxHits	e.g. 100

Processors (2)

Name	Type	Description
Retrieve	workflow	This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction.
Biooptimize_query	workflow	This workflow does four things: 1. it retrieves documents relevant for the query string 2. it discovers entities in those documents, these are considered relevant entities 3. it filters proteins from those entities (on the tag protein_molecule) 4. it removes all terms from the list produced by 3 (query terms temporarily considered proteins) ToDo * Replace step 4 by the following procedure: 1. remove the query terms from the output of NER (probably by a regexp matching on what is inside the tag, possibly case-insensitive) 2. remove tag_as_protein_molecule (obsolete) * Add synonym service/workflow Note that Remove_inputquery has an alternative iteration strategy (dot product instead of cross product). Idem for 'Join' in 'SplitQuery'.

Beanshells (1)

Name	Description	Inputs	Outputs
Prioritise_lucene_query		query_string priority_string	lucene_query

Outputs (1)

Name	Description
relevant_documents

Links (6)

Source	Sink
query_string	Biooptimize_query:query_string
Biooptimize_query:optimized_lucene_query	Retrieve:queryString
document_index	Retrieve:document_index
maxHits	Retrieve:maxHits
search_field	Retrieve:search_field
Retrieve:relevant_documents	relevant_documents

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Marco Roos

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Information Version 2 (latest) (of 2)

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Information Favourited By (1)

Hyde Zhang

Information Statistics

3146 viewings

2630 downloads

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Version History

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Retrieve_bio_documents

Created by Marco Roos on Monday 10 December 2007 22:15:54 (UTC)
Retrieve_bio_documents

Created by Marco Roos on Monday 10 December 2007 22:15:54 (UTC)

Last edited by Marco Roos on Monday 10 December 2007 22:45:49 (UTC)

Revision comment:

Added examples for the inputs

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Comments (2)

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Paul Fisher

Hi Marco,

Could you please add some instructions on what to enter, and maybe some examples.

cheers,

Paul.

Marco Roos	Monday 14 January 2008 12:01:08 (UTC)
	Response to Paul's comment about the instructions. One example for each input is given when you click 'New input' in the run window in Taverna. This is quite minimal; I intend to add more info later and upload a new version.

Other workflows that use similar services (6)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Marco Roos

BioAID_ProteinToDiseases (1)

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This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

Created: 2007-11-14 | Last updated: 2007-11-15

Credits: Marco Roos Martijn Schuemie AID

Attributions: BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Taverna 1

Uploader

Marco Roos

Retrieve_documents_MR1 (1)

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This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction.

Created: 2007-12-10

Credits: Marco Roos Edgar AID