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Retrieve_bio_documents

Workflow Entry: Retrieve_bio_documents

Created at: 10/12/07 @ 22:15:54 Last updated: 10/12/07 @ 22:45:49

Version 2 (latest) (of 2)

Version created on: 10/12/07 @ 22:15:54 by: Marco Roos | Revision comments Expand

Last edited on: 10/12/07 @ 22:45:49 by: Marco Roos

Title: Retrieve_bio_documents

Type: Taverna 1

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Description

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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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/117/download?version=2
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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 Original Uploader

Marco Roos

Information License

All versions of this Workflow are licensed under:

Information Credits (3)

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Information Attributions (0)

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Information Tags (5)

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Information Ratings (2)

Current:

4.5 / 5

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Information Favourited By (0)

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Information Statistics

861 viewings

1023 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Retrieve_bio_documents

Created on: Monday 10 December 2007 @ 22:15:54 (GMT)

Created by: Marco Roos

Revision comments:

None

Latest Version:
[2] - Retrieve_bio_documents

Created on: Monday 10 December 2007 @ 22:15:54 (GMT)

Created by: Marco Roos

Last edited on: Monday 10 December 2007 @ 22:45:49 (GMT)

Last edited by: Marco Roos

Revision comments:

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 (GMT)
	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.

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Taverna 1

Original Uploader

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v11)

Created: 28/05/09 @ 12:21:05

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 454 times | Downloaded: 167 times

Tags (9):

View

Download (v11)

Taverna 1

Original Uploader

Marco Roos

BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter (v4)

Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 4034 times | Downloaded: 616 times

Tags (9):