Find co-occurring documents

Created: 2012-07-13 07:45:39 Last updated: 2014-07-14 10:29:26

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Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts.

Author comments:

This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
ConceptID_1	Concept ID for the input concept.
ConceptID_2	Concept ID for the second concept.
Cutoff_value	The number of co-occurring documents to return.

Processors (6)

Name	Type	Description
findCoOccurringDocuments	wsdl	Wsdl http://ws.biosemantics.org/ConceptRecognizerService?wsdl Wsdl Operation findCoOccurringDocuments
findCoOccurringDocuments_input	xmlsplitter
findCoOccurringDocuments_output	xmlsplitter
findCoOccurringDocuments_return	xmlsplitter
return_SupportingDocumentsList	xmlsplitter
SupportingDocumentsList_SupportingDocumentsList	xmlsplitter

Beanshells (0)

Outputs (2)

Name	Description
Document_ID	The document ID. The example refers to a PubMed ID.
Document_title	The title of the document.

Datalinks (10)

Source	Sink
findCoOccurringDocuments_input:output	findCoOccurringDocuments:parameters
ConceptID_1	findCoOccurringDocuments_input:conceptID1
ConceptID_2	findCoOccurringDocuments_input:conceptID2
Cutoff_value	findCoOccurringDocuments_input:cutoffValue
findCoOccurringDocuments:parameters	findCoOccurringDocuments_output:input
findCoOccurringDocuments_output:return	findCoOccurringDocuments_return:input
findCoOccurringDocuments_return:SupportingDocumentsList	return_SupportingDocumentsList:input
return_SupportingDocumentsList:SupportingDocumentsList	SupportingDocumentsList_SupportingDocumentsList:input
SupportingDocumentsList_SupportingDocumentsList:ID	Document_ID
SupportingDocumentsList_SupportingDocumentsList:title	Document_title

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Kristina Hettne

Information License

All versions of this Workflow are licensed under:

Information Version 2 (of 6)

Information Credits (5)

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Information Tags (3)

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Information Statistics

3740 viewings

4611 downloads

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Citations (0)

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Version History

In chronological order:

Find co-occurring documents

Created by Kristina Hettne on Friday 13 July 2012 07:45:39 (UTC)
Find co-occurring documents

Created by Kristina Hettne on Wednesday 18 July 2012 13:52:39 (UTC)

Revision comment:

Added annotations.
Find co-occurring documents

Created by Kristina Hettne on Friday 14 September 2012 09:44:06 (UTC)
Find co-occurring documents

Created by Kristina Hettne on Friday 14 September 2012 09:51:47 (UTC)
Find co-occurring documents

Created by Kristina Hettne on Tuesday 05 February 2013 20:35:52 (UTC)
Find co-occurring documents

Created by Kristina Hettne on Monday 14 July 2014 10:29:26 (UTC)

Revision comment:

Edited examples to reflect latest concept database update.

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Khalid Belhajjame

This workflow is simple, well document and can ran as of the 7th of September using the Taverna workbench. Well done Kristina.

khalid

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Marco Roos

DatabaseID to ConceptID (7)

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Comments: Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example). CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontol...

Created: 2012-06-25 | Last updated: 2014-07-14

Credits: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

Taverna 2

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Reinout van Schouwen

Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

Find co-occurring documents

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Other workflows that use similar services (18)