Find Supporting Documents

Created: 2012-06-26 10:21:17 Last updated: 2014-07-14 10:47:12

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This workflow finds documents that serve as evidence for the association between two concepts.

Results:

Document titles Document identifiers

Author comment:

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
associatedConceptID	Concept ID for the associated concept.
conceptID	Concept ID for the input concept.
MaxNoOfSupportingDocs	Number of documents to return.

Processors (6)

Name	Type	Description
findSupportingDocuments	wsdl	Wsdl http://ws.biosemantics.org/ConceptRecognizerService?wsdl Wsdl Operation findSupportingDocuments
findSupportingDocuments_input	xmlsplitter
findSupportingDocuments_output	xmlsplitter
findSupportingDocuments_return	xmlsplitter
return_SupportingDocumentsList	xmlsplitter
SupportingDocumentsList_SupportingDocumentsList	xmlsplitter

Beanshells (0)

Outputs (2)

Name	Description
DocumentID	Entrez PubMed Document Identifier
DocumentTitle	Title of document

Datalinks (10)

Source	Sink
findSupportingDocuments_input:output	findSupportingDocuments:parameters
associatedConceptID	findSupportingDocuments_input:associatedConceptCUI
conceptID	findSupportingDocuments_input:conceptCUI
MaxNoOfSupportingDocs	findSupportingDocuments_input:cutoffValue
findSupportingDocuments:parameters	findSupportingDocuments_output:input
findSupportingDocuments_output:return	findSupportingDocuments_return:input
findSupportingDocuments_return:SupportingDocumentsList	return_SupportingDocumentsList:input
return_SupportingDocumentsList:SupportingDocumentsList	SupportingDocumentsList_SupportingDocumentsList:input
SupportingDocumentsList_SupportingDocumentsList:PMID	DocumentID
SupportingDocumentsList_SupportingDocumentsList:title	DocumentTitle

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Kristina Hettne

Information License

All versions of this Workflow are licensed under:

Information Version 4 (of 6)

Information Credits (5)

(People/Groups)

Information Attributions (0)

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None

Information Tags (4)

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Information Shared with Groups (3)

Information Featured In Packs (1)

Functional annotation of SNPs using next-generation text mining

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Information Attributed By (1)

(Workflows/Files)

SNPs to Concept Set through Concept Profile Matching v2

Information Favourited By (0)

No one

Information Statistics

4474 viewings

1544 downloads

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Citations (0)

None

Version History

In chronological order:

Find supporting documents

Created by Kristina Hettne on Tuesday 26 June 2012 10:21:17 (UTC)
Find Supporting Documents

Created by Kristina Hettne on Wednesday 18 July 2012 14:00:02 (UTC)

Revision comment:

Added annotations.
Find Supporting Documents

Created by Kristina Hettne on Tuesday 05 February 2013 20:56:55 (UTC)
Find Supporting Documents

Created by Kristina Hettne on Tuesday 05 February 2013 20:58:29 (UTC)
Find Supporting Documents

Created by Kristina Hettne on Monday 14 July 2014 10:45:00 (UTC)

Revision comment:

Edited examples to reflect latest concept database update. There seems to be a bug in the database since it returns empty results though...
Find Supporting Documents

Created by Kristina Hettne on Monday 14 July 2014 10:47:12 (UTC)

Revision comment:

Updated description to report on the empty values bug.

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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

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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 Supporting Documents

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Other workflows that use similar services (18)