DatabaseID to ConceptID

Created: 2012-06-25 20:48:28 Last updated: 2014-07-14 09:23:46

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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.

Resources:

Table of database identifiers and concept identifiers. Database identifiers from ... EMC ontology compiled from ...

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 (2)

Name	Description
DatabaseID	Identifier for databases, e.g. EG for Entrez Gene
IDvalue	Identifier value, e.g. 3064 for HTT when DatabaseID=EG

Processors (4)

Name	Type	Description
mapDatabaseIDToConceptIDs	wsdl	This Web service takes a database identifier and its value as input and maps it to the corresponding concept id in the Erasmus MC ontology. Wsdl http://ws.biosemantics.org/ConceptRecognizerService?wsdl Wsdl Operation mapDatabaseIDToConceptIDs
mapDatabaseIDToConceptIDs_input	xmlsplitter
mapDatabaseIDToConceptIDs_output	xmlsplitter
mapDatabaseIDToConceptIDs_return	xmlsplitter

Beanshells (0)

Outputs (1)

Name	Description
concepts	Concept Identifiers for the given input, e.g. 3097212 for EG.3064

Datalinks (6)

Source	Sink
mapDatabaseIDToConceptIDs_input:output	mapDatabaseIDToConceptIDs:parameters
IDvalue	mapDatabaseIDToConceptIDs_input:ID
DatabaseID	mapDatabaseIDToConceptIDs_input:database
mapDatabaseIDToConceptIDs:parameters	mapDatabaseIDToConceptIDs_output:input
mapDatabaseIDToConceptIDs_output:return	mapDatabaseIDToConceptIDs_return:input
mapDatabaseIDToConceptIDs_return:conceptSet	concepts

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Marco Roos

Information License

All versions of this Workflow are licensed under:

Information Version 4 (of 7)

Information Credits (4)

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Information Attributions (0)

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None

Information Tags (10)

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Information Shared with Groups (1)

BioSemantics

Information Featured In Packs (2)

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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

4735 viewings

1696 downloads

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Citations (0)

None

Version History

In chronological order:

DatabaseID_to_ConceptID

Created by Marco Roos on Monday 25 June 2012 20:48:28 (UTC)
DatabaseID_to_ConceptID

Created by Kristina Hettne on Wednesday 11 July 2012 15:29:38 (UTC)

Revision comment:

This version reflects a change in the web service interface. The function remains the same.
DatabaseID_to_ConceptID

Created by Kristina Hettne on Wednesday 18 July 2012 13:58:06 (UTC)

Revision comment:

Added annotations.
DatabaseID_to_ConceptID

Created by Kristina Hettne on Friday 14 September 2012 10:03:01 (UTC)
DatabaseID_to_ConceptID

Created by Kristina Hettne on Tuesday 05 February 2013 21:22:28 (UTC)
DatabaseID to ConceptID

Created by Kristina Hettne on Monday 14 July 2014 08:35:00 (UTC)

Revision comment:

Updated examples to newest version of concept database. Modified workflow so that it also supports a list of identifiers separated by the newline character.
DatabaseID to ConceptID

Created by Kristina Hettne on Monday 14 July 2014 09:23:46 (UTC)

Revision comment:

Edited description field.

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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...