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.

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 Ontology, GO:0008219. HG, HGNC, 4851. HMBD, Human Metabolome Database, HMDB01859. KEGD, KEGD, D00217. KEGG, KEGG, C12345. MESH, Medical Subject Headings, D000082. MGI, Mouse Genome Database, 96067. OM, OMIM, 143100. PUBC, PubChem Compound, 1983. PUBS, PubChem Substance, 7847284. RGD, Rat Genome Database, 68337. UG, UniGene, Mm.281700. UMLS, Unified Medical Language System, C0027439. UP, UniProt, P42858.

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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 (6)

Name	Type	Description
mapDatabaseIDToConceptIDs	wsdl	Maps a combination of database identifier and database id to one or more concept ids. Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation mapDatabaseIDToConceptIDs
mapDatabaseIDToConceptIDs_input	xmlsplitter
mapDatabaseIDToConceptIDs_output	xmlsplitter
mapDatabaseIDToConceptIDs_return	xmlsplitter
Split_string_into_string_list_by_regular_expression	localworker	Split the list on newline (\n) character. Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
regex_value	stringconstant	Split on newline (\n) character. Value \n

Beanshells (0)

Outputs (1)

Name	Description
Concept_IDs	Concept Identifiers for the given input, e.g. 3058322 for EG.3064

Datalinks (8)

Source	Sink
mapDatabaseIDToConceptIDs_input:output	mapDatabaseIDToConceptIDs:parameters
DatabaseID	mapDatabaseIDToConceptIDs_input:database
Split_string_into_string_list_by_regular_expression:split	mapDatabaseIDToConceptIDs_input:ID
mapDatabaseIDToConceptIDs:parameters	mapDatabaseIDToConceptIDs_output:input
mapDatabaseIDToConceptIDs_output:return	mapDatabaseIDToConceptIDs_return:input
IDvalue	Split_string_into_string_list_by_regular_expression:string
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
mapDatabaseIDToConceptIDs_return:conceptIDsAsString	Concept_IDs

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Marco Roos

Information License

All versions of this Workflow are licensed under:

Information Version 7 (latest) (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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