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 6 (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

4730 viewings

1690 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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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...