Workflows

EBI_OLS_TermInfo (1)

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Get details of an ontology term given its identifer. This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information.

Created: 2008-07-09

Credits: Hamish McWilliam

getOntologyTerm (1)

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This service takes a MIRIAM compliant URI and looks up all the synonyms for that URI using ChEBI and other services. Service developed and maintained by Neil Swainston at the MCISB in Manchester.

Created: 2009-06-09 | Last updated: 2009-06-09

Credits: Duncan Hull

SNPs to Concept Set through Concept Profil... (6)

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

Created: 2012-06-26 | Last updated: 2013-02-05

Credits: Kristina Hettne Eleni Harish Dharuri Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

Attributions: Find Supporting Documents SNP_ID2EntrezGene_ID DatabaseID to ConceptID Match gene lists based on information in literature Match concept profiles Explain concept scores

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

Get ontology parents (2)

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Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Created: 2015-11-16 | Last updated: 2016-04-26

Credits: Kristina Hettne

Attributions: Get ontology parents

Groovy script to convert (part of) CGN dat... (1)

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Created: 2015-01-22

Credits: Egon Willighagen

Visualize PAV provenance as SVG (1)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2014-05-08

Credits: Katy Wolstencroft Aleksandra Pawlik

Mapping to ontologies (Gene table) (1)

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This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.At the first step, the input table is converted into a table with Ensembl Gene IDs.This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Visualize PAV provenance as SVG (2)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2013-03-05 | Last updated: 2013-04-05

Credits: Stian Soiland-Reyes

Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

Credits: Kristina Hettne Reinout van Schouwen Marco Roos BioSemantics

Attributions: SNPs to Concept Set through Concept Profile Matching v2