myExperiment - Workflows

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User: Kristina Hettne

Wsdl: http://ws.biosemantics.org/ConceptProfileMiningService?wsdl

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Taverna 2

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Kristina Hettne

GWAS to biomedical concept (3)

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Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2013-04-15 | Last updated: 2014-07-14

Credits: Kristina Hettne Harish Dharuri Marco Roos Reinout van Schouwen

Taverna 2

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Kristina Hettne

Find co-occurring documents (6)

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Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts. Author comments: Currently, PubMed is the underlying data source.

Created: 2012-07-13 | Last updated: 2014-07-14

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

Taverna 2

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Kristina Hettne

Find Supporting Documents (6)

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This workflow finds documents that serve as evidence for the association between two concepts. Results: Document titles Document identifiers There seems to be a bug at the moment, since it returns empty values.

Created: 2012-06-26 | Last updated: 2014-07-14

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

Taverna 2

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Kristina Hettne

Prioritize gene list for the Cure game (1)

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This workflow prioritizes a gene list according to its association with the 'concept_id'. Here we are prioritizing a gene list against breast cancer, in order to try to beat Barney in the game The Cure (http://genegames.org/cure/). Note: Before running this workflow the gene names supplied in the game first needs to be mapped to Entrez gene identifiers. This can be done using either this workflow http://www.myexperiment.org/workflows/3722 or a by performing a search in the NCBI Entrez gene d...

Created: 2015-04-29

Credits: Kristina Hettne Eleni

Attributions: Prioritize gene list

Taverna 2

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Kristina Hettne

Match concept profiles with predefined set (2)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2013-02-05 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen BioSemantics

Taverna 2

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Kristina Hettne

Filter concepts with profiles (4)

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Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.

Created: 2012-09-14 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Martijn Schuemie BioSemantics

Taverna 2

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Kristina Hettne

List Concept Sets (3)

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.