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Tag: association Group: BioSemantics
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Pack Concept profile analysis using Anni Web services


Created: 2013-02-06 19:11:26 | Last updated: 2014-07-15 08:17:33

Concept profile analysis is a knowledge discovery method that proved successful in generating hypotheses about molecular mechanisms explaining the results from genotype-phenotype studies. This technology has been implemented in the Anni standalone application (http://biosemantics.org/anni). This pack contains a number of workflows that can be used together to configure and run typical user pipelines from Anni through the Anni Web services (http://www.biocatalogue.org/services/3559).

11 items in this pack

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Workflow Mining the Kegg pathway database with the ... (2)

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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: 2012-08-29 | Last updated: 2013-05-15

Credits: User Harish Dharuri

Workflow 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: User Kristina Hettne User Marco Roos User Reinout van Schouwen User Martijn Schuemie Network-member BioSemantics

Workflow 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: User Kristina Hettne User Eleni

Attributions: Workflow Prioritize gene list

Workflow 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: User Kristina Hettne User Marco Roos User Reinout van Schouwen Network-member BioSemantics

Workflow Match gene lists based on information in l... (7)

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[THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic...

Created: 2012-04-17 | Last updated: 2012-04-25

Credits: User Marco Roos User Reinout van Schouwen User Eleni User Kristina Hettne Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Explain concept scores

Workflow Match concept profiles (6)

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

Created: 2011-12-02 | Last updated: 2014-07-14

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

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