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Tag: profile Group: BioSemantics
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Pack Functional annotation of SNPs using next-generation ...


Created: 2012-06-26 10:41:38 | Last updated: 2015-09-01 14:31:18

This pack implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a ...

12 items in this pack

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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

Comments: 0 | Viewed: 94 times | Downloaded: 14 times

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

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

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

Workflow Get concept information (5)

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The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.

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

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

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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