Pack: Functional annotation of SNPs using next-generation text mining

Created: 2012-06-26 10:41:38      Last updated: 2015-09-01 14:31:18
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Title: Functional annotation of SNPs using next-generation text mining


Information Description

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 list of available concept sets to match the SNPs against. As an example, the concept set GO biological processes is used. Workflow 2973 consist of nine nested workflows (eight different components in the pack, for which one is used twice within the main workflow for different purposes). It reuses the SNP to Entrez gene identifier part of this workflow: http://www.myexperiment.org/workflows/3124, here implemented as a separate workflow (http://www.myexperiment.org/workflows/2971). Workflow 2973 takes a SNP ID and a set of GO biological processes as input together with a set of parameter settings. The outputs give the following information: 1) information about the GO biological process with the highest matching score against the SNPs, 2) if there are any co-occurring documents supporting this finding, and 3) the concepts contributing most to the match (intermediate concepts). The output parameters can be saved in Taverna as an Excel sheet together with the input parameters for interpretation. Documents supporting the relation with the intermediate concepts contributing most to the match can be retrieved with workflow http://www.myexperiment.org/workflows/2972.

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  • Internal item

    Workflow: DatabaseID to ConceptID (Marco Roos)

    Added by Kristina Hettne ... more than 1 year ago (2012-06-26 12:55:35)

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  • Internal item

    Workflow: Explain concept scores (Reinout van Schouwen)

    Added by Kristina Hettne ... more than 1 year ago (2012-06-26 12:56:53)

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  • Internal item

    Workflow: Filter concepts with profiles (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-09-14 10:20:07)

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  • Internal item

    Workflow: Find co-occurring documents (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-07-13 07:50:41)

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  • Internal item

    Workflow: Find Supporting Documents (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-06-26 11:29:02)

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  • Internal item

    Workflow: Get Concept IDs (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-07-06 14:23:48)

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  • Internal item

    Workflow: Get concept information (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-07-06 14:23:22)

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  • Internal item

    Workflow: List Concept Sets (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-07-06 14:26:23)

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  • Internal item

    Workflow: Match concept profiles (Marco Roos)

    Added by Kristina Hettne ... more than 1 year ago (2012-06-26 12:57:59)

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  • Internal item

    Workflow: Match concept profiles with predefined set (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2013-02-05 21:18:52)

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  • Internal item

    Workflow: SNPs to Concept Set through Concept Profile Matching v2 (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-06-26 10:42:02)

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  • Internal item

    Workflow: SNP_ID2EntrezGene_ID (Kristina Hettne)

    Added by Kristina Hettne ... more than 1 year ago (2012-06-26 11:29:13)

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