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Tag: snp

Workflow DataBiNS with Kegg ID (3)

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Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene

Created: 2009-07-09 | Last updated: 2010-11-22

Credits: User Mark Wilkinson User Fong Chun Chan

Workflow Query dbsnp, transform to HTML (1)

This is a XProc worklow. Its input is a list of Entrez queries packed in a html list: See http://plindenbaum.blogspot.com/2009/05/xml-pipelines-xproc-for-bioinformatics.html "snp_gene_clin"[Filter] AND "snp_pubmed_cited"[Filter] AND 2[CHR] (1000[CHRPOS] : 5000[CHRPOS]) AND 2[CHR] AND "homo sapiens"[Organism] it queries entrez, download the SNPs as XML and transform the result as an HTML table:   r...

Created: 2009-05-21 | Last updated: 2009-05-21

Credits: User Pierre Lindenbaum

Workflow snpNeighbours (1)

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My first Taverna workflow:  the input is the SNP "rs25". The Web Services invoked finds its position on the human genome and find its neighbours at 100bp. The XML result is then saved to a local file. The web services used here are under developpement and might be turned off in a near future.

Created: 2009-05-14 | Last updated: 2009-05-14

Credits: User Pierre Lindenbaum

Workflow 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: User Kristina Hettne User Harish Dharuri User Marco Roos User Reinout van Schouwen

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 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

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Workflow NGS : Tuto SNP detection workflow single end (1)

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Generate pileup, Unify Genotypers and create a VCF file from FastQ files of two individuals

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: User Ylebras

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Workflow NGS : flanking SNP regions (1)

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Flank SNP regions using interval format file and a fasta reference file

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: User Ylebras

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Workflow Tuto Galaxy 2013 : CPB2012 - BasicProtocol... (1)

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Workflow used when applying the CPB2012 Basic Protocol 1 tutorial from Galaxy team. It permits to filter Exons with the most SNP density.

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: User Ylebras

Workflow Mining the Kegg pathway database with the ... (1)

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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: 2013-01-30

Credits: User Marco Roos

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