Workflows

NCBI Gi to Kegg Pathway Descriptions (5)

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This workflow accepts a list of NCBI gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2012-01-12 | Last updated: 2013-01-30

Credits: Katy Wolstencroft

Attributions: NCBI Gi to Kegg Pathways

getFirstElementDFS (2)

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Returns the first element of a nested list using depth first search. The maximum depth of the input is set to 2. You can savely increase this by increasing the depth of the workflow input port and the beanshell input port. Taverna will wrap the input into a list with correct depth. However this will create a little overhead.

Created: 2012-01-13 | Last updated: 2012-02-13

Import and convert gene list (1)

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Unigene identifiers

Created: 2012-01-15 | Last updated: 2012-03-12

Credits: Katy Wolstencroft

UnigeneID to KEGG Pathways (3)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2012-01-16 | Last updated: 2012-12-17

Credits: Katy Wolstencroft Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

Reactome pathways (1)

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This workflow returns a list of pathways gene products are involved in, along with their descriptions and Gene Ontology annotations

Created: 2012-01-16

Credits: Katy Wolstencroft

FFmpeg convert audio2aac (REST) (1)

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Converts supported audio files to AAC using FFmpeg through a REST webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

ImageMagick convert image2jp2 (REST) (1)

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Converts supported image files to JPEG2000 using ImageMagick through a REST webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

ImageMagick convert image2jp2 (SOAP) (1)

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Converts supported image files to JPEG2000 using ImageMagick through a SOAP webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

FFmpeg convert audio2aac (SOAP) (1)

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Converts supported audio files to AAC using FFmpeg through a SOAP webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

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: Kristina Hettne Eleni Harish Dharuri Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

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