Workflows

bget (1)

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Retrieve database entries specified by a list of entry_id. Number of entry_id retrieves at a time is restricted up to 100 Example of input: eco:b0002 hin:tRNA-Cys-1

Created: 2008-09-29

Credits: Franck Tanoh

bfind (1)

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Used for searching entries by keywords. User needs to specify a database from those which are supported by DBGET system before keywords. List of databases available at : http://www.genome.jp/dbget/ Example of input parameter: gb E-cadherin human

Created: 2008-09-29 | Last updated: 2008-09-29

Credits: Franck Tanoh

workflow1 (1)

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blast dando o ID de uma proteinablast dando o ID de uma proteina ex: database is ‘SWISS’, for program, ‘blastp’, and for ID ‘1220173blast dando o ID de uma proteina ex: database is SWISS’, for program, blastp, and for ID 1220173

Created: 2009-11-16

Credits: Jorgep

omim and pathways (2)

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This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with

Created: 2009-03-03 | Last updated: 2009-11-02

Credits: Katy Wolstencroft Paul Fisher

Attributions: Get Kegg Gene information

metabolic.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_ontology_diagram.xml (1)

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This workflow builds up a subgraph of the Gene Ontology (http://www.geneontology.org) to show the context for a supplied term or terms. It shows this context by colouring all ancestors of the term, all children and all siblings. By default, ancestors of the supplied term or terms are coloured orange, siblings purple and direct children teal. Other terms appear in the default wheat colour.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

BlastComparer.xml (1)

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Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Entrez Gene to KEGG Pathway (1)

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This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Created: 2014-01-30

Credits: Alice Heliou

Retrieve_Pubmed_Publication_by_kegg_pathwa... (1)

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This workflow shows in your browser pubmed articles related to input pathway

Created: 2012-10-18

Credits: Massimo La Rosa Antonino Fiannaca

Create_SNP_Set (1)

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The purpose of the workflow is to determine SNPs in the vicinity of the genes and create a SNP set for a given set of genes. The user has the freedom to choose the flanking width around the gene for determining the SNPs. The input is in the form of entrez gene ids. Biomart services are used to determine the chromosome and position of the gene as well as determining Affy gene chip 6k ids. The final report is stored as a tab-delimited text file with Affy 6 gene chip ids for the SNP and Kegg inf...

Created: 2012-08-21

Credits: Harish Dharuri