Workflows

Phenotype to pubmed (1)

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2015-09-01

Credits: Heiko Schoof Paul Fisher

Attributions: Phenotype to pubmed

Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: Kristina Hettne Eelke van der Horst BioSemantics

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

Pathway to Pubmed (1)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2013-09-03

Credits: Alan Williams Paul Fisher

Attributions: Pathway to Pubmed

PubMed Search and Solr storage (5)

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Based on the work of Fisher: This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. I extended by removing outputs and text extraction and addded an automatic Solr storage process using a post.jar, specified by the user. Before running this workflow, make sure that a solr server is up and running and the variable attached to the SolrImport process contains the correct path. Dependencies: - Solr

Created: 2013-07-25 | Last updated: 2013-08-26

Credits: Sander van boom

Attributions: PubMed Search

Microbase S3CMD and AWS Workflow to Analys... (1)

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 This workflow is designed to interact with the aws and a specific VM, to carry out commands and analsye next gen sequence data (SFF FASTQ)

Created: 2013-03-08

Credits: ROBSeq Tech. Ltd.

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

Gene_To_Pathways (1)

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 This workflow identifier the pathways that are associated with given Kegg gene identifiers. Example inputs that can be used to run the workflow are eco:b0002, eco:b0078

Created: 2012-08-06 | Last updated: 2012-09-07

Credits: Khalid Belhajjame Stian Soiland-Reyes

Attributions: Hello Anyone

Gene to Pathways (1)

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This is a Taverna workflow that given a gene ID fetches the corespondondings pathways. To do so, the workflow make use of two KEGG web services.

Created: 2012-07-09 | Last updated: 2012-07-10

Credits: Khalid Belhajjame