Workflows

Autodock Vina (1)

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 This workflow requires MGLTools which contains the Vision workflow framework. MGLTools maybe downloaded from https://www.nbcr.net/pub/wiki/index.php?title=CADD_Pipeline. 

Created: 2010-02-04 | Last updated: 2010-02-09

Credits: Jrensp

Get Gene Ids for Human (1)

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This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

Created: 2010-02-04 | Last updated: 2010-02-04

Credits: Paul Fisher

Search TP53 Somatic Mutation catalogue by ... (1)

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This workflow takes the exon, the effect and the TP53 somatic mutation database as input and retrieves the full TP53 somatic mutation description(s) by first retrieving two different outputs and arranging them according to the boolean operators (�and�, �or� and �butnot�): - first output: a TP53 somatic mutation database unique IDs list associated with the input 'exon' (done via a call to the getP53MutationIdsByExon web service) - second output: a TP53 somatic mutation database u...

Created: 2010-01-15

Credits: Achille Zappa

Triplify namespace XREF list from GO, LSRN... (1)

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TAG: banff_manifesto, xref, bio2rdf, rdfTAG: banff_manifesto, xref, bio2rdf, rdf, mashup Triplify namespace XREF list from GO, LSRN, NCBI and UniProt [myexperiment:xref_namespace2rdf] TAG: banff_manifesto, xref, bio2rdf, rdf TAG: banff_manifesto, xref, bio2rdf, rdf

Created: 2009-12-01

Credits: Francois Belleau

Triplify UniProt database external referen... (2)

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Get UniProt external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify NCBI databases external reference... (1)

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Get NCBI external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify UniProt text search results from ... (2)

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Search all UniProt databases using search URL service and merge results into a bmuri list and a ntriples string. 

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: Francois Belleau

Triplify search results from KEGG bfind SO... (3)

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This workflow use KEGG's SOAP service provided to do a BFIND serch within one of the KEGG's official database. The results are returned in RDF ntriples format. 

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: Francois Belleau

Triplify KEGG database list [myexperiments... (2)

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TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf

Created: 2009-11-28 | Last updated: 2009-11-30

Credits: Francois Belleau

Query DBPedia for all entries with an InChI (1)

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Created: 2009-11-20

Credits: Egon Willighagen

Sponge into Virtuoso triplestore the neede... (2)

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query = labrie,f query = labrie query = labrie,f query = labrie query = h1n1 query = morissette,j query = labrie,f query = labrie query = h1n1 Get a list of paper from pubmed.

Created: 2009-11-17 | Last updated: 2009-11-27

Credits: Francois Belleau

Search for citations and related article i... (1)

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graph = http://nur77 bmuri = http://bio2rdf.org/pubmed:18843482 http://bio2rdf.org/pubmed:18466322 http://bio2rdf.org/pubmed:17201484 http://bio2rdf.org/pubmed:14603264 http://bio2rdf.org/pubmed:12629527

Created: 2009-11-17

Credits: Francois Belleau

Get graphs (2)

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Thiw workflow simply returns all the Ondex graphs that are present on a given server (where the web service is)

Created: 2009-11-05

Credits: Paul Fisher

MY_Multi_Alignment_Phylo (1)

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This workflow performs a 'multiple' multiple sequence alignment and phylogenetic analysis.

Created: 2009-11-03

Credits: Achille Zappa

Kabsch Alignment of Small Molecules (1)

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Created: 2009-10-30

Credits: Egon Willighagen

Example 3 (1)

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Search in the Datenbank SWISS the Sequence 1220173

Created: 2009-10-20

Credits: Ruben

Download CAS numbers and save as SD file (1)

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Download molecules from a REST services using the CAS registry number, create 3D coordinates and save the results as a MDL SD file.

Created: 2009-10-15

Credits: Egon Willighagen

Extract RDF from HTML+RDFa (2)

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Small script for Bioclipse that extracts RDF from HTML+RDFa webpages.

Created: 2009-09-30 | Last updated: 2010-06-23

Credits: Egon Willighagen

example of a 2-deep nested workflow (1)

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used for testing provenance as well as experimenting with Scufl2 specfications

Created: 2009-09-11

Credits: Paolo

Sample Entity Converter (1)

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 Disclaimer: This workflow is just a simple example designed for academic purposes.

Created: 2009-09-08 | Last updated: 2009-09-14

Credits: Pedro Lopes