Workflows

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

• Download

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)

• Download

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)

• Download

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)

• Download

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

Created: 2009-11-03

Credits: Achille Zappa

Kabsch Alignment of Small Molecules (1)

• Download

Created: 2009-10-30

Credits: Egon Willighagen

Example 3 (1)

• Download

Search in the Datenbank SWISS the Sequence 1220173

Created: 2009-10-20

Credits: Ruben

Download CAS numbers and save as SD file (1)

• Download

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)

• Download

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)

• Download

used for testing provenance as well as experimenting with Scufl2 specfications

Created: 2009-09-11

Credits: Paolo

Sample Entity Converter (1)

• Download

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

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

Credits: Pedro Lopes

EBI_dbfetch_fetchBatch (1)

• Download

Sample workflow illustrating the use of EBI's WSDbfetch service with Triana.

Created: 2009-08-28

Credits: Hamish McWilliam

EBI_dbfetch_fetchData (1)

• Download

Sample workflow illustrating the use of the EBI's WSDbfetch service in Triana.

Created: 2009-08-28 | Last updated: 2009-08-28

Credits: Hamish McWilliam

Spreadsheet Importer (1)

• Download

This workflow is designed to import a spreadhseet from a local computer. The imported spreadsheet is parsed to extract the first two columns, A and B, for all rows in the spreadsheet. These are returned as two separate outputs.

Created: 2009-08-24

Credits: Paul Fisher

/me is having Bioclipse/XMPP/RDF fun.js (1)

• Download

Created: 2009-08-21

Credits: Egon Willighagen

Retrieve details on genetic marker by UniS... (3)

• Download

The workflow retrieves the marker's primers and the organism name - if available. The organism name may not be unique for a given marker. The primers should be. It would be nice if some good soul could investigate how to retrieve the various mappings from the site. The retrieval of the primers is thought to prepare for a manual mapping of the marker's chromosomal location.

Created: 2009-08-19

Credits: Steffen Möller

SubGraph Filter (2)

This workflow filters a given Ondex graph to return a new ondex sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. ConceptID - The root concept to start at. Valid value range is 1 to 2147483647. FirstRelationType - RelationType limitation for depth 1 (Optional). FirstConceptClass - C...

Created: 2009-08-19

Credits: Paul Fisher

Genomic Filter (1)

This workflow filters a given Ondex graph according to a chromosomal region, or QTL region. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context (Chromosome). From - The start position on the chromosome, e.g. 100. To - The stop pos...

Created: 2009-08-19

Credits: Paul Fisher

CV Filter (1)

This workflow filters a given Ondex graph according to a controlled vocabulary specified by the user. The result is a new Ondex graph with only those concepts that passed the filter. The parameters that can be used with this service graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. CV - A CV to include/exclude Concepts and Relations of (see Exclude param). R...

Created: 2009-08-19

Credits: Paul Fisher

Clean GO Filter (1)

This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph.

Created: 2009-08-19

Credits: Paul Fisher

KEGG Pasrer (1)

This workflow parses a KEGG species database into an Ondex Graph graphId - the ID of the Graph. inputDir - the plugin input directory Species - Use this parameter to specify the species to be loaded from the kegg database. Default value is all. ParseSequences - KEGG species code. Default value is false (boolean) ImportOrthologFillers - Import Ortholog Pathway Fillers. Default value is false (boolean)

Created: 2009-08-19

Credits: Paul Fisher

Rank Phenotype Terms (1)

This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Created: 2009-08-10

Credits: Paul Fisher

Cosine vector space (1)

This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

An example workflow with WSRF service (1)

• Download

An example workflow with WSRF service The service used is http://sidgrid.ci.uchicago.edu:8100/wsrf/services/CounterService The service is included in Globus toolkit installation (ws-core). If the it is down you can host your own and modify the workflow definition file to point to your own. The workflow first creates a counter instance and adds the value 10 for two times to the same counter. Therefore the result should be 20.

Created: 2009-07-28

Credits: Wei Tan Stian Soiland-Reyes

BioQuali asynchronous workflow (1)

• Download

BioQuali: Network Compatibility and products variation inference in a biological network. Help page: http://genoweb2.irisa.fr/claroline/claroline/course/index.php?cid=BIOQUALI Reference: Carito Guziolowski, Annabel Bourdé, Francois Moreews and Anne Siegel BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks BMC Genomics 2009, 10:244 doi:10.1186/1471-2164-10-244 This web service is made available on GenOuest bioinformatics platform (Rennes, ...

Created: 2009-07-06 | Last updated: 2009-07-06

Credits: abretaud GenOUEST Platform

Pipelined list iteration (1)

• Download

Perform multiple iterations of services in order to show pipelining

Created: 2009-07-03

Credits: Stian Soiland-Reyes Ian Dunlop