Workflows

caArray data retrieving (1)

• Download

Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They ca be later used as training and test data set in many classification algorithms.Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They can be later used as training and test data set in many classification algorithms.

Created: 2009-11-23

Credits: Wei Tan

Search for BMURI in PubMed [myexperiment:p... (1)

• Download

test values: subkecttest values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 test values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 query = labrie graph = http://labrie

Created: 2009-11-17

Credits: Francois Belleau

Multiple Choice Quiz (1)

• Download

A multiple choice quiz constructed using the select webservice, control links and looping strategy.

Created: 2009-11-16

Credits: George

workflow1 (1)

• Download

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: Susaninha

getTimololFromMassBank (1)

• Download

This workflow will retrieve a peaklist from a fixed entry (Timolol) from the MassBank spectral library. Note, the API is still in alpha, as of 10.11.2009.  

Created: 2009-11-10 | Last updated: 2009-11-10

Credits: http://sneumann.pip.verisignlabs.com/

Determine the Maximum Common SubStructure ... (1)

• Download

Created: 2009-10-23

Credits: Egon Willighagen

Search GeNS Organism (1)

• Download

 This workflow returns a GeNS identifier for a given organism.    Disclaimer: This workflow is just a simple example designed for academic purposes.

Created: 2009-09-15

Credits: Pedro Lopes

EBI_InterProScan_T2 (1)

• Download

Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2009-09-11

Credits: Steve Crouch Stian Soiland-Reyes

Workflow for provenance testing -- example 1 (1)

• Download

this simply includes a few beanshells and is used for testing our provenance capture and query algorithms

Created: 2009-09-10

Credits: Paolo

Get Bioentity from Organism (1)

• Download

GeNS workflow that lists the identifiers corresponding to a given species and data type. For instance, list all OMIM associated with the human species. Disclaimer: This workflow is just a simple example designed for academic purposes.

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

Credits: Pedro Lopes

chicken_ensembl_gene_id (1)

• Download

Accepts a chromosome eg. 1 and returns the ensembl gene ids for that chromosome

Created: 2009-09-07 | Last updated: 2009-09-09

Credits: Rory

Unconnected Filter (1)

This workflow removes any unconnected nodes from a given Ondex graph through filtering, and returns 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 parameter. If no output graph is specified filtered items will be removed from the input graph. RemoveContextDependencies - Set true to remove context dependencies, otherwise unconnected concepts will still remain in the ...

Created: 2009-08-19

Credits: Paul Fisher

Tranitive Filter (1)

This workflow filters an Ondex graph to extract a sub-graph. The result is a new Ondex graph containing only the transitive 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). If no output graph is specified filtered items will be removed from the input graph. CV - Seed cv that will be used to extract the subgraph (Optional). AttributeName - Seed attribute name that will be us...

Created: 2009-08-19

Credits: Paul Fisher

Significance Filter (1)

This workflow filters a given Ondex graph according to a level of significance set by the user. 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. TargetAttributeName - Target AttributeName to filter for significance. Significance - A significance value to filter relatio...

Created: 2009-08-19

Credits: Paul Fisher

Shortest Path (1)

This workflow filters a given Ondex graph according to the shortest path (graph) algorithm. 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. StartConceptID - The Concept ID that starts the path. Valid value range is 1 to 2147483647. UseWeights - Use gds values as edge ...

Created: 2009-08-19

Credits: Paul Fisher

Relation Type Filter (1)

This workflow filters a pre-existing ONdex graph based on a some paramters provided by the user. 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. TargetRelationType - Target RelationType to filter out. ConceptClassRestriction - Concept Class Restriction as ordered pair representing from/to C...

Created: 2009-08-19

Credits: Paul Fisher

Relation Neighbours Filter (1)

This workflow filters a given Ondex graph based on some neighbour parameters supplied by the user. 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 parameter. If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to ConceptID - The Concept ID to seed th...

Created: 2009-08-19

Credits: Paul Fisher

Pfam Based Ortholog Filter (1)

This workflow filters an Ondex graph based on the occurrence of Pfam orthologs 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. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold...

Created: 2009-08-19

Credits: Paul Fisher

Optimal Paths Filter (1)

This workflow filters a given Ondex graph based on the optimal path between one or more concepts. The result is a new Ondex graph. The parameters that can be used with 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. PathwayDefinition - pathway definition file. StatisticsOutputDir - The directory to output statistics (Optional). Incl...

Created: 2009-08-19

Credits: Paul Fisher

One Pair Shortest Path Filter (1)

This workflow filters a pre-existing Ondex graph using the shortest path algorithm on 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 parameter. If no output graph is specified filtered items will be removed from the input graph. StartConceptID - The Concept ID that starts the path EndConceptID - The Concept ID that ends the path UseWeights -...

Created: 2009-08-19

Credits: Paul Fisher

Isolate Clusters Filter (1)

This workflow filters a given Ondex graph, isolating clusters within the graph and returning only those clusters as a new 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. TargetConceptClass - Target Concept Class to be contained in clusters.

Created: 2009-08-19

Credits: Paul Fisher

Graph Cloner (1)

This workflow clones a given Ondex Graph, based on an Ondex Graph identifier.

Created: 2009-08-19

Credits: Paul Fisher

GDS Value Filter (1)

This workflow filters a given Ondex graph based on a given GDS value supplied by the user. The result is a new Ondex graph with filtered content. 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. AttributeName - AttributeName to filter out. GDSValue - A value which will be matched against the ...

Created: 2009-08-19

Credits: Paul Fisher

Evidence Type Filter (1)

This workflow filters a given Ondex graph according to some user defined evidence values. The result is a new Ondex graph. The parameters that can be used with this web service are given below: 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. EvidenceType - EvidenceType to be taken into consideration. RefactorTrinaries - Where the qualifier of a trinary rel...

Created: 2009-08-19

Credits: Paul Fisher

Context Filter (1)

This workflow filters an Ondex graph according to a given context. The result is a new Ondex graph with only selected contexts. 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 that starts the path. ContextBoolean - Defines two ContextIDs and a boolean operati...

Created: 2009-08-19

Credits: Paul Fisher