Workflows

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

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