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Blob Ondex and Taverna Tutorial

Created: 2009-10-22 13:50:53 | Last updated: 2009-10-22 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

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Blob Ondex Workflows

Created: 2011-09-01 17:17:57 | Last updated: 2011-09-01 17:18:05

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains a large number of Taverna 2 workflows that utilise the Ondex Web Service, for manipulating Ondex graphs.

File type: ZIP archive

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Network-member ONDEX Graphs

Unique name: ONDEX
Created: Tuesday 10 February 2009 10:45:09 (UTC)

A group for sharing ONDEX graphs in oxl format http://ondex.sourceforge.net/ http://www.ondex.org/  

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Network-member SabrOndexProject

Unique name: SabrOndex
Created: Friday 27 February 2009 15:42:55 (UTC)

This group is set up for the SABR Ondex-Taverna integration http://www.ondex.org

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Workflows (26)

Workflow KEGG Pasrer (1)

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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: User Paul Fisher

Workflow Table Parser (1)

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This workflow parsers a table (specified by the user), into an Ondex Graph on the web server.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Tab Parser (1)

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This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow All Pairs Filter (1)

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This workflow filters a given Ondex graph based on the occurrence of directed edges within the graph. Only those concepts that have directional edges are returned to the user, in the form of 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 parameter. If no output graph is specified filtered items will be removed from the input graph. GdsWeight - The name of the GDS type to ...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Clean GO Filter (1)

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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: User Paul Fisher

Workflow Clean UniProt Filter (1)

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This workflow filters a given Ondex graph, removing any erroneous UniProt data. The result is a new Ondex graph that conatains only connected UniProt data. 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.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Concept Class Filter (1)

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This workflow filters a Ondex graph based on a specific concept class. 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. TargetConceptClass - Target Concept Class to filter out. RefactorTrinaries - Where the qualifier of a trinary relation is out of scope create a bina...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Concept Class Neighbours Filter (1)

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This workflow filters a given Ondex graph based on a user defined concept class. The neighbours of the concept class are returned as 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. Depth - The Depth (distance from seed in relations) to apply the filter to. ConceptClass - The Conce...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Context Consensus Filter (1)

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This workflow filters a given Ondex graph according to a consensus with regards to a specific context (concept list). 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. Threshold - Double value representing the share of contexts that qualify a graph element for ...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Context Filter (1)

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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: User Paul Fisher

Workflow CV Filter (1)

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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: User Paul Fisher

Workflow Evidence Type Filter (1)

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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: User Paul Fisher

Workflow GDS Value Filter (1)

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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: User Paul Fisher

Workflow Genomic Filter (1)

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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: User Paul Fisher

Workflow Graph Cloner (1)

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

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Isolate Clusters Filter (1)

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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: User Paul Fisher

Workflow One Pair Shortest Path Filter (1)

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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: User Paul Fisher

Workflow Optimal Paths Filter (1)

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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: User Paul Fisher

Workflow Pfam Based Ortholog Filter (1)

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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: User Paul Fisher

Workflow Relation Neighbours Filter (1)

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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: User Paul Fisher

Workflow Relation Type Filter (1)

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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: User Paul Fisher

Workflow Shortest Path (1)

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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: User Paul Fisher

Workflow Significance Filter (1)

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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: User Paul Fisher

Workflow SubGraph Filter (2)

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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: User Paul Fisher

Workflow Tranitive Filter (1)

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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: User Paul Fisher

Workflow Unconnected Filter (1)

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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: User Paul Fisher

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