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Administrator:

Paul Fisher

SabrOndexProject

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

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Paul Fisher

Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:54 | Last updated: 22/10/09 @ 13:51:52

Credits: George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

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Paul Fisher

KEGG Pasrer (v1)

Created: 19/08/09 @ 16:03:09 | Last updated: 19/08/09 @ 16:03:10

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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)

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Paul Fisher

Tab Parser (v1)

Created: 19/08/09 @ 16:05:21 | Last updated: 19/08/09 @ 16:05:22

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Clean GO Filter (v1)

Created: 19/08/09 @ 16:07:28 | Last updated: 19/08/09 @ 16:07:29

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Paul Fisher

Concept Class Filter (v1)

Created: 19/08/09 @ 16:10:38 | Last updated: 19/08/09 @ 16:10:39

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Context Consensus Filter (v1)

Created: 19/08/09 @ 16:13:12 | Last updated: 19/08/09 @ 16:13:14

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 ...

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Paul Fisher

CV Filter (v1)

Created: 19/08/09 @ 16:15:21 | Last updated: 19/08/09 @ 16:15:23

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

GDS Value Filter (v1)

Created: 19/08/09 @ 16:17:28 | Last updated: 19/08/09 @ 16:17:30

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 ...

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Paul Fisher

Graph Cloner (v1)

Created: 19/08/09 @ 16:22:14 | Last updated: 19/08/09 @ 16:22:16

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Original Uploader

Paul Fisher

One Pair Shortest Path Filter (v1)

Created: 19/08/09 @ 16:24:42 | Last updated: 19/08/09 @ 16:24:44

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 -...

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Paul Fisher

Pfam Based Ortholog Filter (v1)

Created: 19/08/09 @ 16:26:56 | Last updated: 19/08/09 @ 16:26:58

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Relation Type Filter (v1)

Created: 19/08/09 @ 16:29:12 | Last updated: 19/08/09 @ 16:29:13

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Significance Filter (v1)

Created: 19/08/09 @ 16:31:25 | Last updated: 19/08/09 @ 16:31:26

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Tranitive Filter (v1)

Created: 19/08/09 @ 16:34:17 | Last updated: 19/08/09 @ 16:34:18

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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