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Items tagged with "concept" (10)

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Network-member CWA-Working Group 3.2 ConceptWiki

Unique name: ConceptWiki Created: Wednesday 29 July 2009 @ 16:03:54 (BST)

This CWA Working Group is concerned with the CWA ConceptWiki and its relationship to other scientific Wikis. This place on MyExperiment will serve as a common forum for the Working Group.

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Blob PubMed Term Counts

Created: 11/08/09 @ 13:59:35

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in MEDLINE the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.

File type: Plain text

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Blob Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 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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Workflows (7)
Taverna 1

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Workflow Rank Phenotype Terms (v1)

Created: 10/08/09 @ 15:43:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Rank_phenotype_terms
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 ...

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Taverna 1

Original Uploader

Workflow Table Parser (v1)

Created: 19/08/09 @ 16:04:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Taverna 1

Original Uploader

Workflow Tab Parser (v1)

Created: 19/08/09 @ 16:05:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tab_parser
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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Taverna 1

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Workflow Concept Class Filter (v1)

Created: 19/08/09 @ 16:10:36

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concept_class_filter
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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Taverna 1

Original Uploader

Workflow Concept Class Neighbours Filter (v1)

Created: 19/08/09 @ 16:11:56

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concept_class_neighbours_filter
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...

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Taverna 1

Original Uploader

Workflow Context Consensus Filter (v1)

Created: 19/08/09 @ 16:13:11

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Context_consensus_filter
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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Taverna 1

Original Uploader

Workflow SubGraph Filter (v2)

Created: 19/08/09 @ 16:38:17

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Subgraph_filter
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...

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