myExperiment - Content

Taverna 1

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Thomask...

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Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems.

Created: 2010-01-13

Credits: Thomaskelder

Taverna 2

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Paul Fisher

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

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Paul Fisher

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Pathway to Phenotype using Text Mining

Created: 2009-08-10 13:01:47 | Last updated: 2009-08-11 14:51:31

This pack contains a list of workflows and result files obtained from the analysis of candidate pathways believed to play a role in resistance to African Trypanosomiasis in the mouse model organism.

12 items in this pack

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Taverna 2

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Thomask...

Download pathways for external references ... (2)

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Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2009-02-03

Credits: Thomaskelder

Taverna 1

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Paul Fisher

Extract Scientific Terms (1)

This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

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Paul Fisher

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Towards Genotype-Phenotype Correlations

Created: 2009-04-08 13:14:54 | Last updated: 2009-08-11 14:50:01

It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing large datasets, and represent a framework for the re-use and the explicit declaration of experimental methods. In this pack is a paper which describes the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes.&n...

20 items in this pack

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Taverna 1

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Thomask...

Write pathway to disk (2)

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Downloads and writes a pathway from WikiPathways to a local disk in the given file type.

Created: 2008-11-14 | Last updated: 2008-11-14

Credits: Thomaskelder

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Paul Fisher

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Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 14:15:58

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project. Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th...

File type: Plain text

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Tags:

abstracts
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african trypanosomiasis
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authors
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cosine vector space
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data-driven
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enrichment
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esearch
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eutils
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genotype
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kegg
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Kegg Pathways
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pathway
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pathway-driven
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pathways
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phenotype
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pubmed
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition

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Paul Fisher

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Pathway Cosine Scores from Day7 and Tir1 QTL

Created: 2009-08-10 15:55:24

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of all pathways found to be differentially expressed at day 7 post infection in the trypanosomiasis resistance phenotype, which contain genes in the Tir1 QTL. The pathways in this file have been ranked according to the scores obtained after calculating a cosine vector value against the trypanosomiasis resistance phenotype. The higher the score, the more closely linked to a phentype a given pathway is. This allows each pathway to be ranked giving biologists a ...

File type: Excel workbook

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Tags:

abstracts
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african trypanosomiasis
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cosine vector space
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data-driven
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kegg
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Kegg Pathways
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pathway
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pathway-driven
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pathways
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phenotype
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sleeping sickness
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term
|
term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition
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trait

Uploader

Paul Fisher

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Kegg pathways and genes

Created: 2009-04-08 19:26:26 | Last updated: 2009-08-10 11:41:55

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all genes found within the Tir1 QTL region. These are represented as KEGG gene identifiers. Each gene is listed in tab deliminated format along with all KEGG pathway ids in which the gene is involved. These are given as KEGG pathway identifiers. Each gene may be included in zero or more pathways, with multiple instances of the same pathway being included in the file (due to multiple genes included in a single pathway).

File type: Plain text

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