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4399?size=60x60 Gb Paul Fisher
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Pack 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 1
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4399?size=60x60 Gb Paul Fisher

Workflow Extract Scientific Terms (1)

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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: User Paul Fisher

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4399?size=60x60 Gb Paul Fisher
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Pack 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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4399?size=60x60 Gb Paul Fisher
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Pack Genotype to Pathway


Created: 2009-08-11 14:44:16 | Last updated: 2009-08-11 14:52:12

This pack is for investigating links between the genotype of an organisms to possible pathways. This constitutes half of the pathway-driven approach, genotype to pathway, and pathway to phenotype.

18 items in this pack

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4399?size=60x60 Gb Paul Fisher
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Blob Pathway Term Enrichment Scores

Created: 2009-08-11 14:23:49

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of each pathway identified from day 7 post infection and linked to the Tir1 QTL. With each pathway is a list of terms that are common to both pathway and phenotype corpora. These terms were ranked accoring to their enrichement scores. The higher the score, the more significant the term is in relation to correlating the pathway with the African trypanosomiasis resistance phenotype.

File type: Plain text

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4399?size=60x60 Gb Paul Fisher
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Blob PubMed Term Counts

Created: 2009-08-11 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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4399?size=60x60 Gb Paul Fisher
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Blob PubMed Abstract Number

Created: 2009-08-11 13:54:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the number of articles available in MEDLINE, through PubMed, at the time of performing these data analyses. The date of identifying these publications was 25/02/2009.

File type: Plain text

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Term Counts (in Phenotype Corpus)

Created: 2009-08-11 13:34:42 | Last updated: 2009-08-11 13:58:28

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 the phenotype corpus 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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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Concept Profile - Terms

Created: 2009-08-11 13:05:07 | Last updated: 2009-08-11 13:06:51

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model. These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl These terms represent the concept profile for the phenotype.

File type: Plain text

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Abstracts for Trypanosomiasis Resistance

Created: 2009-08-11 12:45:24

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of published abstracts from MEDLINE, that are related to the African Trypanosomiasis resistance phentoype in the mouse. The term used in the PubMed search was: trypanosom* AND (tolerance OR resistance) . The workflow limited the date of the search using PubMed between 31/12/2005 to 01/01/2009, and was restricted to 500 abstracts.

File type: Plain text

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