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Tag: pubmed User: Paul Fisher
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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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4399?size=60x60 Gb Paul Fisher
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Blob Gene Cosine Scores

Created: 2009-08-10 16:00:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora.

File type: Excel workbook

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4399?size=60x60 Gb Paul Fisher
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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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Taverna 2
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4399?size=60x60 Gb Paul Fisher

Workflow XPath Pubmed Ids (2)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

Created: 2011-03-23 | Last updated: 2011-03-30

Credits: User Paul Fisher

Attributions: Workflow XPath Pubmed Ids

Taverna 2
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4399?size=60x60 Gb Paul Fisher

Workflow XPath Pubmed Ids (1)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml

Created: 2011-03-23 | Last updated: 2011-03-23

Credits: User Paul Fisher

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4399?size=60x60 Gb Paul Fisher
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Blob Bilateral Perisylvian Polymicrogyria

Created: 2011-03-17 10:56:15 | Last updated: 2011-03-17 11:16:53

Credits: User Paul Fisher

Attributions: Workflow Pathway and Gene to Pubmed Workflow Pathways and Gene annotations forQTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance each may play in relation to Bilateral Perisylvian Polymicrogyria. If you want to help me identify candidate genes for this disorder, please get i...

File type: ZIP archive

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4399?size=60x60 Gb Paul Fisher
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Blob Trichuriasis Induced Colitis

Created: 2011-02-16 15:16:17 | Last updated: 2011-02-16 15:16:24

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for RefSeq ids Workflow KEGG pathways common to both QTL and microarray based investigations Workflow Pathways and Gene annotations for QTL region Workflow Pathway and Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the results of workflow runs for: identifying genes in each of the 7 QTL regions for Trichuris muris infection; identifying genes differentially expressed in mice challenged with Trichuris muris; and Text mining results (including cosine vector scores and Term Enrichment values).

File type: Trident (Package)

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4399?size=60x60 Gb Paul Fisher
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Pack Trichuriasis induced Colitis


Created: 2011-02-16 12:49:21 | Last updated: 2011-02-16 15:26:36

This pack contains the workflows and data relating to Trichuriasis induced colitis.

5 items in this pack

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