Group: PhD Supplementary Information

Overview

This group is only for examiners of my PhD thesis.

It contains all supplementary information listed in my thesis, and extra information in which to investigate all results a discussed with the thesis.

http://www.slideshare.net/fisherp/a-systematic-approach-to-genotypephenotype-correlations

Created at: Tuesday 11 August 2009 14:41:06 (UTC)

Unique name: FisherpSupplementary

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  1. 4399?size=48x48
    Paul Fisher shared Text Mining Workflows
    This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.
    Wednesday 08 December 2010 11:55:12 (UTC)
  2. 4399?size=48x48
    Paul Fisher shared Extract Scientific Terms
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    This workflow takes in a document containg text and removes and non-ascii characters. The cleaned text is then sent to a service in dresden to extract all scientific terms. These terms represent a profile for the input document. Any null values are also removed.
    Wednesday 08 December 2010 11:50:04 (UTC)
  3. 4399?size=48x48
    Paul Fisher shared Pathway to Pubmed
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    This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.
    Wednesday 08 December 2010 11:47:14 (UTC)
  4. 4399?size=48x48
    Paul Fisher shared Rank Phenotype Terms
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    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 t …
    Wednesday 08 December 2010 11:38:40 (UTC)
  5. 4399?size=48x48
    Paul Fisher shared Cosine vector space
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    This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing added
    Wednesday 08 December 2010 11:35:21 (UTC)
  6. 4399?size=48x48
    Paul Fisher shared KEGG pathways common to both QTL and microarray based investigations
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    This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a m …
    Monday 15 November 2010 12:30:31 (UTC)
  7. 4399?size=48x48
    Paul Fisher shared Pathways and Gene annotations for RefSeq ids
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    This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and …
    Monday 15 November 2010 12:25:17 (UTC)
  8. 4399?size=48x48
    Paul Fisher shared Pathways and Gene annotations for QTL region
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    This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the g …
    Monday 15 November 2010 12:08:34 (UTC)
  9. 4399?size=48x48
    Paul Fisher shared Phenotype to pubmed
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    This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user
    Monday 05 July 2010 14:07:39 (UTC)
  10. 4399?size=48x48
    Paul Fisher shared Gene to Pubmed
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    This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.
    Monday 05 July 2010 13:14:41 (UTC)
  11. 4399?size=48x48
    Paul Fisher shared Genotype to Pathway
    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.
    Tuesday 11 August 2009 14:52:13 (UTC)
  12. 4399?size=48x48
    Paul Fisher shared Pathway to Phenotype using Text Mining
    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.
    Tuesday 11 August 2009 14:51:32 (UTC)

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