myExperiment - Tags - sleeping sickness

Workflows (4)

Taverna 1 Original Uploader Paul Fisher	Extract Scientific Terms (v1) Created: 10/08/09 @ 13:31:07 \| Last updated: 10/08/09 @ 13:32:21 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 119 times \| Downloaded: 0 times Tags (18): abstracts \| authors \| data-driven \| entity recognition \| gene \| getconcepts \| kegg \| Kegg Pathways \| mining \| mouse \| pathway-driven \| pathways \| phenotype \| sleeping sickness \| term extraction \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 2 Original Uploader Paul Fisher	Phenotype to pubmed (v3) Created: 05/07/10 @ 14:07:33 \| Last updated: 11/01/11 @ 12:07:22 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 107 times \| Downloaded: 24 times Tags (18): abstracts \| african trypanosomiasis \| disease \| efetch \| entrez \| esearch \| loci \| ncbi \| phenotype \| pubmed \| qtl \| quanitative \| sleeping sickness \| term \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View Download (v3)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 15/11/10 @ 12:08:18 \| Last updated: 16/11/10 @ 16:07:49 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 10 times Tags (33): african trypanosomiasis \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| kegg \| Kegg Pathways \| KeggID \| loci \| locus \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| region \| sleeping sickness \| species \| trait \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v1) Created: 21/01/11 @ 16:56:47 \| Last updated: 21/01/11 @ 16:58:50 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. 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 genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway data... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 10 times Tags (22): african trypanosomiasis \| bos taurus \| cattle \| chromosome \| cow \| ensembl \| entrez \| gene \| genes \| genotype \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways \| phenotype \| qtl \| quanitative \| re-use \| region \| sleeping sickness \| uniprot	View Download (v1)

Packs (3)

Creator:

Paul Fisher

Towards Genotype-Phenotype Correlations

Created: 08/04/09 @ 13:14:54 | Last updated: 11/08/09 @ 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

Comments: 0 | Viewed: 149 times | Downloaded: 32 times

Tags:

View

Download

Creator:

Paul Fisher

Pathway to Phenotype using Text Mining

Created: 10/08/09 @ 13:01:47 | Last updated: 11/08/09 @ 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

Comments: 0 | Viewed: 186 times | Downloaded: 34 times

Tags:

View

Download

Creator:

Paul Fisher

Genotype to Pathway

Created: 11/08/09 @ 14:44:16 | Last updated: 11/08/09 @ 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

Comments: 0 | Viewed: 86 times | Downloaded: 7 times

Tags:

View

Download

Files (14)

Uploader: Paul Fisher	A Taverna Users Guide Created: 04/08/08 @ 17:40:21 Credits: Paul Fisher Katy Wolstencroft Franck Tanoh License: Creative Commons Attribution-Share Alike 3.0 Unported License No description File type: PowerPoint presentation Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 89 times \| Downloaded: 107 times Tags: bioinformatics \| microarray \| mining \| neuroscience \| newcastle \| sleeping sickness \| summary \| web services	View Download
Uploader: Paul Fisher	A Systematic Strategy for Large-Scale Analysis of Genotype-Phenotype Correlations: Identification of candidate genes involved in African Trypanosomiasis Created: 08/04/09 @ 13:23:03 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This PDF is my personal copy of the NAR publication. File type: Adobe PDF Rating: 0.0 / 5 (0 ratings) \| Comments: 1 \| Viewed: 28 times \| Downloaded: 23 times Tags: african trypanosomiasis \| genotype \| pathway-driven \| phenotype \| sleeping sickness	View Download
Uploader: Paul Fisher	Candidate Gene protocol Created: 08/04/09 @ 13:27:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This protocol provides details on how to identify candidate genes from the returned workflow results. File type: Word document Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 33 times \| Downloaded: 38 times Tags: affymetrix \| african trypanosomiasis \| gene \| gene identifier \| geneid \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness	View Download
Uploader: Paul Fisher	Table of SNP sequenceing results Created: 08/04/09 @ 13:29:32 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains the results of re-sequencing the Daxx gene File type: Word document Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 58 times \| Downloaded: 22 times Tags: african trypanosomiasis \| daxx \| genotype \| mouse \| phenotype \| sleeping sickness \| snp \| snps	View Download
Uploader: Paul Fisher	Tir1 QTL - Day 3 Microarray intersecting pathways Created: 08/04/09 @ 17:56:10 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 3 differentially expressed genes File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 17 times \| Downloaded: 19 times Tags: african trypanosomiasis \| expression \| gene \| microarray \| qtl \| sleeping sickness	View Download
Uploader: Paul Fisher	Tir1 QTL - microarray day 7 intersecting pathways Created: 08/04/09 @ 17:57:57 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 7 differentially expressed genes File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 21 times \| Downloaded: 23 times Tags: affymetrix \| african trypanosomiasis \| gene \| microarray \| pathway \| qtl \| sleeping sickness	View Download
Uploader: Paul Fisher	Pathway Cosine Scores from Day7 and Tir1 QTL Created: 10/08/09 @ 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 1 \| Viewed: 13 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| cosine vector space \| data-driven \| kegg \| Kegg Pathways \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View
Uploader: Paul Fisher	Gene Cosine Scores Created: 10/08/09 @ 16:00:45 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 13 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| cosine vector space \| data-driven \| enrichment \| entity recognition \| gene \| geneid \| genes \| mouse \| ncbi \| phenotype \| pubmed \| ranking \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Phenotype Abstracts for Trypanosomiasis Resistance Created: 11/08/09 @ 12:45:24 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 6 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| cosine vector space \| information \| mining \| pubmed \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Phenotype Concept Profile - Terms Created: 11/08/09 @ 13:05:07 \| Last updated: 11/08/09 @ 13:06:51 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 17 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| concept profile \| cosine vector space \| dresden \| enrichment \| entity recognition \| gene \| mining \| mouse \| protein \| pubmed \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Phenotype Term Counts (in Phenotype Corpus) Created: 11/08/09 @ 13:34:42 \| Last updated: 11/08/09 @ 13:58:28 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 15 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| append term \| authors \| phenotype \| pubmed \| ranking \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	PubMed Abstract Number Created: 11/08/09 @ 13:54:45 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 1 \| Viewed: 16 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| pubmed \| sleeping sickness \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	PubMed Term Counts Created: 11/08/09 @ 13:59:35 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 28 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| concept \| cosine vector space \| pubmed \| sleeping sickness \| term \| term extraction \| terms	View
Uploader: Paul Fisher	Pathway Term Enrichment Scores Created: 11/08/09 @ 14:23:49 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 45 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| concept profile \| cosine vector space \| data-driven \| enrichment \| pubmed \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View

Tag Results

Items tagged with "sleeping sickness" (21)