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Items tagged with "mining" (9)

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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: 125 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 1 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 10/08/09 @ 15:43:48 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 124 times \| Downloaded: 0 times Tags (24): abstracts \| append term \| authors \| concept \| cosine vector space \| data-driven \| enrichment \| gene identifier \| geneid \| genes \| genotype \| information \| mining \| ncbi \| pathways \| phenotype \| pubmed \| ranking \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 2 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 01/02/11 @ 11:22:14 \| Last updated: 01/02/11 @ 11:24:42 Credits: Paul Fisher Attributions: Cosine vector space Rank Phenotype Terms License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 14 times Tags (26): concept \| concept profile \| cosine vector space \| data-driven \| enrichment \| entity recognition \| eutils \| evidence \| getconcepts \| literature \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| significance \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Gene to Pubmed (v4) Created: 08/02/11 @ 13:04:06 \| Last updated: 10/02/11 @ 16:01:41 Credits: Paul Fisher Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 43 times \| Downloaded: 23 times Tags (30): abstracts \| cosine vector space \| data-driven \| disease \| enrichment \| entity recognition \| evidence \| kegg \| Kegg Pathways \| literature \| loci \| locus \| medline \| microarray \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| ranking \| re-use \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trichuris muris	View Download (v4)

Packs (2)

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: 190 times | Downloaded: 34 times

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Creator:

Paul Fisher

Trichuriasis induced Colitis

Created: 16/02/11 @ 12:49:21 | Last updated: 16/02/11 @ 15:26:36

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

5 items in this pack

Comments: 0 | Viewed: 16 times | Downloaded: 2 times

Tags:

annotation
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chromosome
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controlled vocabulary
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cosine vector space
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data integration
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data-driven
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dresden
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efetch
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enrichment
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ensembl
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entity recognition
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esearch
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evidence
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gene expression
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gene identifier
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genotype
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kegg
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Kegg Pathways
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KeggID
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literature
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loci
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locus
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medline
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microarray
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mining
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pathway
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pathway-driven
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phenotype
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pubmed
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qtl
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quanitative
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ranking
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re-use
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significance
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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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trait
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trichuris muris

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Files (3)

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: 109 times

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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
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african trypanosomiasis
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cosine vector space
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information
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mining
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pubmed
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sleeping sickness
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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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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: 18 times | Downloaded: 0 times

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