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Items tagged with "terms" (21)
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Created: 10/08/09 @ 13:19:36 | Last updated: 10/08/09 @ 13:24:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output.
The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype).
A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation.
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Created: 10/08/09 @ 15:43:48
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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: 119 times | Downloaded: 0 times Tags (24): |
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Created: 19/08/09 @ 16:07:27
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). The result is a new Ondex graph. The parameters that can be used with this service are as follows:
graphId - the ID of the input Graph.
outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph.
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Created: 19/08/09 @ 16:26:55
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows:
graphId - the ID of the input Graph.
outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph.
ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100.
AnnotationScoreThreshold - Threshold...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 24 times | Downloaded: 1 time Tags (10): |
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Original Uploader |
Created: 08/12/10 @ 11:35:18 | Last updated: 11/01/11 @ 12:05:41
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 08/12/10 @ 11:50:01 | Last updated: 11/01/11 @ 11:58:09
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Original Uploader |
Created: 01/02/11 @ 11:22:14 | Last updated: 01/02/11 @ 11:24:42
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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 ...
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Original Uploader |
Created: 03/02/11 @ 15:49:07 | Last updated: 03/02/11 @ 15:59:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
THis workflow removes any non-ascii characters from a segment of text. Any characters that are found are removed. Letters either side f the non-ASCII are concatenated - this may cause the loss of word meaning
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Original Uploader |
Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41
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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.
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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: |
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Created: 08/12/10 @ 11:55:03 | Last updated: 01/02/11 @ 11:33:11
This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.
5 items in this pack Comments: 0 | Viewed: 75 times | Downloaded: 12 times Tags: |
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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: 15 times | Downloaded: 2 times Tags: |
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Created: 10/08/09 @ 15:55:24
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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: |
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Created: 10/08/09 @ 16:00:45
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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: |
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Created: 11/08/09 @ 12:45:24
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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: |
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Created: 11/08/09 @ 13:05:07 | Last updated: 11/08/09 @ 13:06:51
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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: |
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Created: 11/08/09 @ 13:34:42 | Last updated: 11/08/09 @ 13:58:28
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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: |
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Created: 11/08/09 @ 13:59:35
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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: |
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Created: 11/08/09 @ 14:08:41 | Last updated: 11/08/09 @ 14:15:58
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project.
Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th...
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Created: 11/08/09 @ 14:23:49
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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.
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Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Biological Data Integration Using Ondex and Taverna: A Tutorial
25/26th November 2009
The University of Manchester
The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.
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