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Pathway Cosine Scores from Day7 and Tir1 QTL

Created: 2009-08-10 15:55:24

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Gene Cosine Scores

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

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Phenotype Abstracts for Trypanosomiasis Resistance

Created: 2009-08-11 12:45:24

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Phenotype Concept Profile - Terms

Created: 2009-08-11 13:05:07 | Last updated: 2009-08-11 13:06:51

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Phenotype Term Counts (in Phenotype Corpus)

Created: 2009-08-11 13:34:42 | Last updated: 2009-08-11 13:58:28

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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PubMed Abstract Number

Created: 2009-08-11 13:54:45

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 14:15:58

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Pathway Term Enrichment Scores

Created: 2009-08-11 14:23:49

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Bilateral Perisylvian Polymicrogyria (Epilepsy)

Created: 2010-12-07 16:34:31 | Last updated: 2010-12-07 16:34:37

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-zip-compressed

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Bilateral Perisylvian Polymicrogyria

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

Credits: Paul Fisher

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Ondex Workflows

Created: 2011-09-01 17:17:57 | Last updated: 2011-09-01 17:18:05

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Open Data: Bilateral Perisylvian Polymicrogyria

Created: 2010-11-16 16:20:43 | Last updated: 2011-09-23 10:55:08

7 items in this pack

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Text Mining Workflows

Created: 2010-12-08 11:55:03 | Last updated: 2011-02-01 11:33:11

5 items in this pack

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Trichuriasis induced Colitis

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

5 items in this pack

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EBI_Whatizit (1)

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Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf). Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.

Created: 2008-07-09

Credits: Hamish McWilliam

Cosine vector space (1)

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.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

Extract Scientific Terms (1)

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.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

Rank Phenotype Terms (1)

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 ...

Created: 2009-08-10

Credits: Paul Fisher

Phenotype to pubmed (3)

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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

Created: 2010-07-05 | Last updated: 2011-01-11

Credits: Paul Fisher

Connect to twitter and analyze the key words (1)

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Hi All, This workflow connects RapidMiner to Twitter and downloads the timeline. It then creates a wordlist from the tweets and breaks them into key words that are mentioned in the tweets. You can then visualize the key words mentioned in the tweets. This workflow can be further modified to review various key events that have been talked about in the twitterland. Do let me know your feedback and feel free to ask me any questions that you may have. Shaily web: http://advanced-analyti...

Created: 2010-07-26 | Last updated: 2010-07-26

Cosine vector space (2)

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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

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Cosine vector space

Rank Phenotype Terms (2)

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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 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 ...

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Rank Phenotype Terms

Pathway to Pubmed (2)

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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.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Extract Scientific Terms (2)

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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.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Rank Phenotype Terms (1)

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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 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 ...

Created: 2011-02-01 | Last updated: 2011-02-01

Credits: Paul Fisher

Attributions: Cosine vector space Rank Phenotype Terms

Gene to Pubmed (4)

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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.

Created: 2011-02-08 | Last updated: 2011-02-10

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

Pathway and Gene to Pubmed (2)

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This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The 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 PubMe...

Created: 2011-02-10 | Last updated: 2011-02-18

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 Gene to Pubmed