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Extract chemical structures from a Beilste... (1)

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 Uses the Oscar4 text mining tool to extract chemical structures from a Beilstein Journal of Organic Chemistry paper and visualizes them in the molecules table. Jericho is used to extract text from the paper's HTML page.

Created: 2011-05-12 | Last updated: 2011-05-12

Credits: Egon Willighagen

Content based recommender system template (1)

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As an input, this workflow takes two distinct example sets: a complete set of items with IDs and appropriate textual attributes (item example set) and a set of IDs of items our user had interaction with (user example set). Also, a macro %{recommendation_no} is defined in the process context, as a required number of outputted recommendations. The first steps of the workflow are to preprocess those example sets; select only textual attributes of item example set, and set ID roles on both of th...

Created: 2011-05-05 | Last updated: 2011-05-09

Credits: Matko Bošnjak Ninoaf

Attributions: Datasets for the pack: RCOMM2011 recommender systems workflow templates

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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

Comments: 0 | Viewed: 75 times | Downloaded: 38 times

Content based recommender (1)

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This process is a special case of the item to item similarity matrix based recommender where the item to item similarity is calculated as cosine similarity over TF-IDF word vectors obtained from the textual analysis over all the available textual data. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations. The process internally uses an example set of...

Created: 2011-03-15 | Last updated: 2011-03-15

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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

Comments: 0 | Viewed: 82 times | Downloaded: 38 times

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

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

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