Egon Willighagen's Workflows

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

Search OpenTox data sets by title. (1)

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 Use of an OpenTox ontology server to find data sets with a particular string in the title, such as 'EPA' as in this case.

Created: 2010-11-14 | Last updated: 2010-11-14

Credits: Egon Willighagen

Run OpenTox models on local data. (1)

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 Runs a remote OpenTox model to predict properties for local data which is uploaded on the fly.

Created: 2010-11-13 | Last updated: 2010-11-13

Credits: Egon Willighagen

Calculate molecular descriptors with OpenT... (1)

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 Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules.

Created: 2010-10-30 | Last updated: 2010-10-30

Credits: Egon Willighagen

Visualize the boiling point data from the ... (1)

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 Downloads the RDF data from a HTML page, extracts the boiling point data, calculates atom counts from SMILES representations, and opens the data in a matrix editor, ready to be visualized in a scatter plot.

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Egon Willighagen

Count the number of MetaPrint2D predicted ... (1)

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 MetaPrint2D (doi: 10.1186/1471-2105-11-362) is used to calculate the number of red, orange, and green markers that indicate how likely an atom in the drug is metabolized (read the paper for the fine prints). It counts them for each molecule and reports them, as a set of three molecular descriptors that could potentially correlate with how well the molecule is metabolized (hypothesis).

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Egon Willighagen

Create an OpenTox API dataset and add mole... (2)

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 Bioclipse script that creates a data set  at an OpenTox API capable server, and adds molecules to it.

Created: 2010-08-04 | Last updated: 2010-11-13

Credits: Egon Willighagen

Resolve an InChIKey on ChemSpider (1)

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 Resolves an InChIKey on ChemSpider and opens the search results in a molecules table.

Created: 2010-06-23 | Last updated: 2010-06-23

Credits: Egon Willighagen

Downloads all Bioclipse Scripting Language... (1)

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 Downloads all Bioclipse Scripting Language scripts uploaded to MyExperiment into the Bioclipse workspace, and opens them in JavaScript editors.

Created: 2010-06-23 | Last updated: 2010-06-23

Credits: Egon Willighagen

Download all data sets from a OpenTox API ... (3)

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 Uses the OpenTox API (REST+RDF) to query all data sets, downloads them as MDL SD file, and opens the results in the Bioclipse molecules table.

Created: 2010-04-01 | Last updated: 2010-11-13

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