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Bioclipse script to Split SDfile

Created: 2010-04-09 14:52:02

Credits: De maas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: JavaScript

Comments: 0 | Viewed: 34 times | Downloaded: 25 times

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filter a sdfile by a list of ids

Created: 2010-10-05 11:17:35 | Last updated: 2010-10-05 11:18:37

Credits: De maas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: JavaScript

Comments: 0 | Viewed: 33 times | Downloaded: 22 times

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filter a sdfile by a list of ids, keep in memory

Created: 2010-10-05 14:40:24 | Last updated: 2010-10-05 14:40:26

Credits: De maas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: JavaScript

Comments: 0 | Viewed: 29 times | Downloaded: 21 times

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Bioclipse

Unique name: bioclipse
Created: Monday 13 September 2010 10:29:24 (UTC)

5 shared items   |   0 announcements

/me is having Bioclipse/XMPP/RDF fun.js (1)

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Created: 2009-08-21

Credits: Egon Willighagen

Lists all Taverna 2 workflows (1)

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Uses Bioclipse and the MyExperiment SPARQL end point.

Created: 2009-08-21 | Last updated: 2009-08-22

Credits: Egon Willighagen

Extract RDF from HTML+RDFa (2)

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Small script for Bioclipse that extracts RDF from HTML+RDFa webpages.

Created: 2009-09-30 | Last updated: 2010-06-23

Credits: Egon Willighagen

Visualize Molecules from DBPedia as Molecu... (3)

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Downloads entries from DBPedia which have a SMILES and creates a molecule table with 2D structures of the hits found with SPARQL.

Created: 2010-03-14

Credits: Egon Willighagen

Open PDB entries in Jmol for hits found fo... (3)

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Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol.

Created: 2010-03-14 | Last updated: 2010-06-23

Credits: Egon Willighagen

Download CAS numbers and save as SD file (1)

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Download molecules from a REST services using the CAS registry number, create 3D coordinates and save the results as a MDL SD file.

Created: 2009-10-15

Credits: Egon Willighagen

Kabsch Alignment of Small Molecules (1)

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Created: 2009-10-30

Credits: Egon Willighagen

Convert a SMILES string into a connection ... (1)

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Created: 2009-12-16

Credits:

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

Credits:

Calculate molecular mass for entries in a ... (1)

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Created: 2010-03-08

Credits:

NMR Spectrum similarity search witn SWI-Pr... (1)

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With the SWI-Prolog (currently in experimental stage, and available from GitHub) plugin Prolog programs can be accessed inside Bioclipse’s scripting environment for querying and other processing of RDF triples. The prolog code in this Bioclipse script performs a simple spectrum similarity search based on a list of peak shift values, for which it tries to find spectra that contain peaks values close to those values, within a certian limit (<0.3 ppm in this case). The data which is u...

Created: 2010-03-13 | Last updated: 2010-03-19

Credits: Samuel Lampa

Download QSAR data sets using the OpenTox ... (1)

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Created: 2010-03-22

Credits: Egon Willighagen

List all algorithms and descriptors an Ope... (2)

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 Uses the OpenTox API 1.1 to discover all the available algorithms and descriptors for a given service.

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

Credits: Egon Willighagen

NMR Shift Dereplication benchmark in Jena ... (1)

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Created: 2010-05-14 | Last updated: 2010-05-14

Credits: Samuel Lampa

NMR Shift Dereplication benchmark in Jena ... (1)

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Created: 2010-05-14 | Last updated: 2010-05-14

Credits: Samuel Lampa

NMR Shift Dereplication benchmark in Pelle... (1)

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Created: 2010-05-14 | Last updated: 2010-05-14

Credits: Samuel Lampa

NMR Shift Dereplication benchmark in SWI-P... (1)

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Created: 2010-05-14 | Last updated: 2010-05-14

Credits: Samuel Lampa

NMR Shift Dereplication benchmark in SWI-P... (1)

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Created: 2010-05-14 | Last updated: 2010-05-14

Credits: Samuel Lampa

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

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

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

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

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

Performing a double sided T-test on Brunn ... (1)

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Created: 2010-09-13 | Last updated: 2010-09-13

Credits: jonalv

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

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

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

Create a molecules table from a list of IU... (1)

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 Scripts that uses OPSIN to convert IUPAC names into chemical structures, which are saved as SD file and openend in the Bioclipse molecules table.

Created: 2011-05-25 | Last updated: 2011-05-25

Credits: Egon Willighagen

Authenticate with the OpenTox network (1)

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 Bioclipse script commands log authenticate with the OpenTox network.

Created: 2011-05-25 | Last updated: 2011-05-25

Credits: Egon Willighagen

Download the ONS solubility data from Goog... (1)

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 Use the Bioclipse scripting langauge to authenticate with Google Docs, and download the Open Notebook Science solubility data into a local data structure.

Created: 2011-06-06 | Last updated: 2011-06-06

Credits: Egon Willighagen

Map a Entrez Gene ID to a Gene Ontology ID (1)

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Created: 2012-01-07

Credits: Egon Willighagen

Find isotopes with a certain exact match (1)

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This script lists all isotopes matching a certain exact mass (given a certain error) and outputs the symbol, atomic number, and exact match of the search hits.

Created: 2013-07-30 | Last updated: 2013-07-31

Credits: Egon Willighagen

Extracts metabolites from a GPML pathway d... (1)

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This Groovy scripts starts with a WikiPathways identifier, downloads the GPML, and uses the Groovy XmlParser to extract metabolites for which it reports the label, and if available, database and identifier.

Created: 2013-08-11 | Last updated: 2013-08-11

Credits: Egon Willighagen

Extracts metabolites from GPML pathway fil... (1)

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Extracts metabolites from a collection of GPML pathway files downloaded from WikiPathways, and opens structures with IUPAC names in a molecules table, using the CDK and OPSIN.

Created: 2013-08-16

Credits: Egon Willighagen

Find Labels in WikiPathways that are IUPAC... (1)

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This scripts parses a directory with WikiPathways GPML files. For each "label" it checks if the label contains an IUPAC name (using OPSIN), calculated the InChIKey (using JNI-InChI/CDK), and looks up a ChemSpider identifiers (using the ChemSpider web service).

Created: 2013-08-20

Credits: Egon Willighagen

Finding nodes in Anopheles gambiae pathway... (1)

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Groovy script to find Anopheles g. metabolites encoded as GPML <Label> with OPSIN and provide ChemSpider identifiers.

Created: 2014-08-24

Credits: Egon Willighagen

Attributions: Extracts metabolites from GPML pathway files downloaded from WikiPathways

Finding nodes in Homo sapiens pathways wit... (1)

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Groovy script to find Homo sapiens metabolites encoded as GPML <Label> with OPSIN and provide ChemSpider identifiers. The results are stored in a report file.

Created: 2014-09-01

Credits: Egon Willighagen

Attributions: Finding nodes in Anopheles gambiae pathways with IUPAC names

Example SPARQL on Wikidata using the Linke... (1)

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This Bioclipse script (in Groovy) uses the Linked Data Fragments (ldf) manager that uses the LDF Java client library to run a SPARQL query on the LDF server wrapping Wikidata.

Created: 2015-01-23 | Last updated: 2015-01-23

Credits: Egon Willighagen

Find concept-literature relationships and ... (1)

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This Bioclipse script (dev version) searches articles titles for the given concept and creates QuickStatements to create Wikidata statements that that article is about that concept.

Created: 2018-09-01

Credits: Egon Willighagen