User: Egon Willighagen

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

• Download

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

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

• Download

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

Groovy script to convert (part of) CGN dat... (1)

• Download

Created: 2015-01-22

Credits: Egon Willighagen

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

• Download

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

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

• Download

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

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

• Download

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

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

• Download

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

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

• Download

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

Find isotopes with a certain exact match (1)

• Download

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

List all human metabolites in Wikipathways (1)

• Download

Created: 2013-03-08

Credits: Egon Willighagen

List all Kegg identifiers used for metabol... (1)

• Download

Created: 2013-03-08

Credits: Egon Willighagen

List all sources from which metabolite ide... (1)

• Download

 List all sources from which metabolite identifiers are used, sorted by use.

Created: 2013-03-08

Credits: Egon Willighagen

List all Metabolites in WikiPathways (1)

• Download

Created: 2013-03-08 | Last updated: 2013-03-08

Credits: Egon Willighagen

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

• Download

Created: 2012-01-07

Credits: Egon Willighagen

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

• Download

 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

Authenticate with the OpenTox network (1)

• Download

 Bioclipse script commands log authenticate with the OpenTox network.

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

Credits: Egon Willighagen

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

• Download

 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

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

• Download

 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)

• Download

 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)

• Download

 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)

• Download

 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)

• Download

 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)

• Download

 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)

• Download

 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)

• Download

 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)

• Download

 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

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

• Download

 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

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

• Download

 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:

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

• Download

Created: 2010-03-22

Credits: Egon Willighagen

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

• Download

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

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

• Download

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

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

• Download

Created: 2010-03-08

Credits:

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

• Download

Created: 2009-12-16

Credits:

Query DBPedia for all entries with an InChI (1)

• Download

Created: 2009-11-20

Credits: Egon Willighagen

Kabsch Alignment of Small Molecules (1)

• Download

Created: 2009-10-30

Credits: Egon Willighagen

Determine the Maximum Common SubStructure ... (1)

• Download

Created: 2009-10-23

Credits: Egon Willighagen

Download CAS numbers and save as SD file (1)

• Download

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

Extract RDF from HTML+RDFa (2)

• Download

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

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

Credits: Egon Willighagen

Lists all Taverna 2 workflows (1)

• Download

Uses Bioclipse and the MyExperiment SPARQL end point.

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

Credits: Egon Willighagen

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

• Download

Created: 2009-08-21

Credits: Egon Willighagen

Run XMPP cloud services. (2)

• Download

Basic workflow indicating how a XMPP service can be called with XML input and output. Source code for the activity is available from: github.com/egonw/xws-taverna/tree/master That page explains you how to install the plugin you must install on top of Taverna 2.0. The workflow will not work otherwise.

Created: 2009-04-25 | Last updated: 2010-03-22

Credits: Egon Willighagen

Download from ChemSpider using Accurate Mass (2)

• Download

No description

Created: 2007-11-26 | Last updated: 2008-02-05

Credits: Egon Willighagen