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Showing 32 results. Use the filters on the left and the search box below to refine the results.
Tag: bioclipse User: Egon Willighagen

Workflow 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: User Egon Willighagen

Workflow 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: User Egon Willighagen

Attributions: Workflow Finding nodes in Anopheles gambiae pathways with IUPAC names

Workflow 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: User Egon Willighagen

Attributions: Workflow Extracts metabolites from GPML pathway files downloaded from WikiPathways

Workflow 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: User Egon Willighagen

Workflow 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: User Egon Willighagen

Workflow 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: User Egon Willighagen

Workflow 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: User Egon Willighagen

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

 BSL Groovy script that uses BridgeDB to convert a Entrez Gene identifier into a Gene ontology identifier.

Created: 2012-01-07

Credits: User Egon Willighagen

Workflow 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: User Egon Willighagen

Workflow 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: User Egon Willighagen

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