Tag Results

View Download Add New Item

WikiPathways workflows

Created: 2008-09-16 11:43:57 | Last updated: 2009-02-03 12:47:00

5 items in this pack

Comments: 0 | Viewed: 210 times | Downloaded: 49 times

Download pathways for external references ... (2)

• Download

Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2008-11-14

Credits: Thomaskelder

Attributions: CloneItemsInList

Write pathway to disk (2)

• Download

Downloads and writes a pathway from WikiPathways to a local disk in the given file type.

Created: 2008-11-14 | Last updated: 2008-11-14

Credits: Thomaskelder

Get pathways by external reference (3)

• Download

Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems.

Created: 2010-01-13

Credits: Thomaskelder

Download pathways for external references ... (2)

• Download

Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2009-02-03

Credits: Thomaskelder

List all Metabolites in WikiPathways (1)

• Download

Created: 2013-03-08 | Last updated: 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 Kegg identifiers used for metabol... (1)

• Download

Created: 2013-03-08

Credits: Egon Willighagen

List all human metabolites in Wikipathways (1)

• Download

Created: 2013-03-08

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

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

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

Use Case C, Worflow 1 (1)

• Download

Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  This workflow can be used to get approved drugs from a pathway of interest using the Open PHACTS APIRequirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts...

Created: 2014-05-26 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Use Case C, Worflow 2 (1)

• Download

Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes version 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- D...

Created: 2014-05-26 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Use Case C, Worflow 3 (1)

• Download

Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Use Case C, Worflow 4 (1)

• Download

Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

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

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