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Items tagged with "enzyme" (8)

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Files (2)

Uploader

Paul Fisher

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Ondex Workflows

Created: 2011-09-01 17:17:57 | Last updated: 2011-09-01 17:18:05

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains a large number of Taverna 2 workflows that utilise the Ondex Web Service, for manipulating Ondex graphs.

File type: ZIP archive

Comments: 0 | Viewed: 62 times | Downloaded: 0 times

Tags:

annotation
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compound
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enzyme
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gene identifier
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general data store
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graph
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ismb
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ondex
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ovtk
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oxl
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parser
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pubmed
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text
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text mining; term extraction; entity recognition

Uploader

Pablo Carbonell

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Pathway example for Selenzyme

Created: 2017-08-18 08:35:57 | Last updated: 2017-08-23 11:13:20

Credits: Pablo Carbonell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example of an input file containing information about a metabolic pathway to query the KNIME workflow for Selenzyme, an enzyme selection tool for pathway design.The file contains a list of reactions or generic reactions expressed in SMILES or SMARTS (SMIRKS) format. In the example, the list of reactions correspond to the different steps of a biosynthetic pathway.

File type: text/csv

Comments: 0 | Viewed: 36 times | Downloaded: 12 times

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Packs (1)

Creator

Pablo Carbonell

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Selenzyme

Created: 2017-08-18 08:23:47 | Last updated: 2017-08-23 11:12:00

Enzyme selection workflow for pathway design

2 items in this pack

Comments: 0 | Viewed: 40 times | Downloaded: 19 times

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Workflows (5)

Taverna 1

Uploader

Franck Tanoh

get_enzymes_by_compound (1)

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Retrieve all enzymes which have a link to a given compound id Input example: cpd:C00345

Created: 2008-10-08

Credits: Franck Tanoh

Taverna 1

Uploader

Franck Tanoh

get_enzymes_by_gene (1)

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Retrieve all the EC numbers which are assigned to a given gene Input example: eco:b0002

Created: 2008-10-08

Credits: Franck Tanoh

KNIME

Uploader

Pablo Carbonell

Workflow for Selenzyme v 1.0 (2)

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No description

Created: 2017-08-18 | Last updated: 2017-09-08

Credits: Pablo Carbonell

KNIME

Uploader

Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

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KNIME Workflow for RetroRules and SelenzymeThis worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction and selecting enzyme sequences using the Selenzyme tool.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Each reaction rule queries Selenzyem and outputs the selected Uniprot sequences for each rule.4. Resulting list of selected...

Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell

KNIME

Uploader

Pablo Carbonell

KNIME Workflow for RetroRules and Retropat... (3)

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KNIME Workflow for RetroRules and RetroPath2.0This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Resulting list of rulesenzymes is stored in a csv file in RetroPath2.0 format.Installation notesThe workflow runs a Python scrpt that requires pandas: Python Data A...

Created: 2018-07-26 | Last updated: 2018-08-11

Credits: Pablo Carbonell

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Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/146

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