Workflows

Clustering of Molecular Compounds with Bio... (4)

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This workflow downloads an input set of molecular compounds in SMILES format, using Chemspider service. The most frequent molecular fragments are extracted by means of MoSS tool (see http://www.borgelt.net/moss.html) , in order to obtain a set of features for each compound. Then a clustering and a visual exploration of the input dataset is performed by BioDICE service (see http://biolab.pa.icar.cnr.it/biodice.html), implementing Fast Learning Self-Organized Map (FLSOM) algorithm. Finally the ...

Created: 2013-05-29 | Last updated: 2014-01-09

Credits: Antonino Fiannaca Massimo La Rosa

Attributions: Get compound information Simple search

Scoring small molecules for metabolite lik... (2)

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: Kalai

KEGG:Get PW for met (1)

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The purpose of the workflow is to retrieve all the pathways that the input metabolite(s) participates in.

Created: 2016-06-21

Credits: Kristina Hettne Harish Dharuri

Attributions: KEGG:Pathway Scheme

chebi2keggID (1)

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This workflow converts a (list of) chebi identifiers to kegg compound identifiers.

Created: 2016-06-21

Credits: Kristina Hettne

Get targets for compound (1)

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This workflow retrieves single protein targets for a compound from open PHACTS.

Created: 2016-02-22

Credits: Kristina Hettne Eelke van der Horst Aylin Metzner

Get ontology parents (2)

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Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Created: 2015-11-16 | Last updated: 2016-04-26

Credits: Kristina Hettne

Attributions: Get ontology parents

Metabolite pathway search (1)

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The workflow searches for metabolomic pathways that match the entered keywords and returns information about the chosen pathway

Created: 2014-12-18

Credits: Alan Williams

Find compounds pharmacology targets in Ope... (2)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTS API https://dev.openphacts.org/docs/1.5. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors. Until there is a Local worker to filter out...

Created: 2013-10-16 | Last updated: 2015-11-19

Credits: Stian Soiland-Reyes

Attributions: Find compounds pharmacology and align against target sequences

Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree

Download Structures from PubChem given che... (1)

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem