Workflows

Q10:For a given compound, summarize all si... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Chemical Structure Search: Similarity with filters searchOptions.SimilarityType=0 and searchOptions.Threshold=0.80, followe by Com...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q9:For a given compound, give me the inter... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Compound Pharmacology with filter activity_type=IC50|EC50|AC50|Ki|Kd|Potency to answer scientific competency question Q9: For a gi...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q8:Identify all known protein-protein inte... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Class Pharmacology and filters target_type=ppi and minEx-pChembl=5 to answer scientific competency question Q8: Identify al...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q7: For a target, give me all active compo... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Pharmacology and filter minEx-pChembl=5 to answer scientific competency question Q7; For a target, give me all active compo...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q6:For a specific target family, retrieve ... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Class Pharmacology to answer scientific competency question Q6; For a specific target family, retrieve all compounds in spe...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q3: Given a target find me all actives aga... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Pharmacology with filter minEx-pChembl=5 followed by Compound Pharmacology with minEx-pChembl=0. to answer scientific compe...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q1: Give me all oxidoreductase inhibitors ... (2)

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A new version of the Open PHACTS drug discovery question 1 workflow (answers the question: Give me all oxidoreductase inhibitors active <100nM in human and mouse) with improvements contributed by Ellert van Koperen.  To run workflow the parameters for Human and Mouse in the OPS_Swagger node must be re-entered. They become corrupted upon on export to zip file.

Created: 2014-10-22 | Last updated: 2015-06-02

Credits: Christine Chichester Daniela Digles Open PHACTS

HPO-UMLS-ConceptID mapping (1)

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Generate HPO-Concept profiles via HPO-UMLS mappings. The result is a list of Concept IDs corresponding to Concept profiles for UMLS concepts that approximate HPO concepts. The output is a table of UMLS-ID, HPO- ID, COncept-ID rows.

Created: 2014-10-20

Credits: Marco Roos BioSemantics

Get HPO concept label and synonym (1)

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This workflow queries bioportal for label and synonyms of Human Phenotype Ontology concepts.Note: this workflow requires a BioPortal API key to work. It can be requested from bioportal.bioontology.org

Created: 2014-10-20 | Last updated: 2014-10-20

Credits: Rajireturn BioSemantics

Match concept to HPO profiles (1)

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This workflow matches a query concept to the list of Human Phenotypes. The Human Phenotypes are the subset of the Human Phenotype Ontology for which we have a mapped UMLS concept available and a concept profile. HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/5.pdf Concept Profile Database: July 2012

Created: 2014-10-20

Credits: Marco Roos BioSemantics

Attributions: Match concept profiles Get concept information