Get similar phenotypes for a disease and a gene

Created: 2016-02-22 19:50:02

This workflow retrieves the similar phenotypes between a disease and a gene based on the Monarch services at http://monarchinitiative.org/page/services. Phenotype similarity is calculated based on OwlSim, see http://owlsim.org.

Option 1:

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http://myexperiment.org/workflows/4796/download?version=1
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Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
disease_id	Input disease identifier.
gene_id	Input gene identifier.

Processors (8)

Name	Type	Description
common_phenotypes	rest	Monarch REST service for calculating similar phenotypes between a disease and a gene based on OwlSim.
JsonPath	jsonpath
JsonPath_2	jsonpath
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
JsonPath_3	jsonpath
Flatten_List_2	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
JsonPath_4	jsonpath
Flatten_List_2_2	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);

Beanshells (0)

Outputs (3)

Datalinks (12)

Source	Sink
disease_id	common_phenotypes:id1
gene_id	common_phenotypes:id2
common_phenotypes:responseBody	JsonPath:json_text
JsonPath:nodelistAsJSON	JsonPath_2:json_text
JsonPath_2:nodelist	Flatten_List:inputlist
JsonPath:nodelistAsJSON	JsonPath_3:json_text
JsonPath_3:nodelist	Flatten_List_2:inputlist
JsonPath:nodelistAsJSON	JsonPath_4:json_text
JsonPath_4:nodelist	Flatten_List_2_2:inputlist
Flatten_List:outputlist	label
Flatten_List_2:outputlist	IC
Flatten_List_2_2:outputlist	phenotype_id