Get similar phenotypes for a disease and a gene
Created: 2016-02-22 19:50:02
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Workflow Components
Authors (1)
Titles (1)
| Get similar phenotypes for a disease and a gene |
Descriptions (1)
| 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. |
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 |
Scriptflatten(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 |
Scriptflatten(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 |
Scriptflatten(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); |
Outputs (3)
| Name |
Description |
| label |
Phenotype name
|
| IC |
Information Content score
|
| phenotype_id |
Phenotype identifier
|
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 |
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licensed under:
Version 1
(of 1)
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How does one run the Json_Paths?