Find compounds pharmacology targets in Open PHACTS
Created: 2013-10-16 14:18:06
Last updated: 2015-11-19 11:44:45
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.
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 Errors, the best way to view only the results is to manually select "View results" for each output port - after the workflow run has finished. Note that some of the ports have XML outputs.
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Authors (1)
Titles (1)
Find compounds pharmacology targets in Open PHACTS |
Descriptions (1)
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.
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 Errors, the best way to view only the results is to manually select "View results" for each output port - after the workflow run has finished. Note that some of the ports have XML outputs. |
Dependencies (0)
Inputs (1)
Name |
Description |
query |
Freetext name of concept to match, e.g. "aspirin" or "water"
|
Processors (11)
Name |
Type |
Description |
Map_free_text_to_a_concept_URL |
rest |
|
app_id_value |
stringconstant |
Value161aeb7d |
app_key_value |
stringconstant |
Valuecffc292726627ffc50ece1dccd15aeaf |
concept_URL |
xpath |
Xpath Expression/result/primaryTopic/result/item/@href |
concept_labels |
xpath |
Xpath Expression/result/primaryTopic/result/item/prefLabel[1] |
matches |
xpath |
Xpath Expression/result/primaryTopic/result/item/exactMatch/item/url/@href |
target |
xpath |
Xpath Expression/result/items/item/hasAssay/hasTarget/@href |
target_info |
rest |
|
compound_pharmacology |
rest |
|
target_sequence |
xpath |
Xpath Expression/result/primaryTopic/exactMatch/item/sequence |
emailAddress_value |
stringconstant |
Valuestian@s11.no |
Outputs (8)
Name |
Description |
mapped_concept |
|
concept_URL |
|
concept_label |
|
matches |
|
pharmacology |
|
target |
|
target_info |
|
target_sequence |
|
Datalinks (22)
Source |
Sink |
app_id_value:value |
Map_free_text_to_a_concept_URL:app_id |
app_key_value:value |
Map_free_text_to_a_concept_URL:app_key |
query |
Map_free_text_to_a_concept_URL:query |
Map_free_text_to_a_concept_URL:responseBody |
concept_URL:xml_text |
Map_free_text_to_a_concept_URL:responseBody |
concept_labels:xml_text |
Map_free_text_to_a_concept_URL:responseBody |
matches:xml_text |
compound_pharmacology:responseBody |
target:xml_text |
app_id_value:value |
target_info:app_id |
app_key_value:value |
target_info:app_key |
target:nodelist |
target_info:target_uri |
concept_URL:nodelist |
compound_pharmacology:compound_uri |
app_id_value:value |
compound_pharmacology:app_id |
app_key_value:value |
compound_pharmacology:app_key |
target_info:responseBody |
target_sequence:xml_text |
Map_free_text_to_a_concept_URL:responseBody |
mapped_concept |
concept_URL:nodelist |
concept_URL |
concept_labels:nodelist |
concept_label |
matches:nodelist |
matches |
compound_pharmacology:responseBody |
pharmacology |
target:nodelist |
target |
target_info:responseBody |
target_info |
target_sequence:nodelist |
target_sequence |
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