karafecho
commented
5 years ago ROBOKOP queries can be pre-computed for this workflow using all available ICEES phenotypes/diagnoses. Example ICEES queries are included below as an FYI:
curl -k -XPOST https://localhost:8080/1.0.0/patient/2010/cohort/COHORT:22/associations_to_all_features -H "Content-Type: application/json" -d '{"feature":{"TotalEDInpatientVisits":{"operator":"<", "value":2}},"maximum_p_value":0.1}' -H "Accept: application/json"
curl -k -XPOST https://localhost:8080/1.0.0/patient/2010/cohort/COHORT:22/associations_to_all_features -H "Content-Type: application/json" -d '{"feature":{"ur":{"operator":"=", "value":"U"}},"maximum_p_value":0.1}' -H "Accept: application/json"
curl -k -XPOST https://localhost:8080/1.0.0/patient/2010/cohort/COHORT:22/associations_to_all_features -H "Content-Type: application/json" -d '{"feature":{"Sex2":{"operator":"=", "value":"Male"}},"maximum_p_value":0.1}' -H "Accept: application/json"
WORKFLOW INPUT:
See ICEES_FeatureVariables and ICEES_Identifiers here for diagnoses. Note that these docs are updated as new variables are added to the ICEES integrated feature tables.
WORKFLOW QUESTION TEMPLATE:
Note that the second gene hop was added per ROBOKOP Neo4J constraints. If we can avoid this, great; if not, that's fine, too.
{ "name": "Gamma WF4 template", "natural_question": "disease or phenotypic feature to gene to biological process/activity to gene to drug", "notes": "", "machine_question": { "nodes": [ { "id": "n0", "curie": "MONDO:0008300", "name": "ObesityDx", "type": "disease or phenotypic feature" }, { "id": "n1", "type": "gene" }, { "id": "n2", "type": "biological_process_or_activity" }, { "id": "n3", "type": "gene" }, { "id": "n4", "type": "drug" } ], "edges": [ { "id": "e0", "source_id": "n0", "target_id": "n1" }, { "id": "e1", "source_id": "n1", "target_id": "n2" }, { "id": "e2", "source_id": "n2", "target_id": "n3" } ] } }