pharma_drugs_targets

= Pharmaceutical Drugs and their Targets
Josh Kunken <joshkunken@gmail.com>
v1.0, 14-Dec-2013
:neo4j-version: 2.0.0-RC1
:author: Josh Kunken
:twitter: joshkunken
 
== Domain
 
A pharmaceutical portfolio is a collection of drug compounds, their respective indications, and their targets.
 
A pharmaceutical company or drugstore organizes its pharmaceutical products into one or more portfolios. A drug portfolio thus contains multiple pharmaceuticals, with each pharmaceutical containing a link to one or more of its targets in the human body. This lends itself to be modeled as a graph. Each pharmaceutical and drug target can also have a distinct set of attributes which also fit nicely into the property graph model. Within the examples found in this use case, most drug targets happen to be G-protein coupled receptors (GPCRs), for which structures have only recently been solved in the last several years.
 
A drug can have one or more targets. A target can be targetted by one or more drugs. This is not a complete solution for all the drug portfolio use cases but provides a good starting point. 
  
image::http://www.sohosci.com/drug_portfolio.PNG[Domain Model]
 
 
== Setup
 
The sample data set uses a pharmaceutical portfolio.
 
//hide
//setup
//output
[source,cypher]
----
CREATE (drugPortfolio:Portfolio{ name:'Pharmaceutical Portfolio' })
 
CREATE (drugs:Category { name:'Drugs' }) 
CREATE drugs-[:PARENT]->drugPortfolio 

CREATE (antipsychotic_agents:Category { name:'Antipsychotic Agents' }) 
CREATE antipsychotic_agents-[:PARENT]->drugs
CREATE (antiparkinson_agents:Category { name:'Antiparkinson Agents' }) 
CREATE antiparkinson_agents-[:PARENT]->drugs
CREATE (antimigraine_agents:Category { name:'Antimigraine Agents' }) 
CREATE antimigraine_agents-[:PARENT]->drugs
CREATE (antidepressive_agents:Category { name:'Antidepressive Agents' }) 
CREATE antidepressive_agents-[:PARENT]->drugs
CREATE (antiallergic_agents:Category { name:'Antiallergic Agents' }) 
CREATE antiallergic_agents-[:PARENT]->drugs
CREATE (cns_stimulants:Category { name:'CNS Stimulants' }) 
CREATE cns_stimulants-[:PARENT]->drugs
CREATE (bronchodilator_agents:Category { name:'Bronchodilator Agents' }) 
CREATE bronchodilator_agents-[:PARENT]->drugs
CREATE (vasodilator:Category { name:'Vasodilator' }) 
CREATE vasodilator-[:PARENT]->drugs

CREATE (HUMAN_5HT1A:DrugTarget{ name:'5HT1A_HUMAN' })
CREATE (HUMAN_5HT1B:DrugTarget{ name:'5HT1B_HUMAN' })
CREATE (HUMAN_5HT2A:DrugTarget{ name:'5HT2A_HUMAN' })
CREATE (HUMAN_AA1R:DrugTarget{ name:'AA1R_HUMAN' })
CREATE (HUMAN_AA2AR:DrugTarget{ name:'AA2AR_HUMAN' })
CREATE (HUMAN_AA2BR:DrugTarget{ name:'AA2BR_HUMAN' })

CREATE (clozapine:Product { name:'Clozapine' })
CREATE clozapine-[:OF_TYPE]->antipsychotic_agents
CREATE clozapine-[:Targets]->HUMAN_5HT1A

CREATE (aripiprazole:Product { name:'Aripiprazole' })
CREATE aripiprazole-[:OF_TYPE]->antipsychotic_agents
CREATE aripiprazole-[:Targets]->HUMAN_5HT1A 
 
CREATE (lisuride:Product { name:'Lisuride' })
CREATE lisuride-[:OF_TYPE]->antiparkinson_agents
CREATE lisuride-[:Targets]->HUMAN_5HT1A 

CREATE (methysergide:Product { name:'Methysergide' })
CREATE methysergide-[:OF_TYPE]->antimigraine_agents
CREATE methysergide-[:Targets]->HUMAN_5HT1A 

CREATE (almotriptan:Product { name:'Almotriptan' })
CREATE almotriptan-[:OF_TYPE]->antimigraine_agents
CREATE almotriptan-[:Targets]->HUMAN_5HT1B 

CREATE (eletriptan:Product { name:'Eletriptan' })
CREATE eletriptan-[:OF_TYPE]->antimigraine_agents
CREATE eletriptan-[:Targets]->HUMAN_5HT1B 

CREATE (ergotamine:Product { name:'Ergotamine' })
CREATE ergotamine-[:OF_TYPE]->antimigraine_agents
CREATE ergotamine-[:Targets]->HUMAN_5HT1B 

CREATE (frovatriptan:Product { name:'Frovatriptan' })
CREATE frovatriptan-[:OF_TYPE]->antimigraine_agents
CREATE frovatriptan-[:Targets]->HUMAN_5HT1B 

CREATE (naratriptan:Product { name:'Naratriptan' })
CREATE naratriptan-[:OF_TYPE]->antimigraine_agents
CREATE naratriptan-[:Targets]->HUMAN_5HT1B 

CREATE (chlorprothixene:Product { name:'Chlorprothixene' })
CREATE chlorprothixene-[:OF_TYPE]->antipsychotic_agents
CREATE chlorprothixene-[:Targets]->HUMAN_5HT2A 

CREATE clozapine-[:OF_TYPE]->antipsychotic_agents
CREATE clozapine-[:Targets]->HUMAN_5HT2A

CREATE (cyclobenzaprine:Product { name:'Cyclobenzaprine' })
CREATE cyclobenzaprine-[:OF_TYPE]->antidepressive_agents
CREATE cyclobenzaprine-[:Targets]->HUMAN_5HT2A 

CREATE (cyproheptadine:Product { name:'Cyclobenzaprine' })
CREATE cyproheptadine-[:OF_TYPE]->antiallergic_agents
CREATE cyproheptadine-[:Targets]->HUMAN_5HT2A 

CREATE (caffeine:Product { name:'Caffeine' })
CREATE caffeine-[:OF_TYPE]->cns_stimulants
CREATE caffeine-[:Targets]->HUMAN_AA1R 
CREATE caffeine-[:Targets]->HUMAN_AA2AR 

CREATE (theophylline:Product { name:'Theophylline' })
CREATE theophylline-[:OF_TYPE]->bronchodilator_agents
CREATE theophylline-[:Targets]->HUMAN_AA1R 
CREATE theophylline-[:Targets]->HUMAN_AA2AR 
CREATE theophylline-[:Targets]->HUMAN_AA2BR

CREATE (regadenoson:Product { name:'Regadenoson' })
CREATE regadenoson-[:OF_TYPE]->vasodilator
CREATE regadenoson-[:Targets]->HUMAN_AA2AR 
----
 
=== Try other queries yourself!
//console
 
== Use Cases
 
== All portfolios
[source,cypher]
----
MATCH (c:Portfolio) RETURN c.name AS Portfolios
----
 
//table
 
== All categories by Depth
[source,cypher]
----
MATCH p=(cats:Category)-[:PARENT|PARENT*]->(cat:Portfolio) 
WHERE cat.name='Pharmaceutical Portfolio' 
RETURN LENGTH(p) AS Depth, COLLECT(cats.name) AS Categories 
ORDER BY Depth ASC
----
 
//table
 
== All categories of a given level
[source,cypher]
----
MATCH p=(cats:Category)-[:PARENT*]->(cat:Portfolio) 
WHERE cat.name='Pharmaceutical Portfolio' AND length(p)=1
RETURN cats.name AS CategoriesOfGivenLevel 
ORDER BY CategoriesOfGivenLevel
----
 
//table
 
== All sub-categories of a given category
[source,cypher]
----
MATCH p=(cats:Category)-[:PARENT]->(parentCat:Category), (parentCat)-[:PARENT*]->(c:Portfolio) 
WHERE parentCat.name='Drugs' AND c.name='Pharmaceutical Portfolio' 
RETURN collect(cats.name) AS SubCategories
----
 
//table
 
== All Parent and their child categories
[source,cypher]
----
MATCH p=(child:Category)-[:PARENT*]->(parent) 
RETURN parent.name, collect(child.name)
----
 
//table
 
== All parent and their IMMEDIATE children
[source,cypher]
----
MATCH p=(child:Category)-[:PARENT]->(parent) 
RETURN labels(parent), parent.name, collect(child.name)
----
 
//table