https://github.com/sobakavosne/chemist

Chemist Graph DB
https://github.com/sobakavosne/chemist

docker hasbolt haskell neo4j

Last synced: 2 months ago
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Chemist Graph DB

• Host: GitHub
• URL: https://github.com/sobakavosne/chemist
• Owner: sobakavosne
• Created: 2024-07-23T20:41:58.000Z (5 months ago)
• Default Branch: master
• Last Pushed: 2024-09-27T02:14:50.000Z (3 months ago)
• Last Synced: 2024-09-30T07:20:11.395Z (3 months ago)
• Topics: docker, hasbolt, haskell, neo4j
• Language: Haskell
• Homepage: https://sobakavosne.github.io/chemist/
• Size: 1000 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.txt

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README

        
:Chemist Graph DB

   • Create .env file from examples/

     NEO4J_HOST=neo4j     -- launching project via Docker 

     NEO4J_HOST=localhost -- launching project locally

   • For Unix-like systems (Linux, macOS, BSD):

     > chmod +x run.sh

     > ./run.sh

   • Documentation:

     https://sobakavosne.github.io/chemist/

:Issues

   • If you encounter a "permissions" error while Docker is running:

     

     > sudo chown -R $USER:$USER neo4j_db/

     > sudo chmod -R 755 neo4j_db/

   • When changing Neo4j versions, remember to remove the "neo4j_db/plugins" directory to 

     avoid potential issues ("java.lang.UnsupportedClassVersionError: apoc/ApocSignatures 

     has been compiled by a more recent version of the Java Runtime" error)

:Notes

   ! Not all of the reactions are real

   • Reaction example with 3d-metal oxides as catalysts was referenced from an article 

     available on Springer: https://link.springer.com/article/10.1134/S096554412306018X

   • Any reaction has conditions (temperature and pressure) and should be supplied with 

     a catalyst or an empty catalyst node since the "conditions" element is a bond

   • The standard migration batch contains 20 reactions available by IDs [1..20]

   • Currently, only the 4th process is available and contains a mechanism

   • After running the Dockerized application, the Neo4j GUI is available at 

     http://localhost:7474/browser/

:Queries

   

   •  Ethene hydration mechanism is available by ID=4 (the only mechanism added). The full

      process can be queried using the following query:

      MATCH 

             (reaction:Reaction { id: 4 })<-[accelerate:ACCELERATE]-(catalyst:Catalyst),

             (reaction)-[product_from:PRODUCT_FROM]->(product:Molecule),

             (reaction)<-[reagent_in:REAGENT_IN]-(reagent:Molecule),

             (reaction)-[follow:FOLLOW]->(mechanism:Mechanism),

             (mechanism)-[has_stage:HAS_STAGE]->(stage:Stage),

             (stage)<-[include:INCLUDE]-(participant)

      

      RETURN 

             mechanism, reaction, accelerate, catalyst, product, reagent, product_from,

             reagent_in, follow, has_stage, stage, include, participant;

:Next

   • Mechanism should utilize the only relationship for ":Stage" (1st stage) to specify the starting 

     point with ":START_WITH" relationship

   

   • Products should be pointed out with ":Ion" or ":Molecule"