Merge pull request #4 from y1zhou/metacyc: MetaCyc to graph database

- Setup graph database in Neo4j with proper constraints.
- Parse MetaCyc SBML file and add `Compartment`, `Compound`, `GeneProduct`, `Reaction`, and `RDF` nodes.
- Parse MetaCyc `reactions.dat` file and add standard Gibbs free energy, standard reduction potential, reaction direction, reaction balance status, systematic name, comment attributes to `Reaction` nodes. Also link `Reaction` nodes to `Pathway` and `Citation` nodes.
- Parse MetaCyc `pathways.dat` file and:
  - Add synonyms, types, comments, common names to `Pathway` nodes.
  - Link `Pathway` nodes to super-pathway `Pathway` and taxonomy `Taxa` nodes.
  - Link `Reaction` nodes within the pathway with `isPrecedingEvent` relationships.
  - Link `Pathway` nodes with their rate limiting steps (`Reaction` nodes).
  - Link `Pathway` nodes with primary reactant and product `Compound` nodes.
  - For `Reaction` nodes, add `isPrimary[Reactant|Product]InPathway` labels in their links to `Compound` nodes.
- Parse MetaCyc `compounds.dat` file and add standard Gibbs free energy, logP, molecular weight, monoisotopic molecular weight, polar surface area, pKa {1,2,3}, comment, and synonyms to `Compound` nodes. Also add SMILES and INCHI strings to related `RDF` nodes, and links the `Compound` nodes to `Citation` nodes.
- Parse MetaCyc `pubs.dat` file and add DOI, PUBMED, MEDLINE IDs, title, source, year, URL, and `REFERENT-FRAME` to `Citation` nodes.
- Parse MetaCyc `classes.dat` file and:
  - Add common name and synonyms to `Compartment` nodes.
  - Add common name, strain name, comment, and synonyms to `Taxa` nodes.

README.rst

@@ -1,9 +1,8 @@
 Metabolic reprogramming Knowledgebase
 ========================
 
-A Python package that aggregates the data from BRENDA_, BioCyc_ and Reactome_ into one unified `graph database`_.
+A Python package that aggregates the data from BRENDA_ and BioCyc_ into one unified `graph database`_.
 
 .. _BRENDA: https://brenda-enzymes.org/
 .. _BioCyc: https://biocyc.org/
-.. _Reactome: https://reactome.org/
 .. _graph database: https://neo4j.com/

docs/index.rst

@@ -6,6 +6,13 @@
 Welcome to metabolike's documentation!
 ======================================
 
+The MetaCyc (BioCyc) database is imported to a graph database using the provided SBML file.
+
+.. image:: _static/metacyc_schema.svg
+    :alt: Schema of the MetaCyc database
+    :align: center
+
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:

docs/source/metabolike.parser.rst

@@ -20,6 +20,14 @@ metabolike.parser.brenda\_transformer module
    :undoc-members:
    :show-inheritance:
 
+metabolike.parser.metacyc module
+--------------------------------
+
+.. automodule:: metabolike.parser.metacyc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 

metabolike/db.py

@@ -1,4 +1,4 @@
-from neo4j import GraphDatabase, Neo4jDriver, Transaction
+from neo4j import GraphDatabase, Neo4jDriver, Session, Transaction
 from neo4j.work.result import Result