Revamp installation instructions

Author: JDRomano2

README.md

@@ -19,24 +19,87 @@ AlzKB is designed and developed by the following authors (in alphabetical order)
 
 ## Installation
 
-(Note: Implementation not yet complete)
+To build a copy of AlzKB's graph database, you can either:
+
+- Download a dump of the Neo4j database and import it into Neo4j
+
+- Build the knowledge base from its original third-party sources and populate
+  an empty Neo4j graph database
+
+### Install from database dump (easy)
+
+- Before doing anything else, make sure you have an up-to-date version of Neo4j
+  installed on the new database server. This can be Neo4j Desktop or Neo4j
+  Server, depending on your intended use.
+
+- Visit the [Releases page](https://github.com/EpistasisLab/AlzKB/releases) and
+  find the version of AlzKB you want to install. Unless you have a particular
+  reason to do otherwise, this should probably be the most recent release.
+  Follow the link in the release notes to the corresponding database dump (it
+  will redirect to an external page).
+
+- Once you have downloaded the dump, extract the archive. 
+
+- If you haven't already done so, create an empty database in Neo4j.
+
+- Stop any running Neo4j database instances (you can only import the dump when
+  the destination database is shut down).
+
+- Use the `neo4j-admin` utility (included with Neo4j) to import the database
+  from the dump. You may need to add the program to your `PATH` variable or
+  similar; if using Neo4j Desktop you can open a terminal window from within the
+  application and use `cd bin` to access the directory where the `neo4j-admin`
+  program is located. **(If you are installing on Neo4j Server the following
+  command needs to be run by the appropriate user; this is often `neo4j`)**
+  Assuming that `neo4j-admin` is accessible in your current directory, an
+  example import command for UNIX-based operating systems could look like this
+  (substitute database name and dump location as needed):
+
+  `$ neo4j-admin load --verbose --force --database=neo4j --from=~/Downloads/alzkb.dump`
+
+- Start the Neo4j database and open it to verify everything looks good.
+
+### Build from scratch (less easy)
+
+Start by installing the Python package, which includes the necessary scripts:
 
-Install AlzKB:
 ```{bash}
+$ git clone https://github.com/EpistasisLab/AlzKB
+$ cd AlzKB
 $ pip install .
 ```
 
-Download public data sources:
+#### Download the third-party database sources
+
+First, install MySQL and make sure it is running, as some of the source
+databases are only available as MySQL dumps.
+
+We've created a script that will fetch all of the source files and put them into
+the expected directory structure. We will try to keep this script as updated as
+possible, but if you encounter any issues we suggest looking at the script and
+making sure it points to entities that still exist.
+
 ```{bash}
 $ alzkb bootstrap
 ```
 
-Build the RDF/XML knowledge base
+#### Populate the ontology
+
+We use the external `ista` library to populate the OWL ontology. This should
+be pretty much entirely automated:
+
 ```{bash}
 $ alzkb build
 ```
 
-Install knowledge base to an instance of Neo4j
+#### Load the ontology contents into Neo4j
+
+This script will import the OWL 2 ontology contents into an empty Neo4j database
+and clean up unnecessary artifacts left over by the OWL 2 standard:
+
 ```{bash}
 $ alzkb install
-```
+```
+
+After this, check the Neo4j database (which will now be turned on) and make sure
+everything looks alright.