Update README.md

README.md

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 # i2o-transform
-### PCORnet Ontology to OMOP - under construction!
-
+### PCORnet Ontology to OMOP 
 An experimental fork of the i2b2-to-PCORNET transform that targets OMOP, for the [Precision Medicine Initiative](https://www.nih.gov/research-training/allofus-research-program).
 
-[See OMOP documentation and DDL here.](https://github.com/OHDSI/CommonDataModel)
+Written by Jeffrey Klann, PhD; Matthew Joss; Kevin Embree; Aaron Abend; Arturo Torres
+
+### To set this up:
+1. Create a database for your OMOP tables and perform the next two major numbered steps on that database.
+2. Download the [OMOP DDL](https://github.com/OHDSI/CommonDataModel) to create the OMOP tables.
+3. Download and run the MSSQL version of the transform. (Oracle version not currently available.)
+    1. Create a database for your OMOP tables. Our transform requires that they be on the same server as your i2b2 instance - though you can move them later.
+    2. Make sure the database user that will be running the scripts can also read from your i2b2 data and ontology databases. 
+    3. From your new OMOP database, open the OMOPLoader.sql script.  Edit the preamble to match your local setup, according to the instructions in the file. This now includes the following:
+        * synonym names 
+        * the USE line 
+        * Change 'LOINC:' in the lab results procedure to whatever term your local site uses. 
+    4. This script will delete your existing OMOP tables. If you do not want this behavior, please back them up.
+    5. Run the script.
+
+4. From your i2b2 database: Download, install, and map your i2b2 data to v3.1 or later of the [SCILHS Ontology](https://github.com/SCILHS/scilhs-ontology/blob/master/Documentation/INSTALL.md)
+
+### Each time you want to transform your data:
+1. From your OMOP database, execute the run script in the MSSQL directory of our GitHub to transform your data.