added usage example to readme

README.md

@@ -144,7 +144,7 @@ Here's a well-structured **README.md** example with the series of steps you prov
 
 Follow these steps to initialize and manage a phenotype using `acmc`. In this example, we use a source concept code list for the Concept Set `Abdominal Pain` created from [ClinicalCodes.org](ClinicalCodes.org). The source concept codes are is read2. We genereate versioned phenotypes for read2 and then translate to snomed with a another version.  
 
-### **1. Initialize the Phenotype in the Workspace**
+1. **Initialize a phenotype in the workspace**
 
 Use the followijng acmc command to initialize the phenotype in a local Git repository:
 
@@ -152,23 +152,23 @@ Use the followijng acmc command to initialize the phenotype in a local Git repos
 acmc phen init
 ```
 
-### **2. Copy Example Medical Code Lists to the Phenotype Code Directory**
+2. **Copy example medical code lists to the phenotype codes directory**
 
-Copy medical code lists to the phenotype code directory:
+From the command prompt, copy medical code lists `/examples/codes`to the phenotype code directory:
 
 ```bash
 cp -r ./examples/codes/* ./workspace/phen/codes
 ```
 
-### **3. Copy the Example Phenotype Configuration Files**
+3. **Copy the example phenotype configuration file to the phenotype directory**
 
-Copy example phenotype configuration files (`.json`) to the phenotype directory:
+From the command prompt, copy example phenotype configuration files `/examples/config.json` to the phenotype directory:
 
 ```bash
 cp -r ./examples/config.json ./workspace/phen
 ```
 
-### **4. Validate the Phenotype Configuration**
+4. **Validate the phenotype configuration**
 
 Use the followijng acmc command to validate the phenotype configuration to ensure it's correct:
 
@@ -176,7 +176,7 @@ Use the followijng acmc command to validate the phenotype configuration to ensur
 acmc phen validate
 ```
 
-### **5. Generate Phenotype in Read2 Format**
+5. **Generate phenotype in read2 code format**
 
 Use the followijng acmc command to generate the phenotype in `read2` format:
 
@@ -184,39 +184,41 @@ Use the followijng acmc command to generate the phenotype in `read2` format:
 acmc phen map -t read2
 ```
 
-### **6. Publish the Phenotype at an Initial Version**
+6. **Publish phenotype at an initial version**
 
-Use the followijng acmc command to publish the phenotype at an initial version:
+Use the following `acmc` command to publish the phenotype at an initial version:
 
 ```bash
 acmc phen publish
 ```
 
-### **7. Generate Phenotype in SNOMED Format**
+7. **Generate phenotype in SNOWMED code format**
 
-Generate the phenotype in `SNOMED` format:
+Generate the phenotype in `snomed` format:
 
 ```bash
 acmc phen map -t snomed
 ```
 
-### **8. Get a Copy of the Previous Version in the Repo**
+8. **Get a copy of the previous version from the repo**
 
-Retrieve a copy of the previous version (`v1.0.3`) from the repository:
+Use the following `acmc` command to retrieve a copy of the previous version (`v1.0.3`) from the repository:
 
 ```bash
 acmc phen copy -v v1.0.3
 ```
 
-### **9. Compare the Previous Version `v1.0.3` with the Latest Version**
-Compare the previous version (`v1.0.3`) with the latest version in the repository:
+9. **Compare the previous version `v1.0.3` with the latest version**
+
+Use the following `acmc` command to compare the previous version (`v1.0.3`) with the latest version in the repository:
+
 ```bash
 python acmc.py phen diff -old ./workspace/v1.0.3/
 ```
 
-### **10. Publish the Phenotype at the Next Version**
+10. **Publish the phenotype at the next version**
 
-Use the followijng acmc command to publish the phenotype at the next version:
+Use the following `acmc` command to publish the phenotype at the next version:
 
 ```bash
 acmc phen publish