diff --git a/acmc/phen.py b/acmc/phen.py
index d4a95d0946008eba0a856bdd26cd2bfc67128998..f2111ac7c0fb311fb64b64a973cefc75aea84b13 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -32,7 +32,7 @@ DEFAULT_PHEN_PATH = Path("./workspace") / PHEN_DIR
 
 CONCEPTS_DIR = "concepts"
 MAP_DIR = "map"
-CONCEPT_SET_DIR = "concept-set"
+CONCEPT_SET_DIR = "concept-sets"
 CSV_PATH = Path(CONCEPT_SET_DIR) / "csv"
 OMOP_PATH = Path(CONCEPT_SET_DIR) / "omop"
 DEFAULT_PHEN_DIR_LIST = [CONCEPTS_DIR, MAP_DIR, CONCEPT_SET_DIR]
diff --git a/docs/index.md b/docs/index.md
index fd3ad6772f70dda5410009f6c769f25badd902e4..910d1f870bdf9215ba2b9c45c7cab80e5cb161b0 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -45,8 +45,8 @@ The tool supports verification and mapping across diagnostic coding formats belo
 ```
 workspace/                          # Default workspace directory
 ├── phen/                           # Default phenotype directory
-│   ├── codes/                      # Phenotype source concept code lists directory
-│   ├── concept-set/                # Processed phenotype concept sets
+│   ├── concepts/                   # Phenotype source concept code lists directory
+│   ├── concept-sets/               # Processed phenotype concept sets
 │   │   ├── csv/                    # Processed phenotype concept sets in ACMC CSV format
 │   │   ├── omop/                   # Processed phenotype concept sets in OMOP CDM database exported as CSV files
 │   ├── map/                        # Process mapping from source to target code types