diff --git a/.gitignore b/.gitignore
index 7d61b28..40f2d5c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,13 @@ uv.lock
 plantuml-images
 docs
 
+# Generated vocabulary documentation (but keep readme.md files)
+models/generated/vocabularies/*.qmd
+models/generated/vocabularies/*.md
+!models/generated/vocabularies/readme.md
+models/generated/extensions/*.md
+!models/generated/extensions/readme.md
+
 # Large data files
 *.parquet
 
diff --git a/models/generated/extensions/readme.md b/models/generated/extensions/readme.md
index 37a8299..7c77b9f 100644
--- a/models/generated/extensions/readme.md
+++ b/models/generated/extensions/readme.md
@@ -1 +1 @@
-this folder contains markdown output for extension vocabularies
\ No newline at end of file
+this folder contains markdown output for extension vocabularies
diff --git a/models/index.qmd b/models/index.qmd
index dc17d94..dcbae0d 100644
--- a/models/index.qmd
+++ b/models/index.qmd
@@ -37,10 +37,10 @@ The iSamples taxonomies are used to characterize three fundamental concepts pert
 
 Three taxonomies are currently defined :
 
-[Material Sample (specimen) Type Vocabulary](https://isamplesorg.github.io/metadata/vocabularies/specimentype.html)
+[Material Sample (specimen) Type Vocabulary](generated/vocabularies/material_sample_object_type.html)
 
-[Materials Vocabulary](https://isamplesorg.github.io/metadata/vocabularies/materialtype.html)
+[Materials Vocabulary](generated/vocabularies/material_type.html)
 
-[Sampled Feature (context) Type vocabulary](https://isamplesorg.github.io/metadata/vocabularies/sampledfeature.html)
+[Sampled Feature (context) Type vocabulary](generated/vocabularies/sampled_feature_type.html)
 
 
diff --git a/scripts/generate_vocab_docs.sh b/scripts/generate_vocab_docs.sh
index 20d9b22..5eff275 100755
--- a/scripts/generate_vocab_docs.sh
+++ b/scripts/generate_vocab_docs.sh
@@ -6,7 +6,6 @@
 
 # get the core sample type vocabularies
 SCRIPT_FOLDER="$(dirname ${0})"
-#SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata/develop/src/vocabularies/"
 
 SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/"
 
@@ -16,8 +15,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.qmd"
     echo "Generating ${fname}..."
-#    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
-    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 #
@@ -35,8 +33,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.md"
     echo "Generating ${fname}..."
-#    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
-    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/"
@@ -46,8 +43,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.md"
     echo "Generating ${fname}..."
-#    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
-    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/"
@@ -57,8 +53,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.md"
     echo "Generating ${fname}..."
-#    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
-    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 echo "Done."