diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml
new file mode 100644
index 00000000..4536dc44
--- /dev/null
+++ b/.github/workflows/generate-schema.yml
@@ -0,0 +1,35 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will build a Java project with Gradle and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-gradle
+
+name: Java CI with Gradle
+
+on:
+  push:
+    branches: [ "data-model-separation" ]
+  workflow_dispatch:
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 21
+        uses: actions/setup-java@v4
+        with:
+          java-version: '21'
+          distribution: 'temurin'
+
+      # Configure Gradle for optimal use in GitHub Actions, including caching of downloaded dependencies.
+      # See: https://github.com/gradle/actions/blob/main/setup-gradle/README.md
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@af1da67850ed9a4cedd57bfd976089dd991e2582 # v4.0.0
+
+      - name: Build with Gradle Wrapper
+        run: generator/gradlew validate
diff --git a/.gitignore b/.gitignore
index bc07f967..a8dfde9e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,7 @@
 .settings/
 .idea
 .vscode/
+.idea
 
 /_temp
 brapi_blueprint.apib
diff --git a/generator/.gitignore b/generator/.gitignore
new file mode 100644
index 00000000..2e384376
--- /dev/null
+++ b/generator/.gitignore
@@ -0,0 +1,3 @@
+.gradle
+build
+!gradle/wrapper/gradle-wrapper.jar
\ No newline at end of file
diff --git a/generator/README.md b/generator/README.md
new file mode 100644
index 00000000..9ec3ea71
--- /dev/null
+++ b/generator/README.md
@@ -0,0 +1,38 @@
+
+# BrAPI Schema Generator
+
+Generates the OpenAPI Specification, GraphQL Schema and OWL Model from the JSON Schema.
+The files are generated in the Specification/Generated directory.
+
+### How to use
+
+To generate all use the following
+
+    * In windows
+
+    ```powershell
+    ./gradlew generateAll
+    ```
+
+    * In Linux or macOS
+
+    ```shell
+    ./gradle generateAll
+    ```
+For individual tasks try
+
+* *generateGraphQL* to generate the GraphQL Schema from the JSON Schema
+* *generateOpenAPI* to generate the OpenAPI Specification from the JSON Schema
+* *generateOWL* to generate the OWL Model from the JSON Schema
+* *validate* to validate the JSON Schema without generating any file 
+
+The files are generated in the Specification/Generated directory.
+
+to change the version of BrAPI used in the file name edit the *brapiVersion* in
+[Settings](settings.gradle).
+
+### Configuration
+
+To configure the generator see https://github.com/plantbreeding/brapi-schema-tools
+
+
diff --git a/generator/build.gradle b/generator/build.gradle
new file mode 100644
index 00000000..c9acfb9b
--- /dev/null
+++ b/generator/build.gradle
@@ -0,0 +1,72 @@
+apply plugin : "java"
+ext {
+  javaMainClass = 'org.brapi.schematools.cli.BrAPICommand'
+  brapiSchemaToolsVersion = '0.10.0-SNAPSHOT'
+  brapiVersion = 'v2_1'
+}
+
+repositories {
+  mavenCentral()
+  maven {url 'https://s01.oss.sonatype.org/content/repositories/snapshots/'}
+}
+
+dependencies {
+  implementation "org.brapi:brapi-schema-tools-cli:$brapiSchemaToolsVersion"
+}
+
+tasks.register("validate", JavaExec) {
+  group = 'BrAPI'
+  description = 'Validate the Json Schema'
+  classpath = sourceSets.main.runtimeClasspath
+  mainClass = javaMainClass
+  workingDir = '../'
+  args = ['validate', 'Specification/BrAPI-Schema', '-x']
+}
+
+tasks.register("generateGraphQL", JavaExec) {
+  group = 'BrAPI'
+  description = 'Generate GraphQL schema from the Json Schema'
+  classpath = sourceSets.main.runtimeClasspath
+  mainClass = javaMainClass
+  workingDir = '../'
+  def filename = "Specification/Generated/brapi_" + brapiVersion + ".graphqls"
+  args = ['generate',
+          'Specification/BrAPI-Schema',
+          '-l', 'GRAPHQL',
+          '-f', filename,
+          '-x']
+}
+
+tasks.register("generateOpenAPI", JavaExec) {
+  group = 'BrAPI'
+  description = 'Generate OpenAPI schema from the Json Schema'
+  classpath = sourceSets.main.runtimeClasspath
+  mainClass = javaMainClass
+  workingDir = '../'
+  def filename = "Specification/Generated/brapi_" + brapiVersion + ".json"
+  args = ['generate', 'Specification/BrAPI-Schema',
+          '-l', 'OPEN_API',
+          '-f', filename,
+          '-c', 'Specification/OpenAPI-Components',
+          '-x']
+}
+
+tasks.register("generateOWL", JavaExec) {
+  group = 'BrAPI'
+  description = 'Generate OWL schema from the Json Schema'
+  classpath = sourceSets.main.runtimeClasspath
+  mainClass = javaMainClass
+  workingDir = '../'
+  def filename = "Specification/Generated/brapi_" + brapiVersion + ".ttl"
+  args = ['generate', 'Specification/BrAPI-Schema',
+          '-l', 'OWL',
+          '-f', filename,
+          '-m', 'generator/ont-model-metadata.yaml',
+          '-x']
+}
+
+tasks.register("generateAll") {
+  dependsOn generateGraphQL
+  dependsOn generateOpenAPI
+  dependsOn generateOWL
+}
\ No newline at end of file
diff --git a/generator/gradle/wrapper/gradle-wrapper.jar b/generator/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 00000000..e6441136
Binary files /dev/null and b/generator/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/generator/gradle/wrapper/gradle-wrapper.properties b/generator/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 00000000..b82aa23a
--- /dev/null
+++ b/generator/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,7 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
diff --git a/generator/gradlew b/generator/gradlew
new file mode 100644
index 00000000..1b6c7873
--- /dev/null
+++ b/generator/gradlew
@@ -0,0 +1,234 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
+done
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&2
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD=$JAVA_HOME/jre/sh/java
+    else
+        JAVACMD=$JAVA_HOME/bin/java
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
+exec "$JAVACMD" "$@"
diff --git a/generator/gradlew.bat b/generator/gradlew.bat
new file mode 100644
index 00000000..25da30db
--- /dev/null
+++ b/generator/gradlew.bat
@@ -0,0 +1,92 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%"=="" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if %ERRORLEVEL% equ 0 goto execute
+
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if %ERRORLEVEL% equ 0 goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega
diff --git a/generator/settings.gradle b/generator/settings.gradle
new file mode 100644
index 00000000..78864991
--- /dev/null
+++ b/generator/settings.gradle
@@ -0,0 +1,10 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * The settings file is used to specify which projects to include in your build.
+ * For more detailed information on multi-project builds, please refer to https://docs.gradle.org/8.7/userguide/multi_project_builds.html in the Gradle documentation.
+ */
+
+rootProject.name = 'org.brapi.schema.generator'
+
+