diff --git a/api/poetry.lock b/api/poetry.lock
index 0527507bff..9bfeec30d7 100644
--- a/api/poetry.lock
+++ b/api/poetry.lock
@@ -9584,4 +9584,4 @@ cffi = ["cffi (>=1.11)"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<3.13"
-content-hash = "165e4af9cfbce83ee831dd0e82159446ef595d7a7850ee8644c8e2d24dd7040d"
+content-hash = "a74c7b6a72145d5074aa84581df6e543ea422810caf0ba1561cd2d35497243ca"
diff --git a/api/pyproject.toml b/api/pyproject.toml
index f0df3e5a0e..82ccd0b202 100644
--- a/api/pyproject.toml
+++ b/api/pyproject.toml
@@ -156,6 +156,7 @@ markdown = "~3.5.1"
 novita-client = "^0.5.6"
 numpy = "~1.26.4"
 openai = "~1.29.0"
+openpyxl = "~3.1.5"
 oss2 = "2.18.5"
 pandas = { version = "~2.2.2", extras = ["performance", "excel"] }
 psycopg2-binary = "~2.9.6"
@@ -173,7 +174,6 @@ readabilipy = "0.2.0"
 redis = { version = "~5.0.3", extras = ["hiredis"] }
 replicate = "~0.22.0"
 resend = "~0.7.0"
-safetensors = "~0.4.3"
 scikit-learn = "^1.5.1"
 sentry-sdk = { version = "~1.44.1", extras = ["flask"] }
 sqlalchemy = "~2.0.29"
@@ -187,10 +187,16 @@ werkzeug = "~3.0.1"
 xinference-client = "0.13.3"
 yarl = "~1.9.4"
 zhipuai = "1.0.7"
-rank-bm25 = "~0.2.2"
-openpyxl = "^3.1.5"
+# Before adding new dependency, consider place it in alphabet order (a-z) and suitable group.
+
+############################################################
+# Related transparent dependencies with pinned verion
+# required by main implementations
+############################################################
+[tool.poetry.group.indriect.dependencies]
 kaleido = "0.2.1"
-elasticsearch = "8.14.0"
+rank-bm25 = "~0.2.2"
+safetensors = "~0.4.3"
 
 ############################################################
 # Tool dependencies required by tool implementations
@@ -198,6 +204,7 @@ elasticsearch = "8.14.0"
 
 [tool.poetry.group.tool.dependencies]
 arxiv = "2.1.0"
+cloudscraper = "1.2.71"
 matplotlib = "~3.8.2"
 newspaper3k = "0.2.8"
 duckduckgo-search = "^6.2.6"
@@ -209,26 +216,25 @@ twilio = "~9.0.4"
 vanna = { version = "0.5.5", extras = ["postgres", "mysql", "clickhouse", "duckdb"] }
 wikipedia = "1.4.0"
 yfinance = "~0.2.40"
-cloudscraper = "1.2.71"
 
 ############################################################
 # VDB dependencies required by vector store clients
 ############################################################
 
 [tool.poetry.group.vdb.dependencies]
+alibabacloud_gpdb20160503 = "~3.8.0"
+alibabacloud_tea_openapi = "~0.3.9"
 chromadb = "0.5.1"
+clickhouse-connect = "~0.7.16"
+elasticsearch = "8.14.0"
 oracledb = "~2.2.1"
 pgvecto-rs = { version = "~0.2.1", extras = ['sqlalchemy'] }
 pgvector = "0.2.5"
 pymilvus = "~2.4.4"
-pymysql = "1.1.1"
 tcvectordb = "1.3.2"
 tidb-vector = "0.0.9"
 qdrant-client = "1.7.3"
 weaviate-client = "~3.21.0"
-alibabacloud_gpdb20160503 = "~3.8.0"
-alibabacloud_tea_openapi = "~0.3.9"
-clickhouse-connect = "~0.7.16"
 
 ############################################################
 # Dev dependencies for running tests
@@ -252,5 +258,5 @@ pytest-mock = "~3.14.0"
 optional = true
 
 [tool.poetry.group.lint.dependencies]
-ruff = "~0.6.1"
 dotenv-linter = "~0.5.0"
+ruff = "~0.6.1"