diff --git a/docs/python_api/datasets/biosample_index.md b/docs/python_api/datasets/biosample_index.md
new file mode 100644
index 000000000..d3e4ee2c8
--- /dev/null
+++ b/docs/python_api/datasets/biosample_index.md
@@ -0,0 +1,9 @@
+---
+title: Biosample index
+---
+
+::: gentropy.dataset.biosample_index.BiosampleIndex
+
+## Schema
+
+--8<-- "assets/schemas/biosample_index.md"
diff --git a/docs/python_api/datasources/_datasources.md b/docs/python_api/datasources/_datasources.md
index e6e081b21..43b212e50 100644
--- a/docs/python_api/datasources/_datasources.md
+++ b/docs/python_api/datasources/_datasources.md
@@ -26,7 +26,7 @@ This section contains information about the data source harmonisation tools avai
 2. GWAS catalog's [harmonisation pipeline](https://www.ebi.ac.uk/gwas/docs/methods/summary-statistics#_harmonised_summary_statistics_data)
 3. Ensembl's [Variant Effect Predictor](https://www.ensembl.org/info/docs/tools/vep/index.html)
 
-## Linkage desiquilibrium
+## Linkage disequilibrium
 
 1. [GnomAD](gnomad/_gnomad.md) v2.1.1 LD matrixes (7 ancestries)
 
@@ -37,3 +37,8 @@ This section contains information about the data source harmonisation tools avai
 ## Gene annotation
 
 1. [Open Targets Platform Target Dataset](open_targets/target.md) (derived from Ensembl)
+
+## Biological samples
+
+1. [Uberon](biosample_ontologies/_uberon.md)
+2. [Cell Ontology](biosample_ontologies/_cell_ontology.md)
diff --git a/docs/python_api/datasources/biosample_ontologies/_cell_ontology.md b/docs/python_api/datasources/biosample_ontologies/_cell_ontology.md
new file mode 100644
index 000000000..5798e032b
--- /dev/null
+++ b/docs/python_api/datasources/biosample_ontologies/_cell_ontology.md
@@ -0,0 +1,5 @@
+---
+title: Cell Ontology
+---
+
+The [Cell Ontology](http://www.obofoundry.org/ontology/cl.html) is a structured controlled vocabulary for cell types. It is used to annotate cell types in single-cell RNA-seq data and other omics data.
diff --git a/docs/python_api/datasources/biosample_ontologies/_uberon.md b/docs/python_api/datasources/biosample_ontologies/_uberon.md
new file mode 100644
index 000000000..4bb47305a
--- /dev/null
+++ b/docs/python_api/datasources/biosample_ontologies/_uberon.md
@@ -0,0 +1,5 @@
+---
+title: Uberon
+---
+
+The [Uberon](http://uberon.github.io/) ontology is a multi-species anatomy ontology that integrates cross-species ontologies into a single ontology.
diff --git a/docs/python_api/steps/biosample_index_step.md b/docs/python_api/steps/biosample_index_step.md
new file mode 100644
index 000000000..d8f7abbb4
--- /dev/null
+++ b/docs/python_api/steps/biosample_index_step.md
@@ -0,0 +1,5 @@
+---
+title: biosample_index
+---
+
+::: gentropy.biosample_index.BiosampleIndexStep
diff --git a/poetry.lock b/poetry.lock
index 226311a8b..296f07145 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.0 and should not be changed by hand.
 
 [[package]]
 name = "aiodns"
@@ -3952,6 +3952,7 @@ files = [
     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
     {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"},
     {file = "PyYAML-6.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9"},
+    {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a08c6f0fe150303c1c6b71ebcd7213c2858041a7e01975da3a99aed1e7a378ef"},
     {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0"},
     {file = "PyYAML-6.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4"},
     {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"},
diff --git a/src/gentropy/assets/schemas/biosample_index.json b/src/gentropy/assets/schemas/biosample_index.json
new file mode 100644
index 000000000..1d68762ac
--- /dev/null
+++ b/src/gentropy/assets/schemas/biosample_index.json
@@ -0,0 +1,83 @@
+{
+  "type": "struct",
+  "fields": [
+    {
+      "name": "biosampleId",
+      "type": "string",
+      "nullable": false,
+      "metadata": {}
+    },
+    {
+      "name": "biosampleName",
+      "type": "string",
+      "nullable": true,
+      "metadata": {}
+    },
+    {
+      "name": "description",
+      "type": "string",
+      "nullable": true,
+      "metadata": {}
+    },
+    {
+      "name": "xrefs",
+      "type": {
+        "type": "array",
+        "elementType": "string",
+        "containsNull": true
+      },
+      "nullable": true,
+      "metadata": {}
+    },
+    {
+      "name": "synonyms",
+      "type": {
+        "type": "array",
+        "elementType": "string",
+        "containsNull": true
+      },
+      "nullable": true,
+      "metadata": {}
+    },
+    {
+      "name": "parents",
+      "type": {
+        "type": "array",
+        "elementType": "string",
+        "containsNull": true
+      },
+      "nullable": true,
+      "metadata": {}
+    },
+    {
+      "name": "ancestors",
+      "type": {
+        "type": "array",
+        "elementType": "string",
+        "containsNull": true
+      },
+      "nullable": true,
+      "metadata": {}
+    },
+    {
+      "name": "descendants",
+      "type": {
+        "type": "array",
+        "elementType": "string",
+        "containsNull": true
+      },
+      "nullable": true,
+      "metadata": {}
+    },
+    {
+      "name": "children",
+      "type": {
+        "type": "array",
+        "elementType": "string",
+        "containsNull": true
+      },
+      "nullable": true,
+      "metadata": {}
+    }
+  ]
+}
diff --git a/src/gentropy/biosample_index.py b/src/gentropy/biosample_index.py
new file mode 100644
index 000000000..e85c2e135
--- /dev/null
+++ b/src/gentropy/biosample_index.py
@@ -0,0 +1,34 @@
+"""Step to generate biosample index dataset."""
+from __future__ import annotations
+
+from gentropy.common.session import Session
+from gentropy.datasource.biosample_ontologies.utils import extract_ontology_from_json
+
+
+class BiosampleIndexStep:
+    """Biosample index step.
+
+    This step generates a Biosample index dataset from the various ontology sources. Currently Cell Ontology and Uberon are supported.
+    """
+
+    def __init__(
+        self,
+        session: Session,
+        cell_ontology_input_path: str,
+        uberon_input_path: str,
+        biosample_index_path: str,
+    ) -> None:
+        """Run Biosample index generation step.
+
+        Args:
+            session (Session): Session object.
+            cell_ontology_input_path (str): Input cell ontology dataset path.
+            uberon_input_path (str): Input uberon dataset path.
+            biosample_index_path (str): Output gene index dataset path.
+        """
+        cell_ontology_index = extract_ontology_from_json(cell_ontology_input_path, session.spark)
+        uberon_index = extract_ontology_from_json(uberon_input_path, session.spark)
+
+        biosample_index = cell_ontology_index.merge_indices([uberon_index])
+
+        biosample_index.df.write.mode(session.write_mode).parquet(biosample_index_path)
diff --git a/src/gentropy/config.py b/src/gentropy/config.py
index 4d1174d6b..a1d0cdfc6 100644
--- a/src/gentropy/config.py
+++ b/src/gentropy/config.py
@@ -51,6 +51,16 @@ class GeneIndexConfig(StepConfig):
     _target_: str = "gentropy.gene_index.GeneIndexStep"
 
 
+@dataclass
+class BiosampleIndexConfig(StepConfig):
+    """Biosample index step configuration."""
+
+    cell_ontology_input_path: str = MISSING
+    uberon_input_path: str = MISSING
+    biosample_index_path: str = MISSING
+    _target_: str = "gentropy.biosample_index.BiosampleIndexStep"
+
+
 @dataclass
 class GWASCatalogStudyCurationConfig(StepConfig):
     """GWAS Catalog study curation step configuration."""
@@ -505,6 +515,7 @@ class StudyValidationStepConfig(StepConfig):
     study_index_path: list[str] = MISSING
     target_index_path: str = MISSING
     disease_index_path: str = MISSING
+    biosample_index_path: str = MISSING
     valid_study_index_path: str = MISSING
     invalid_study_index_path: str = MISSING
     invalid_qc_reasons: list[str] = MISSING
@@ -545,6 +556,7 @@ def register_config() -> None:
     cs.store(group="step", name="colocalisation", node=ColocalisationConfig)
     cs.store(group="step", name="eqtl_catalogue", node=EqtlCatalogueConfig)
     cs.store(group="step", name="gene_index", node=GeneIndexConfig)
+    cs.store(group="step", name="biosample_index", node=BiosampleIndexConfig)
     cs.store(
         group="step",
         name="gwas_catalog_study_curation",
diff --git a/src/gentropy/dataset/biosample_index.py b/src/gentropy/dataset/biosample_index.py
new file mode 100644
index 000000000..35c65a491
--- /dev/null
+++ b/src/gentropy/dataset/biosample_index.py
@@ -0,0 +1,73 @@
+"""Biosample index dataset."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from functools import reduce
+from typing import TYPE_CHECKING
+
+import pyspark.sql.functions as f
+from pyspark.sql import DataFrame
+from pyspark.sql.types import ArrayType, StringType
+
+from gentropy.common.schemas import parse_spark_schema
+from gentropy.dataset.dataset import Dataset
+
+if TYPE_CHECKING:
+    from pyspark.sql.types import StructType
+
+
+@dataclass
+class BiosampleIndex(Dataset):
+    """Biosample index dataset.
+
+    A Biosample index dataset captures the metadata of the biosamples (e.g. tissues, cell types, cell lines, etc) such as alternate names and relationships with other biosamples.
+    """
+
+    @classmethod
+    def get_schema(cls: type[BiosampleIndex]) -> StructType:
+        """Provide the schema for the BiosampleIndex dataset.
+
+        Returns:
+            StructType: The schema of the BiosampleIndex dataset.
+        """
+        return parse_spark_schema("biosample_index.json")
+
+    @classmethod
+    def merge_indices(
+        cls: type[BiosampleIndex],
+        biosample_indices : list[BiosampleIndex]
+        ) -> BiosampleIndex:
+        """Merge a list of biosample indices into a single biosample index.
+
+        Where there are conflicts, in single values - the first value is taken. In list values, the union of all values is taken.
+
+        Args:
+            biosample_indices (list[BiosampleIndex]): Biosample indices to merge.
+
+        Returns:
+            BiosampleIndex: Merged biosample index.
+        """
+        # Extract the DataFrames from the BiosampleIndex objects
+        biosample_dfs = [biosample_index.df for biosample_index in biosample_indices] + [cls.df]
+
+        # Merge the DataFrames
+        merged_df = reduce(DataFrame.unionAll, biosample_dfs)
+
+        # Determine aggregation functions for each column
+        # Currently this will take the first value for single values and merge lists for list values
+        agg_funcs = []
+        for field in merged_df.schema.fields:
+            if field.name != "biosampleId":  # Skip the grouping column
+                if field.dataType == ArrayType(StringType()):
+                    agg_funcs.append(f.array_distinct(f.flatten(f.col(field.name))).alias(field.name))
+                else:
+                    agg_funcs.append(f.first(f.col(field.name), ignorenulls=True).alias(field.name))
+
+        # Perform aggregation
+        aggregated_df = merged_df.groupBy("biosampleId").agg(*agg_funcs)
+
+        return BiosampleIndex(
+            _df=aggregated_df,
+            _schema=BiosampleIndex.get_schema()
+            )
diff --git a/src/gentropy/dataset/study_index.py b/src/gentropy/dataset/study_index.py
index ac637f137..768a83dad 100644
--- a/src/gentropy/dataset/study_index.py
+++ b/src/gentropy/dataset/study_index.py
@@ -19,6 +19,7 @@
     from pyspark.sql import Column, DataFrame
     from pyspark.sql.types import StructType
 
+    from gentropy.dataset.biosample_index import BiosampleIndex
     from gentropy.dataset.gene_index import GeneIndex
 
 
@@ -29,6 +30,7 @@ class StudyQualityCheck(Enum):
         UNRESOLVED_TARGET (str): Target/gene identifier could not match to reference - Labelling failing target.
         UNRESOLVED_DISEASE (str): Disease identifier could not match to referece or retired identifier - labelling failing disease
         UNKNOWN_STUDY_TYPE (str): Indicating the provided type of study is not supported.
+        UNKNOWN_BIOSAMPLE (str): Flagging if a biosample identifier is not found in the reference.
         DUPLICATED_STUDY (str): Flagging if a study identifier is not unique.
         NO_GENE_PROVIDED (str): Flagging QTL studies if the measured
     """
@@ -36,6 +38,7 @@ class StudyQualityCheck(Enum):
     UNRESOLVED_TARGET = "Target/gene identifier could not match to reference."
     UNRESOLVED_DISEASE = "No valid disease identifier found."
     UNKNOWN_STUDY_TYPE = "This type of study is not supported."
+    UNKNOWN_BIOSAMPLE = "Biosample identifier was not found in the reference."
     DUPLICATED_STUDY = "The identifier of this study is not unique."
     NO_GENE_PROVIDED = "QTL study doesn't have gene assigned."
 
@@ -408,3 +411,36 @@ def validate_target(self: StudyIndex, target_index: GeneIndex) -> StudyIndex:
         )
 
         return StudyIndex(_df=validated_df, _schema=StudyIndex.get_schema())
+
+    def validate_biosample(self: StudyIndex, biosample_index: BiosampleIndex) -> StudyIndex:
+        """Validating biosample identifiers in the study index against the provided biosample index.
+
+        Args:
+            biosample_index (BiosampleIndex): Biosample index containing a reference of biosample identifiers e.g. cell types, tissues, cell lines, etc.
+
+        Returns:
+            StudyIndex: with flagged studies if biosampleIndex could not be validated.
+        """
+        biosample_set = biosample_index.df.select("biosampleId", f.lit(True).alias("isIdFound"))
+
+        validated_df = (
+            self.df.join(biosample_set, self.df.biosampleFromSourceId == biosample_set.biosampleId, how="left")
+            .withColumn(
+                "isIdFound",
+                f.when(
+                    f.col("isIdFound").isNull(),
+                    f.lit(False),
+                ).otherwise(f.lit(True)),
+            )
+            .withColumn(
+                "qualityControls",
+                StudyIndex.update_quality_flag(
+                    f.col("qualityControls"),
+                    ~f.col("isIdFound"),
+                    StudyQualityCheck.UNKNOWN_BIOSAMPLE,
+                ),
+            )
+            .drop("isIdFound").drop("biosampleId")
+        )
+
+        return StudyIndex(_df=validated_df, _schema=StudyIndex.get_schema())
diff --git a/src/gentropy/datasource/biosample_ontologies/__init__.py b/src/gentropy/datasource/biosample_ontologies/__init__.py
new file mode 100644
index 000000000..d3fa6b416
--- /dev/null
+++ b/src/gentropy/datasource/biosample_ontologies/__init__.py
@@ -0,0 +1,3 @@
+"""Biosample index data source."""
+
+from __future__ import annotations
diff --git a/src/gentropy/datasource/biosample_ontologies/utils.py b/src/gentropy/datasource/biosample_ontologies/utils.py
new file mode 100644
index 000000000..e02c82cb7
--- /dev/null
+++ b/src/gentropy/datasource/biosample_ontologies/utils.py
@@ -0,0 +1,130 @@
+"""Utility functions for Biosample ontology processing."""
+from pyspark.sql import DataFrame, SparkSession
+from pyspark.sql import functions as f
+from pyspark.sql.types import ArrayType, StringType
+from pyspark.sql.window import Window
+
+from gentropy.dataset.biosample_index import BiosampleIndex
+
+
+def extract_ontology_from_json(
+    ontology_json : str,
+    spark : SparkSession
+) -> BiosampleIndex:
+    """Extracts the ontology information from a JSON file. Currently only supports Uberon and Cell Ontology.
+
+    Args:
+        ontology_json (str): Path to the JSON file containing the ontology information.
+        spark (SparkSession): Spark session.
+
+    Returns:
+        BiosampleIndex: Parsed and annotated biosample index table.
+    """
+
+    def json_graph_traversal(
+        df : DataFrame,
+        node_col : str,
+        link_col: str,
+        traversal_type: str
+    ) -> DataFrame:
+        """Traverse a graph represented in a DataFrame to find all ancestors or descendants.
+
+        Args:
+            df (DataFrame): DataFrame containing the graph data.
+            node_col (str): Column name for the node.
+            link_col (str): Column name for the link.
+            traversal_type (str): Type of traversal - "ancestors" or "descendants".
+
+        Returns:
+            DataFrame: DataFrame with the result column added.
+        """
+        # Collect graph data as a map
+        graph_map = df.select(node_col, link_col).rdd.collectAsMap()
+        broadcasted_graph = spark.sparkContext.broadcast(graph_map)
+
+        def get_relationships(
+            node : str
+        ) -> list[str]:
+            """Get all relationships for a given node.
+
+            Args:
+                node (str): Node ID.
+
+            Returns:
+                list[str]: List of relationships.
+            """
+            relationships = set()
+            stack = [node]
+            while stack:
+                current = stack.pop()
+                if current in broadcasted_graph.value:
+                    current_links = broadcasted_graph.value[current]
+                    stack.extend(current_links)
+                    relationships.update(current_links)
+            return list(relationships)
+
+        # Choose column name based on traversal type
+        result_col = "ancestors" if traversal_type == "ancestors" else "descendants"
+
+        # Register the UDF based on traversal type
+        relationship_udf = f.udf(get_relationships, ArrayType(StringType()))
+
+        # Apply the UDF to create the result column
+        return df.withColumn(result_col, relationship_udf(f.col(node_col)))
+
+    # Load the JSON file
+    df = spark.read.json(ontology_json, multiLine=True)
+
+    # Exploding the 'graphs' array to make individual records easier to access
+    df_graphs = df.select(f.explode_outer("graphs").alias("graph"))
+
+    # Exploding the 'nodes' array within each graph
+    df_nodes = df_graphs.select(
+        f.col("graph.id").alias("graph_id"),
+        f.explode_outer("graph.nodes").alias("node"))
+
+    # Exploding the 'edges' array within each graph for relationship data
+    df_edges = df_graphs.select(
+        f.col("graph.id").alias("graph_id"),
+        f.explode_outer("graph.edges").alias("edge")
+    ).select(
+        f.col("edge.sub").alias("subject"),
+        f.col("edge.pred").alias("predicate"),
+        f.col("edge.obj").alias("object")
+    )
+    df_edges = df_edges.withColumn("subject", f.regexp_replace(f.col("subject"), "http://purl.obolibrary.org/obo/", ""))
+    df_edges = df_edges.withColumn("object", f.regexp_replace(f.col("object"), "http://purl.obolibrary.org/obo/", ""))
+
+    # Extract the relevant information from the nodes
+    transformed_df = df_nodes.select(
+    f.regexp_replace(f.col("node.id"), "http://purl.obolibrary.org/obo/", "").alias("biosampleId"),
+    f.col("node.lbl").alias("biosampleName"),
+    f.col("node.meta.definition.val").alias("description"),
+    f.collect_set(f.col("node.meta.xrefs.val")).over(Window.partitionBy("node.id")).getItem(0).alias("xrefs"),
+    f.collect_set(f.col("node.meta.synonyms.val")).over(Window.partitionBy("node.id")).getItem(0).alias("synonyms"))
+
+
+    # Extract the relationships from the edges
+    # Prepare relationship-specific DataFrames
+    df_parents = df_edges.filter(f.col("predicate") == "is_a").select("subject", "object").withColumnRenamed("object", "parent")
+    df_children = df_edges.filter(f.col("predicate") == "is_a").select("object", "subject").withColumnRenamed("subject", "child")
+
+    # Aggregate relationships back to nodes
+    df_parents_grouped = df_parents.groupBy("subject").agg(f.array_distinct(f.collect_list("parent")).alias("parents"))
+    df_children_grouped = df_children.groupBy("object").agg(f.array_distinct(f.collect_list("child")).alias("children"))
+
+    # Get all ancestors
+    df_with_ancestors = json_graph_traversal(df_parents_grouped, "subject", "parents", "ancestors")
+    # Get all descendants
+    df_with_descendants = json_graph_traversal(df_children_grouped, "object", "children", "descendants")
+
+    # Join the ancestor and descendant DataFrames
+    df_with_relationships = df_with_ancestors.join(df_with_descendants, df_with_ancestors.subject == df_with_descendants.object, "full_outer").withColumn("biosampleId", f.coalesce(df_with_ancestors.subject, df_with_descendants.object)).drop("subject", "object")
+
+    # Join the original DataFrame with the relationship DataFrame
+    final_df = transformed_df.join(df_with_relationships, ["biosampleId"], "left")
+
+    return BiosampleIndex(
+        _df=final_df,
+        _schema=BiosampleIndex.get_schema()
+        )
diff --git a/src/gentropy/study_validation.py b/src/gentropy/study_validation.py
index 5bfb83fe0..6f905f89b 100644
--- a/src/gentropy/study_validation.py
+++ b/src/gentropy/study_validation.py
@@ -5,6 +5,7 @@
 from pyspark.sql import functions as f
 
 from gentropy.common.session import Session
+from gentropy.dataset.biosample_index import BiosampleIndex
 from gentropy.dataset.gene_index import GeneIndex
 from gentropy.dataset.study_index import StudyIndex
 
@@ -22,6 +23,7 @@ def __init__(
         study_index_path: list[str],
         target_index_path: str,
         disease_index_path: str,
+        biosample_index_path: str,
         valid_study_index_path: str,
         invalid_study_index_path: str,
         invalid_qc_reasons: list[str] = [],
@@ -33,12 +35,14 @@ def __init__(
             study_index_path (list[str]): Path to study index file.
             target_index_path (str): Path to target index file.
             disease_index_path (str): Path to disease index file.
+            biosample_index_path (str): Path to biosample index file.
             valid_study_index_path (str): Path to write the valid records.
             invalid_study_index_path (str): Path to write the output file.
             invalid_qc_reasons (list[str]): List of invalid quality check reason names from `StudyQualityCheck` (e.g. ['DUPLICATED_STUDY']).
         """
         # Reading datasets:
         target_index = GeneIndex.from_parquet(session, target_index_path)
+        biosample_index = BiosampleIndex.from_parquet(session, biosample_index_path)
         # Reading disease index and pre-process.
         # This logic does not belong anywhere, but gentorpy has no disease dataset yet.
         disease_index = (
@@ -63,6 +67,7 @@ def __init__(
             .validate_study_type()  # Flagging non-supported study types.
             .validate_target(target_index)  # Flagging QTL studies with invalid targets
             .validate_disease(disease_index)  # Flagging invalid EFOs
+            .validate_biosample(biosample_index)  # Flagging studies with invalid biosamples
         ).persist()  # we will need this for 2 types of outputs
 
         study_index_with_qc.valid_rows(
diff --git a/tests/gentropy/conftest.py b/tests/gentropy/conftest.py
index 629f3a505..35fcc6e24 100644
--- a/tests/gentropy/conftest.py
+++ b/tests/gentropy/conftest.py
@@ -13,6 +13,7 @@
 
 from gentropy.common.Liftover import LiftOverSpark
 from gentropy.common.session import Session
+from gentropy.dataset.biosample_index import BiosampleIndex
 from gentropy.dataset.colocalisation import Colocalisation
 from gentropy.dataset.gene_index import GeneIndex
 from gentropy.dataset.intervals import Intervals
@@ -559,6 +560,35 @@ def mock_gene_index(spark: SparkSession) -> GeneIndex:
     return GeneIndex(_df=data_spec.build(), _schema=gi_schema)
 
 
+@pytest.fixture()
+def mock_biosample_index(spark: SparkSession) -> BiosampleIndex:
+    """Mock biosample index dataset."""
+    bi_schema = BiosampleIndex.get_schema()
+
+    # Makes arrays of varying length with random integers between 1 and 100
+    array_expression = "transform(sequence(1, 1 + floor(rand() * 9)), x -> cast((rand() * 100) as int))"
+
+    data_spec = (
+        dg.DataGenerator(
+            spark,
+            rows=400,
+            partitions=4,
+            randomSeedMethod="hash_fieldname",
+        )
+        .withSchema(bi_schema)
+        .withColumnSpec("biosampleName", percentNulls=0.1)
+        .withColumnSpec("description", percentNulls=0.1)
+        .withColumnSpec("xrefs", expr=array_expression, percentNulls=0.1)
+        .withColumnSpec("synonyms", expr=array_expression, percentNulls=0.1)
+        .withColumnSpec("parents", expr=array_expression, percentNulls=0.1)
+        .withColumnSpec("ancestors", expr=array_expression, percentNulls=0.1)
+        .withColumnSpec("descendants", expr=array_expression, percentNulls=0.1)
+        .withColumnSpec("children", expr=array_expression, percentNulls=0.1)
+    )
+
+    return BiosampleIndex(_df=data_spec.build(), _schema=bi_schema)
+
+
 @pytest.fixture()
 def liftover_chain_37_to_38(spark: SparkSession) -> LiftOverSpark:
     """Sample liftover chain file."""
diff --git a/tests/gentropy/data_samples/cell_ontology_sample.json b/tests/gentropy/data_samples/cell_ontology_sample.json
new file mode 100644
index 000000000..5e73bfdee
--- /dev/null
+++ b/tests/gentropy/data_samples/cell_ontology_sample.json
@@ -0,0 +1,351 @@
+{
+  "graphs": [
+    {
+      "id": "http://purl.obolibrary.org/obo/cl.json",
+      "meta": {
+        "basicPropertyValues": [
+          {
+            "pred": "http://purl.obolibrary.org/obo/IAO_0000700",
+            "val": "http://purl.obolibrary.org/obo/CL_0000000"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/description",
+            "val": "An ontology of cell types."
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/title",
+            "val": "Cell Ontology"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0001-5208-3432"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0001-9114-8737"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0001-9990-8331"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0002-2244-7917"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0002-6601-2165"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0002-7073-9172"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0002-8688-6599"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0002-9900-7880"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/contributor",
+            "val": "https://orcid.org/0000-0003-1980-3228"
+          },
+          {
+            "pred": "http://purl.org/dc/terms/license",
+            "val": "http://creativecommons.org/licenses/by/4.0/"
+          },
+          {
+            "pred": "http://www.w3.org/2000/01/rdf-schema#comment",
+            "val": "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo."
+          },
+          {
+            "pred": "http://www.w3.org/2002/07/owl#versionInfo",
+            "val": "2024-08-16"
+          }
+        ],
+        "version": "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/cl.json"
+      },
+      "nodes": [
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000653",
+          "lbl": "podocyte",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "A specialized kidney epithelial cell, contained within a glomerulus, that contains \"feet\" that interdigitate with the \"feet\" of other podocytes.",
+              "xrefs": ["GOC:tfm", "https://doi.org/10.1101/2021.10.10.463829"]
+            },
+            "subsets": [
+              "http://purl.obolibrary.org/obo/cl#cellxgene_subset",
+              "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"
+            ],
+            "synonyms": [
+              {
+                "pred": "hasBroadSynonym",
+                "val": "epithelial cell of visceral layer of glomerular capsule",
+                "xrefs": ["FMA:70967"]
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "glomerular podocyte",
+                "xrefs": ["FMA:70967"]
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "glomerular visceral epithelial cell"
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "kidney podocyte"
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "renal podocyte"
+              }
+            ],
+            "xrefs": [
+              {
+                "val": "BTO:0002295"
+              },
+              {
+                "val": "FMA:70967"
+              },
+              {
+                "val": "ZFA:0009285"
+              }
+            ],
+            "basicPropertyValues": [
+              {
+                "pred": "http://purl.obolibrary.org/obo/RO_0002175",
+                "val": "http://purl.obolibrary.org/obo/NCBITaxon_9606"
+              },
+              {
+                "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso",
+                "val": "https://github.com/obophenotype/cell-ontology/issues/1460"
+              }
+            ]
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000654",
+          "lbl": "primary oocyte",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "A primary oocyte is an oocyte that has not completed female meosis I.",
+              "xrefs": ["GOC:tfm", "ISBN:0721662544"]
+            },
+            "subsets": [
+              "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"
+            ],
+            "synonyms": [
+              {
+                "pred": "hasRelatedSynonym",
+                "val": "primary oogonium"
+              }
+            ],
+            "xrefs": [
+              {
+                "val": "BTO:0000512"
+              },
+              {
+                "val": "FMA:18645"
+              }
+            ],
+            "basicPropertyValues": [
+              {
+                "pred": "http://purl.obolibrary.org/obo/RO_0002175",
+                "val": "http://purl.obolibrary.org/obo/NCBITaxon_9606"
+              }
+            ]
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000655",
+          "lbl": "secondary oocyte",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "A secondary oocyte is an oocyte that has not completed meiosis II.",
+              "xrefs": ["GOC:tfm", "ISBN:0721662544"]
+            },
+            "synonyms": [
+              {
+                "pred": "hasRelatedSynonym",
+                "val": "primary oogonium"
+              }
+            ],
+            "xrefs": [
+              {
+                "val": "BTO:0003094"
+              },
+              {
+                "val": "FMA:18646"
+              }
+            ]
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000656",
+          "lbl": "primary spermatocyte",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes.",
+              "xrefs": ["GOC:tfm", "ISBN:0721662544"]
+            },
+            "xrefs": [
+              {
+                "val": "BTO:0001115"
+              },
+              {
+                "val": "CALOHA:TS-2194"
+              },
+              {
+                "val": "FMA:72292"
+              }
+            ]
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000657",
+          "lbl": "secondary spermatocyte",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids.",
+              "xrefs": ["GOC:tfm", "ISBN:0721662544"]
+            },
+            "xrefs": [
+              {
+                "val": "BTO:0000709"
+              },
+              {
+                "val": "CALOHA:TS-2195"
+              },
+              {
+                "val": "FBbt:00004941"
+              },
+              {
+                "val": "FMA:72293"
+              }
+            ]
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000658",
+          "lbl": "cuticle secreting cell",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "An epithelial cell that secretes cuticle.",
+              "xrefs": ["GOC:tfm"]
+            }
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000659",
+          "lbl": "eggshell secreting cell",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "An extracellular matrix secreting cell that secretes eggshell.",
+              "xrefs": ["GOC:tfm"]
+            }
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_1000451",
+          "lbl": "obsolete epithelial cell of visceral layer of glomerular capsule",
+          "type": "CLASS",
+          "meta": {
+            "basicPropertyValues": [
+              {
+                "pred": "http://purl.obolibrary.org/obo/IAO_0100001",
+                "val": "http://purl.obolibrary.org/obo/CL_0000653"
+              }
+            ],
+            "deprecated": true
+          }
+        }
+      ],
+      "edges": [
+        {
+          "sub": "http://purl.obolibrary.org/obo/UBERON_0005751",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000051",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000653"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/GO_1903210",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000066",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000653"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/GO_0090521",
+          "pred": "http://purl.obolibrary.org/obo/RO_0002565",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000653"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/GO_0072015",
+          "pred": "http://purl.obolibrary.org/obo/RO_0002296",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000653"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_4030008",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000653"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002525",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000653"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002523",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000653"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000653",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0002522"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000653",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_1000450"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000653",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000050",
+          "obj": "http://purl.obolibrary.org/obo/UBERON_0005751"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000655",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000023",
+          "meta": {
+            "basicPropertyValues": [
+              {
+                "pred": "http://www.geneontology.org/formats/oboInOwl#is_inferred",
+                "val": "true"
+              }
+            ]
+          }
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000655",
+          "pred": "http://purl.obolibrary.org/obo/CL_4030044",
+          "obj": "http://purl.obolibrary.org/obo/GO_0007147"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000655",
+          "pred": "http://purl.obolibrary.org/obo/RO_0002202",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000654"
+        }
+      ]
+    }
+  ]
+}
diff --git a/tests/gentropy/data_samples/uberon_sample.json b/tests/gentropy/data_samples/uberon_sample.json
new file mode 100644
index 000000000..7dedfa23c
--- /dev/null
+++ b/tests/gentropy/data_samples/uberon_sample.json
@@ -0,0 +1,889 @@
+{
+  "graphs": [
+    {
+      "id": "http://purl.obolibrary.org/obo/uberon.json",
+      "meta": {
+        "basicPropertyValues": [
+          {
+            "pred": "http://purl.obolibrary.org/obo/IAO_0000700",
+            "val": "http://purl.obolibrary.org/obo/UBERON_0000104"
+          },
+          {
+            "pred": "http://purl.obolibrary.org/obo/IAO_0000700",
+            "val": "http://purl.obolibrary.org/obo/UBERON_0001062"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0001-5839-6798"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0001-7972-3866"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0001-9114-8737"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0002-1810-9886"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0002-6601-2165"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0002-7356-1779"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0002-9611-1279"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0003-3162-7490"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/creator",
+            "val": "https://orcid.org/0000-0003-3308-6245"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/description",
+            "val": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/publisher",
+            "val": "http://uberon.org"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://dbpedia.org"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://palaeos.com"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://www.brain-map.org"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://braininfo.rprc.washington.edu/"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://en.wikipedia.org/wiki/"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://pons.incf.org/wiki/Common_Upper_Mammalian_Brain_Ontology_%28Cumbo%29"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/aao.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/aba.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/aeo.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/bila.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/bto.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/caro.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/cl.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/ehdaa2.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/emapa.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/fbbt.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/fma.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/go.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/hp.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/ma.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/mp.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/tao.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/vhog.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/vsao.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/wbbt.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/xao.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://purl.obolibrary.org/obo/zfa.owl"
+          },
+          {
+            "pred": "http://purl.org/dc/elements/1.1/source",
+            "val": "http://uri.neuinfo.org/nif/nifstd"
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+              {
+                "pred": "hasRelatedSynonym",
+                "val": "rectal glandular cell",
+                "xrefs": ["CALOHA:TS-1281"]
+              },
+              {
+                "pred": "hasRelatedSynonym",
+                "val": "rectum glandular cells",
+                "xrefs": ["CALOHA:TS-1281"]
+              }
+            ],
+            "xrefs": [
+              {
+                "val": "CALOHA:TS-1281"
+              }
+            ]
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_1001596",
+          "lbl": "salivary gland glandular cell",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts.",
+              "xrefs": ["HPA:HPA", "NPX:PDR"]
+            },
+            "synonyms": [
+              {
+                "pred": "hasRelatedSynonym",
+                "val": "salivary gland glandular cells",
+                "xrefs": ["CALOHA:TS-1282"]
+              }
+            ],
+            "xrefs": [
+              {
+                "val": "CALOHA:TS-1282"
+              }
+            ]
+          }
+        },
+        {
+          "id": "http://purl.obolibrary.org/obo/CL_0000653",
+          "lbl": "podocyte",
+          "type": "CLASS",
+          "meta": {
+            "definition": {
+              "val": "A specialized kidney epithelial cell, contained within a glomerulus, that contains \"feet\" that interdigitate with the \"feet\" of other podocytes.",
+              "xrefs": ["GOC:tfm", "https://doi.org/10.1101/2021.10.10.463829"]
+            },
+            "subsets": [
+              "http://purl.obolibrary.org/obo/cl#cellxgene_subset",
+              "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"
+            ],
+            "synonyms": [
+              {
+                "pred": "hasBroadSynonym",
+                "val": "epithelial cell of visceral layer of glomerular capsule",
+                "xrefs": ["FMA:70967"]
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "glomerular podocyte",
+                "xrefs": ["FMA:70967"]
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "glomerular visceral epithelial cell"
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "kidney podocyte"
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "renal podocyte"
+              }
+            ],
+            "xrefs": [
+              {
+                "val": "BTO:0002295"
+              },
+              {
+                "val": "FMA:70967"
+              }
+            ],
+            "basicPropertyValues": [
+              {
+                "pred": "http://purl.obolibrary.org/obo/RO_0002175",
+                "val": "http://purl.obolibrary.org/obo/NCBITaxon_9606"
+              },
+              {
+                "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso",
+                "val": "https://github.com/obophenotype/cell-ontology/issues/1460"
+              }
+            ]
+          }
+        }
+      ],
+      "edges": [
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_1001596",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000150"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_1001596",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000152"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_1001596",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0002251"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_1001596",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000050",
+          "obj": "http://purl.obolibrary.org/obo/UBERON_0001044"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_1001596",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000050",
+          "obj": "http://purl.obolibrary.org/obo/UBERON_0004809"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002623",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000622",
+          "meta": {
+            "basicPropertyValues": [
+              {
+                "pred": "http://www.geneontology.org/formats/oboInOwl#is_inferred",
+                "val": "true"
+              }
+            ]
+          }
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002623",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_1001596"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002623",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000050",
+          "obj": "http://purl.obolibrary.org/obo/UBERON_0001044"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002623",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_0000622",
+          "meta": {
+            "basicPropertyValues": [
+              {
+                "pred": "http://www.geneontology.org/formats/oboInOwl#is_inferred",
+                "val": "true"
+              }
+            ]
+          }
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002623",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_1001596"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0002623",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000050",
+          "obj": "http://purl.obolibrary.org/obo/UBERON_0001044"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000653",
+          "pred": "is_a",
+          "obj": "http://purl.obolibrary.org/obo/CL_1000450"
+        },
+        {
+          "sub": "http://purl.obolibrary.org/obo/CL_0000653",
+          "pred": "http://purl.obolibrary.org/obo/BFO_0000050",
+          "obj": "http://purl.obolibrary.org/obo/UBERON_0005751"
+        }
+      ]
+    }
+  ]
+}
diff --git a/tests/gentropy/dataset/test_biosample_index.py b/tests/gentropy/dataset/test_biosample_index.py
new file mode 100644
index 000000000..c647710d1
--- /dev/null
+++ b/tests/gentropy/dataset/test_biosample_index.py
@@ -0,0 +1,8 @@
+"""Tests on Biosample index."""
+
+from gentropy.dataset.biosample_index import BiosampleIndex
+
+
+def test_biosample_index_creation(mock_biosample_index: BiosampleIndex) -> None:
+    """Test biosample index creation with mock biosample index."""
+    assert isinstance(mock_biosample_index, BiosampleIndex)
diff --git a/tests/gentropy/datasource/biosample_ontologies/test_biosample_ontology.py b/tests/gentropy/datasource/biosample_ontologies/test_biosample_ontology.py
new file mode 100644
index 000000000..b88623b0d
--- /dev/null
+++ b/tests/gentropy/datasource/biosample_ontologies/test_biosample_ontology.py
@@ -0,0 +1,50 @@
+"""Tests for biosample index dataset."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from gentropy.dataset.biosample_index import BiosampleIndex
+from gentropy.datasource.biosample_ontologies.utils import extract_ontology_from_json
+
+if TYPE_CHECKING:
+    from pyspark.sql import SparkSession
+
+
+class TestOntologyParger:
+    """Testing ontology parser."""
+
+    SAMPLE_CELL_ONTOLOGY_PATH = "tests/gentropy/data_samples/cell_ontology_sample.json"
+    SAMPLE_UBERON_PATH = "tests/gentropy/data_samples/uberon_sample.json"
+
+    def test_cell_ontology_parser(
+        self: TestOntologyParger, spark: SparkSession
+    ) -> None:
+        """Test cell ontology parser."""
+        cell_ontology = extract_ontology_from_json(
+            self.SAMPLE_CELL_ONTOLOGY_PATH, spark
+        )
+        assert isinstance(
+            cell_ontology, BiosampleIndex
+        ), "Cell ontology subset is not parsed correctly to BiosampleIndex."
+
+    def test_uberon_parser(self: TestOntologyParger, spark: SparkSession) -> None:
+        """Test uberon parser."""
+        uberon = extract_ontology_from_json(self.SAMPLE_UBERON_PATH, spark)
+        assert isinstance(
+            uberon, BiosampleIndex
+        ), "Uberon subset is not parsed correctly to BiosampleIndex."
+
+    def test_merge_biosample_indices(
+        self: TestOntologyParger, spark: SparkSession
+    ) -> None:
+        """Test merging of biosample indices."""
+        cell_ontology = extract_ontology_from_json(
+            self.SAMPLE_CELL_ONTOLOGY_PATH, spark
+        )
+        uberon = extract_ontology_from_json(self.SAMPLE_UBERON_PATH, spark)
+
+        merged = cell_ontology.merge_indices([uberon])
+        assert isinstance(
+            merged, BiosampleIndex
+        ), "Merging of biosample indices is not correct."