Knowledge Graph: How To Tutorial In Python, LLM Comparison & 23 Tools & Libraries

by | Nov 14, 2023 | Data Science, Natural Language Processing

What is a Knowledge Graph?

Knowledge Graph is a structured representation of knowledge that incorporates entities, relationships, and attributes to create a network of interconnected information. Unlike traditional databases, which primarily store data in tables, knowledge graphs focus on organizing information to reflect the inherent relationships between different entities.

Entities are the core building blocks of a knowledge graph. They can represent anything, from people and places to concepts and events. Each entity is assigned a unique identifier.

Relationships: Relationships define the connections between entities. They establish links that convey specific meanings, helping to contextualize the information. Relationships often come with attributes that provide additional details.

Attributes: Attributes provide more granular information about entities or relationships. They include properties, characteristics, or descriptive elements associated with a particular entity or relationship.

Components of a Knowledge Graph

Nodes and edges in a knowledge graph


  • Entity Nodes: Represent individual entities in the knowledge graph.
  • Literal Nodes: Represent values or attributes associated with entities or relationships.


  • Relationship Edges: Connect entities and represent the nature of their relationship.
  • Attribute Edges: Connect entities to their attributes, indicating specific details.


  • Entity Properties: Characteristics or features associated with individual entities.
  • Relationship Properties: Additional information about the nature of relationships.

How Knowledge Graphs Differ from Traditional Databases

Graph Structure:

Traditional databases use tabular structures, whereas knowledge graphs employ a graph structure, enabling a more flexible and nuanced representation of relationships.

Semantic Understanding:

Knowledge graphs focus on semantic understanding, capturing not just data but the meaning and context behind the data.

Querying and Traversal:

Knowledge graphs allow for complex queries and traversals, making extracting specific information and uncovering hidden relationships easier.

A knowledge graph is a powerful tool for organizing, connecting, and deriving insights from diverse datasets, making it an invaluable asset in various fields, from artificial intelligence to data management.

How Does a Knowledge Graph Work?

Data Integration

Knowledge graphs excel at integrating data from diverse sources, creating a unified and interconnected information ecosystem.

Data Sources:

  • Knowledge graphs aggregate data from structured databases, unstructured text, and external sources.
  • Integration tools are employed to harmonize disparate data formats and structures.

Data Mapping:

  • Entities and relationships from different sources are mapped to a standard schema within the knowledge graph.
  • This mapping process involves aligning terminology and resolving semantic inconsistencies.

Semantic Interoperability

Semantic interoperability is crucial to knowledge graphs, ensuring that data meaning is preserved and understood consistently.


  • Knowledge graphs often rely on ontologies, which define the concepts, relationships, and rules in a specific domain.
  • Ontologies provide a shared understanding of the data semantics, facilitating interoperability.

Linked Data Principles:

  • Knowledge graphs adhere to linked data principles, enabling seamless integration and interlinking of information on the web.
  • Uniform Resource Identifiers (URIs) are used to identify entities and concepts uniquely.

Querying and Traversing

Knowledge graphs enable powerful querying and traversal capabilities, allowing users to explore and extract meaningful insights.

SPARQL Queries:

  • SPARQL (SPARQL Protocol and RDF Query Language) is commonly used to query knowledge graphs.
  • It allows users to retrieve specific information, traverse relationships, and filter results based on complex conditions.

Graph Algorithms:

  • Graph algorithms, such as shortest path or centrality analysis, are applied to uncover patterns and relationships within the knowledge graph.
  • These algorithms provide valuable insights into the structure and dynamics of the interconnected data.

Inference and Reasoning:

  • Knowledge graphs support inference and reasoning mechanisms, allowing the system to deduce new information based on existing knowledge.
  • Logical rules and ontological axioms contribute to automated reasoning.

Natural Language Processing (NLP):

  • Integrating NLP techniques enhances the understanding of unstructured text, enabling the extraction of valuable information to enrich the knowledge graph.

Knowledge graphs integrate diverse data sources, adhere to semantic interoperability through ontologies, and empower users with advanced querying and traversal capabilities to extract meaningful insights from the interconnected data landscape.

What are the Benefits of a Knowledge Graph?

Knowledge graphs offer a range of advantages that make them a powerful tool in various domains. Understanding these benefits is crucial for appreciating knowledge graphs’ impact and potential applications.

1. Improved Data Connectivity

Relationship Awareness:

Knowledge graphs capture intricate relationships between entities, providing a comprehensive understanding of data context.

This relationship awareness enhances the connectedness of information, enabling a holistic view of the data landscape.

Cross-Domain Integration:

Knowledge graphs facilitate the integration of data from diverse domains, breaking down silos and fostering a more interconnected and comprehensive knowledge base.

2. Enhanced Search and Discovery

Contextualized Search:

Knowledge graphs enable more context-aware search functionalities, allowing users to find information within a specific context or related to particular entities.

Recommendation Systems:

Knowledge graphs power recommendation systems by understanding relationships and patterns suggesting relevant content or connections based on user preferences and behaviour.

3. Flexibility and Scalability


Knowledge graphs are highly adaptable to changes in data structures and evolving requirements. This flexibility makes them suitable for dynamic and growing datasets.


As the volume of data increases, knowledge graphs maintain scalability, ensuring efficient storage and retrieval of information without compromising performance.

Use Cases in Various Industries

1. Healthcare:

Knowledge graphs connect patient records, medical research, and treatment protocols, enhancing collaboration and improving healthcare outcomes.

2. Finance:

Knowledge graphs assist in fraud detection, risk assessment, and portfolio management in the financial sector by providing a unified view of diverse financial data.

3. E-commerce:

Knowledge graphs benefit e-commerce platforms through enhanced product recommendations, supply chain optimization, and customer profiling.

4. Life Sciences:

Knowledge graphs, which integrate and analyze complex biological data, play a crucial role in genomics, drug discovery, and clinical research.

5. Smart Cities:

In urban planning, knowledge graphs connect transportation, infrastructure, and public services data to support intelligent decision-making.

Top 3 Future Trends in Knowledge Graphs

1. Machine Learning Integration:

Integrating machine learning techniques enhances knowledge graphs by enabling predictive analytics, anomaly detection, and continuous learning.

2. Decentralized Knowledge Graphs:

The emergence of decentralized technologies, such as blockchain, may influence the development of decentralized knowledge graphs, which can ensure data integrity and security.

3. Industry-Specific Knowledge Graphs:

A growing trend is tailoring knowledge graphs to specific industries and domains. This optimizes the technology for more targeted and practical applications.

In conclusion, knowledge graphs’ benefits extend from improved data connectivity to industry-specific applications, making them pivotal technologies for navigating the complexities of interconnected information in the digital age.

What are the Challenges of Implementing a Knowledge Graph?

While knowledge graphs offer substantial benefits, their implementation is not without challenges. Addressing these challenges is crucial for maximizing the potential of knowledge graph technologies.

1. Data Quality and Integration Issues

Data Inconsistency:

Inconsistencies in data formats, semantics, and quality across different sources can pose challenges during integration and affect the knowledge graph’s accuracy and reliability.

Data Cleaning and Preprocessing:

Cleaning and preprocessing large datasets to ensure consistency and relevance require significant effort and resources, mainly when dealing with unstructured or semi-structured data.

2. Maintenance and Updates

Dynamic Data Environments:

Maintaining a knowledge graph’s integrity and relevance in rapidly changing environments can be challenging. However, regular updates are necessary to reflect the latest information accurately.

Schema Evolution:

As data evolves, the schema of the knowledge graph may need to be updated. Managing schema changes without disrupting existing applications or data structures requires careful planning.

3. Privacy and Security Concerns

Sensitive Information Handling:

Incorporating sensitive data into knowledge graphs requires robust security measures to protect privacy and comply with data protection regulations.

Access Control:

Implementing adequate access controls is vital to prevent unauthorized access and ensure that sensitive information is only accessible to authorized users.

4. Lack of Standards

Interoperability Challenges:

The absence of standardized formats and protocols for knowledge graphs can hinder interoperability between systems and limit the seamless exchange of information.

Ontology Design:

Designing a comprehensive and practical ontology can be challenging, as it requires balancing domain-specific specificity with the need for broader interoperability.

5. Resource Intensiveness

Computational Resources:

Building and maintaining knowledge graphs, especially in large-scale applications, may require significant computational resources. These include storage, processing power, and memory.

Expertise and Training:

Effective knowledge graph development and management require a skilled workforce with data science, semantics, and graph technologies expertise. Training personnel to work with these technologies can be resource-intensive.

6. Resistance to Change

Organizational Culture:

Overcoming resistance to change within organizations is a common challenge. Adopting knowledge graphs may require a shift in mindset and operational practices.

Integration with Existing Systems:

Integrating knowledge graphs into existing IT infrastructure can be complex, especially when legacy systems are in place. Ensuring compatibility and minimizing disruptions is a significant challenge.

Addressing these challenges involves a combination of technological solutions, organizational strategies, and ongoing commitment to refining and optimizing knowledge graph implementations. By doing so, organizations can unlock the full potential of knowledge graphs while mitigating potential obstacles.

What are the Real-World Applications of a Knowledge Graph?

Knowledge graphs have found diverse and impactful applications across various industries, transforming how organizations manage and derive insights from their data. Here are notable real-world applications that showcase the versatility and effectiveness of knowledge graphs:

1. Google’s Knowledge Graph Semantic Search:

  • Google’s Knowledge Graph enhances search results by understanding the context of user queries, providing more relevant and nuanced information.
  • It connects entities like people, places, and concepts to deliver a more comprehensive search experience.

2. Social Media Platforms

Content Recommendations:

  • Social media platforms leverage knowledge graphs to analyze user interactions, identify preferences, and deliver personalized content recommendations.
  • This enhances user engagement and satisfaction by tailoring content to individual interests.

Entity Recognition:

  • Knowledge graphs assist in entity recognition and disambiguation, helping platforms understand and connect diverse user-generated content.

3. Healthcare and Life Sciences

Clinical Decision Support:

  • Knowledge graphs integrate medical literature, patient records, and treatment protocols to provide clinicians with comprehensive and up-to-date information for informed decision-making.

Drug Discovery:

  • In pharmaceutical research, knowledge graphs connect biological pathways, drug interactions, and genetic data, accelerating drug discovery.

4. E-commerce and Recommendation Systems

Product Recommendations:

  • E-commerce platforms utilize knowledge graphs to understand customer preferences, analyze product attributes, and generate accurate and timely product recommendations.

Supply Chain Optimization:

  • Knowledge graphs optimize supply chain processes by connecting suppliers, inventory, and logistics information, enabling more efficient operations.

5. Smart Cities

Urban Planning:

  • Knowledge graphs assist urban planning by integrating data on transportation, infrastructure, public services, and environmental factors.
  • This integration enhances decision-making for city planners and policymakers.

6. Financial Services

Fraud Detection:

  • Knowledge graphs help detect fraudulent activities by connecting patterns in financial transactions, identifying anomalies, and enhancing the accuracy of fraud detection algorithms.

Risk Assessment:

  • In risk management, knowledge graphs provide a holistic view of market trends, regulatory changes, and financial data, aiding in more informed risk assessments.

7. Knowledge Management in Enterprises

Enterprise Knowledge Graphs:

  • Organizations use knowledge graphs to connect internal knowledge repositories, facilitating efficient knowledge discovery and employee sharing.

Human Resources:

  • Knowledge graphs assist in talent management, employee skill mapping, and organizational planning by connecting diverse HR data.

These real-world applications underscore the versatility and impact of knowledge graphs across industries. As technology continues to evolve, the scope and depth of knowledge graph applications will likely expand, offering innovative solutions to complex challenges in various domains.

How to Implement a Knowledge Graph

To implement a knowledge graph, you need to follow these steps:

  1. Define your objectives. What problems do you want your knowledge graph to solve? What questions do you want it to answer? Once you clearly understand your goals, you can start designing the structure of your knowledge graph and identifying the necessary data sources.
  2. Gather your data. Knowledge graphs can be built from various data sources, including text documents, databases, and APIs. You must collect and clean your data before loading it into your knowledge graph.
  3. Extract entities and relationships. Entities are the basic building blocks of a knowledge graph. They represent objects, concepts, or events in the real world. Relationships are the links between entities. You can use natural language processing (NLP) techniques to extract entities and relationships from your data.
  4. Load your data into a knowledge graph database. Several knowledge graph databases, such as Neo4j, Stardog, and Blazegraph, are available. Choose a database that is appropriate for your needs and budget.
  5. Query and visualize your knowledge graph. Once your knowledge graph is populated with data, you can query it to answer your questions and generate insights. You can also use visualization tools to create interactive graphs and charts representing your knowledge graph data.

Here are some additional tips for implementing knowledge graphs:

  • Start small. It is better to start with a small, focused knowledge graph than to build a comprehensive one immediately. You can continually expand your knowledge graph later, as needed.
  • Use ontologies. Ontologies are formal representations of knowledge that can be used to structure your knowledge graph and ensure that your data is consistent and unambiguous.
  • Use a knowledge graph development platform. These platforms can make building and maintaining your knowledge graph easier and provide various features, such as tools for data extraction, entity linking, and knowledge graph visualization.

List of Tools and Libraries to Build Knowledge Graphs

There are many tools and libraries available for implementing knowledge graphs. Here is a list of some of the most popular options:

Knowledge graph databases

  • Neo4j
  • Stardog
  • Blazegraph
  • Ontotext GraphDB
  • ArangoDB

Knowledge graph development platforms

  • Google Cloud Dataproc
  • Amazon Neptune
  • Microsoft Azure Cosmos DB Gremlin API
  • Knowledge Graph Studio
  • TopQuadrant Enterprise Knowledge Graph

Python libraries

  • PyKEEN
  • scikit-kge
  • OpenNRE

JavaScript libraries

  • KeyLines
  • ReGraph
  • Cytoscape.js
  • Sigma.js

Graph visualization tools

  • Gephi
  • Cytoscape
  • Linkurious
  • KeyLines
  • ReGraph

The best tools and libraries for you will depend on your specific needs and budget. If you are just starting with knowledge graphs, start with a free and open-source option, such as Neo4j or PyKEEN. You can upgrade to a more powerful tool or platform as your needs grow.

How To Implement a Knowledge Graph In Python Example

Creating a knowledge graph in Python involves using various libraries and tools to model, store, and query the graph. Here, I’ll provide a simple example using the NetworkX library for creating and visualizing graphs.

1. Install Required Libraries

Make sure you have the required libraries installed. You can install them using:

pip install networkx matplotlib 

2. Create a Simple Knowledge Graph

import networkx as nx
import matplotlib.pyplot as plt

# Create an empty directed graph
knowledge_graph = nx.DiGraph()

# Add nodes representing entities
knowledge_graph.add_node("Person", label="Entity")
knowledge_graph.add_node("City", label="Entity")
knowledge_graph.add_node("BornIn", label="Relationship")

# Add edges representing relationships between entities
knowledge_graph.add_edge("Person", "BornIn", label="Location")
knowledge_graph.add_edge("City", "BornIn", label="Location")

# Visualize the graph
pos = nx.spring_layout(knowledge_graph)
labels = nx.get_edge_attributes(knowledge_graph, 'label')
nx.draw_networkx(knowledge_graph, pos, with_labels=True, node_size=2000, node_color="skyblue", font_size=10)
nx.draw_networkx_edge_labels(knowledge_graph, pos, edge_labels=labels)
knowledge graph python example plot with nodes and edges

This code creates a basic directed graph using NetworkX. It represents a simple knowledge graph with nodes for entities (“Person,” “City”) and a relationship (“BornIn”) between them.

3. Query the Knowledge Graph

NetworkX provides basic graph querying functionalities. For more advanced querying, especially in semantic graph databases, you might want to explore libraries like RDFLib or use a dedicated graph database like Neo4j.

# Example query: Find all entities related to "BornIn"
related_entities = [node for node, neighbors in knowledge_graph.adjacency() if "BornIn" in neighbors]

print("Entities related to 'BornIn':", related_entities)

4. Extend with Attributes and More Complex Relationships

You can extend the graph by adding attributes to nodes and edges and incorporating more complex relationships and entities.

# Adding attributes to nodes
knowledge_graph.nodes["Person"]["gender"] = "Male"
knowledge_graph.nodes["City"]["population"] = 5000000

# Adding attributes to edges
knowledge_graph.edges["Person", "BornIn"]["year"] = 1990

# Visualize the updated graph
pos = nx.spring_layout(knowledge_graph)
labels = nx.get_edge_attributes(knowledge_graph, 'label')
nx.draw_networkx(knowledge_graph, pos, with_labels=True, node_size=2000, node_color="skyblue", font_size=10)
nx.draw_networkx_edge_labels(knowledge_graph, pos, edge_labels=labels)

This example adds attributes to nodes and edges, providing additional information about entities and relationships in the knowledge graph.

Remember, for more complex knowledge graphs and querying capabilities. You might want to explore dedicated graph databases or use RDF libraries for semantic data.

How to combine Large Language Models (LLMs) with a Knowledge Graph

Knowledge graphs and large language models (LLMs) are powerful technologies with different strengths and weaknesses. Knowledge graphs are structured representations of knowledge, while LLMs are statistical models that can generate and understand text.

Knowledge graphs

  • Strengths:
    • Accurate and reliable representation of knowledge
    • It can be used to power a variety of applications, such as search engines, question-answering systems, and recommendation systems.
  • Weaknesses:
    • It can be difficult and time-consuming to build and maintain
    • Not as good at generating text or understanding natural language as LLMs

Large Language Models (LLMs)

  • Strengths:
    • Can generate text that is indistinguishable from human-written text
    • Can understand natural language and answer questions in a comprehensive and informative way
  • Weaknesses:
    • Not as accurate or reliable as knowledge graphs when representing structured knowledge
    • It can be more challenging to control and generate biased or inaccurate results.

Knowledge graphs vs LLMs

CharacteristicKnowledge graphLarge Language Model (LLM)
Accurate and reliableYesNo (can be biased or inaccurate)
Good at generating textNoYes
Good at understanding natural languageNoYes
Easy to build and maintainNoYes

When to use knowledge graphs

Knowledge graphs are a good choice for a reliable and accurate structured knowledge representation. For example, you might use one to power a search engine or a question-answering system.

When to use LLMs

LLMs are an excellent choice to generate text or understand natural language. For example, you might use an LLM to develop a creative text format of text content, like poems, code, scripts, musical pieces, emails, letters, etc., or to answer questions in a comprehensive and informative way, even if they are open-ended, challenging, or strange.

Combining knowledge graphs and LLMs

Knowledge graphs and LLMs can be used together to improve the performance of various tasks. For example, you could use a knowledge graph to provide an LLM with additional information that can help it generate more accurate and informative results. You could also use an LLM to extract data from existing text and add this information to a knowledge graph.

Knowledge graphs and LLMs are complementary technologies with different strengths and weaknesses. You can achieve the best possible results by choosing the right technology.


Knowledge graphs and large language models represent a powerful synergy in information processing and natural language understanding. With their structured representation of entities, relationships, and attributes, knowledge graphs offer a means to organize and contextualize information. On the other hand, large language models, such as GPT-3, showcase remarkable capabilities in understanding and generating human-like text.

The integration of knowledge graphs and large language models holds promise across various applications:

  • Enhanced Contextual Understanding: Knowledge graphs provide a structured context that can augment the ability of large language models to understand and respond to queries in a more contextually aware manner.
  • Improved Information Retrieval: By accessing the structured relationships within knowledge graphs, language models can more accurately retrieve relevant information, contributing to more informed responses.
  • Domain-specific Expertise: Knowledge graphs offer a way to encode domain-specific knowledge, enabling large language models to exhibit expertise in particular areas by leveraging the structured information available.
  • Dynamic Content Generation: Integrating knowledge graphs with language models allows for generating linguistically coherent content grounded in factual and structured information.
  • Advancements in Question-Answering Systems: The combined use of knowledge graphs and large language models can elevate the performance of question-answering systems, offering more precise and informed responses.

As technology evolves, the collaboration between knowledge graphs and large language models will likely drive innovations in diverse fields, from information retrieval and content creation to advanced artificial intelligence applications. The ongoing exploration of this synergy is expected to lead to more intelligent systems capable of understanding and generating content in a way that closely aligns with human cognition and contextual reasoning.

About the Author

Neri Van Otten

Neri Van Otten

Neri Van Otten is the founder of Spot Intelligence, a machine learning engineer with over 12 years of experience specialising in Natural Language Processing (NLP) and deep learning innovation. Dedicated to making your projects succeed.

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