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References: Graph Databases and Query Languages

  1. Graph Database - Wikipedia - Overview of graph database technology including property graph and RDF models, comparison with relational databases, and use cases in knowledge management and network analysis.

  2. Neo4j - Wikipedia - History and architecture of the Neo4j graph database management system, covering its property graph model, ACID compliance, Cypher query language, and adoption in life sciences.

  3. SPARQL - Wikipedia - Describes the SPARQL query language for RDF data, including graph pattern matching, CONSTRUCT queries, and federated queries across distributed biological knowledge bases.

  4. Graph Databases (2nd Edition) - Ian Robinson - O'Reilly Media - Practical guide to graph database concepts, data modeling with property graphs, Cypher query patterns, and application architecture for connected data problems.

  5. Knowledge Graphs: Fundamentals, Techniques, and Applications - Mayank Kejriwal - MIT Press - Covers knowledge graph construction, RDF and ontology frameworks, query languages, and embedding techniques relevant to biomedical graph database applications.

  6. Neo4j Documentation - Neo4j Inc. - Official documentation covering Neo4j installation, Cypher query language reference, graph data modeling, indexing, and the Python driver for programmatic database access.

  7. Cypher Query Language Reference - Neo4j Inc. - Complete reference for the Cypher graph query language including MATCH, CREATE, MERGE patterns, aggregation functions, and path-finding operations for biological networks.

  8. W3C RDF Primer - World Wide Web Consortium - Introduction to the Resource Description Framework data model, explaining triples, URIs, literals, and named graphs used in biological linked data and ontology systems.

  9. GQL Standard Overview - GQL Standards - Information about the ISO GQL graph query language standard, which unifies property graph querying and will shape the future of biological graph database interactions.

  10. Bio4j: Bioinformatics Graph Database - Bio4j Project - Open-source graph database integrating UniProt, Gene Ontology, NCBI Taxonomy, and RefSeq data, demonstrating practical graph database applications in bioinformatics.