The RDF model of the Gene Ontology, demystified

The Gene Ontology (GO) is a controlled vocabulary of terms describing genes and gene products. It facilitates the integration of biological and biomedical data and is widely used in bioinformatics.

The ontology defines terms (GO terms) and relationships between those terms. The terms can be thought of as tags that can be assigned to gene products. An individual gene can also be annotated with multiple GO terms.

Gene Ontology in RDF

The GO terms and relationships between them form a graph which can be described in RDF.

In the RDF representation of the Gene Ontology, each term has the IRI of the form http://purl.obolibrary.org/obo/GO_XXXXXXX. For example, the term "mitochondrion inheritance" is represented by the node http://purl.obolibrary.org/obo/GO_0000001 (obo:GO_0000001). Here is an excerpt of the ontology showing information about obo:GO_0000001:

Running SPARQL queries against the Gene Ontology data

A SPARQL query interface provided by the Gene Ontology project and powered by Blazegraph makes it possible to issue queries against the GO RDF dataset directly in the browser. For example, this query returns all superclasses of mitochondrion inheritance:

Query result:

What does it mean?

An instance of a Linked Data set, the Gene Ontology RDF graph is a step towards the more efficient sharing and reuse of biological information. While the GO terms provide the common language for annotating genes, RDF enables the interoperability and integration of those annotations with other datasets and ontologies.

See also

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• SNOMED CT RF2 to OWL - Convert SNOMED CT RF2 to OWL online.
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• WebLogo in the browser - Bringing WebLogo to the browser + demo of a pure client side sequence logo maker.
• BLAST WASM - Compiling the BLAST sequence search/alignment tool to WASM.
• DESeq2 in the browser - Running DESeq2 in the browser.
• Genome Browser - Explore the human genome.
• Sequence Alignment Viewer - Open FASTA files in the browser.
• Phylogenetic Tree Editor - An online visual editor for phylogenetic trees (WIP).
• Phylogenetic Tree Builder - Reconstruct phylogenetic trees from protein or DNA/RNA sequence alignments.
• Plasmid Map Generator - A tool to generate plasmid maps from GenBank files.
• WikiPathways: A Wikipedia for biological pathways - An overview of the collaboratively edited structured pathway encyclopedia.
• The ambitious challenge of finishing the human genome - Generating a complete human genome sequence, chromosome by chromosome.
• Scalable genomic alignment with Progressive Cactus - How progressive alignment makes it possible to efficiently align hundreds to thousands of large genomes.
• GenBank to FASTA - Convert GenBank flat files to FASTA format.
• ABI to FASTA - Convert AB1 files (Applied Biosystems/ABI trace files) to FASTA format.
• Awesome bioinformatics - A curated list of awesome resources on bioinformatics.
• What is FASTA and how is it used? - Learn about the FASTA format and its applications.
• FASTA Editor - A FASTA editor for creating and editing FASTA files.
• FASTA Parse Tree Viewer - Visualize the parse tree of FASTA files.
• FASTQ to FASTA Converter - Convert FASTQ files to FASTA format.
• FASTQ Editor - A FASTQ editor for creating and editing FASTQ files.
• Newick Editor - An online editor for phylogenetic trees in the Newick format.
• Newick Parse Tree Viewer - View the parse trees of Newick strings.
• PDB Editor - Edit PDB files online.
• PDB to FASTA - Extract protein/nucleotide sequences from PDB files.
• Bioinformatics Crossword - A daily crossword puzzle for bioinformatics terms.
• Bioinformatics pronunciation guide - A pronunciation guide for bioinformatics terms.
• RDF graphs - Intro to RDF graph visualization + demo.
• RDF* and the onset of Linked Data* and the Semantic Web* - The evolution of RDF and the related technologies fuelled by the need to make statements about statements.
• The building blocks of OWL - What makes up OWL ontologies and how do they support logical inference?
• SPARQL Playground (RDF Playground) - Experiment with running SPARQL queries against RDF data.
• SPARQL Client - Query SPARQL endpoints online.
• Why federation is a game-changing feature of SPARQL - SPARQL federation is an incredibly useful feature for querying distributed RDF graphs.
• Introduction to SPARQL - SPARQL is a query language for graph data. The graph model of thinking fits well a lot of use cases.
• SPARQL Parse Tree Viewer - Visualize the parse tree of SPARQL queries.
• Turtle Editor - Edit Turtle documents online.
• Turtle Inspector - Inspect the RDF content of Turtle files.
• Turtle Parse Tree Viewer - Visualize the parse tree of Turtle syntax.
• Wikidata's ontology - Inspecting the ontology of Wikidata.
• SHACL Validator - Validate RDF data against SHACL shapes.
• Semantic Web Browser - Look up entities on the Semantic Web.
• Let's explore the Nobel Prize dataset - An overview of the official Nobel Prize Linked Data dataset with some example SPARQL queries.
• Data exploration on linked COVID-19 datasets - An overview of the available RDF datasets and discovery tools for COVID-19.
• Creating an Amazon Neptune database using AWS CDK v2 - Provisioning a graph database cluster in AWS using TypeScript.