SIBiLS RDF is built on the data underlying SIBiLS services. The RDF is accessible via a SPARQL endpoint that you can query directly. The RDF dataset includes a collection of publications from MedLine and PMC Central. Each publication is semantically annotated with concepts extracted from standard ontologies or terminologies.
Annotations link a concept to a publication and to a specific location within the document (e.g., title, keywords, abstract, or sentence in the full text when available). The set of annotated publications available here represents the union of publications referenced by key SIB resources such as UniProtKB, Rhea, SwissLipids, and Cellosaurus. These resources also have their own SPARQL endpoints. Together, this enables federated queries that connect curated statements with the semantic content of supporting publications.
The pages on this website are designed to help you become familiar with the SIBiLS RDF dataset, connect to its services, and query the system. Below is a brief description of the content you will find on each page accessible from the website’s menu.
this page :)
A sandbox to learn how to programmatically access some low-level functionalities of the SPARQL endpoint, such as:
in various formats.
[Go to API Methods page]The documentation page of the SIBiLS RDF ontology. An RDF ontology is a formal, structured representation of knowledge based on the Resource Description Framework (RDF) model. It explicitly defines domain-specific concepts - such as classes and properties - enabling data to be described with meaningful semantics that both humans and machines can interpret. The SIBiLS ontology is expressed in OWL (Web Ontology Language). Its classes and properties are specifically designed to describe all the information regarding the annotated publications contained in the SIBiLS RDF dataset.
[Go to Ontology page]The Concept Hopper, a data model browser, is a tool that provides an alternative view of the SIBiLS RDF ontology and data. It focuses on a single concept at a time - either a class or a property - and shows how that concept is linked to others within the ontology, as well as how it appears in the data. For example, it reveals how many times a particular class is instantiated or which properties are used to describe instances of that class.
[Go to Concept Hopper page]The RDF dereferencing service is the mechanism that, given a URI, returns an RDF description of the resource identified by that URI, enabling clients to retrieve structured, machine-readable data about the resource from the web in different formats. For example, if a URI identifies a publication, dereferencing that URI via the dereferencing service returns a collection of RDF triples describing that publication’s properties. This enables applications to navigate and combine data dynamically from multiple sources. The page describes more into the details how to use the service.
[Go to Dereferencing page]The page gives access to the files that you need if you are interested of downloading the full SIBiLS RDF for example to load it into your own triple store.
[Go to Downloads page]The SPARQL Editor is a tool designed to assist users in developing their SPARQL queries. Its primary function is to send queries to the SIBiLS SPARQL service, but it also offers several useful features, including multiple reusable and editable query examples, automatic prefix insertion, context-aware autocomplete while editing, and local storage of user queries.
[Go to SPARQL Editor page]This page explains how to connect programmatically to the SPARQL service including bash and python code example.
[Go to SPARQL service page]