Glossary

Knowledge Graph

A collection of subject, predicate object relation triples.

Ontology

Studer, Benjamins, and Fensel (1998) describes an ontology as being a ‘formal, explicit specification of a shared conceptualisation’. This refers to the understanding of a topic, being a machine readable version of a model obtained by consensus. An ontology is commonly used to store the rules of a graph database

SPARQL Protocol And RDF Query Language (SPARQL)

A query language for RDF files. An example of an SPARQL query might be:

PREFIX abc: <nul://sparql/exampleOntology#> .
SELECT ?capital ?country
WHERE {
  # All things that have a city name and are a capital.
  ?x abc:cityname ?capital ;
     abc:isCapitalOf ?y.
  # All things that have a country name and are in Africa.
  ?y abc:countryname ?country ;
     abc:isInContinent abc:Africa.
}

Which retrieves a list of African countries and their capital city. For further reading see

“Wikidata:SPARQL Tutorial - Wikidata” (n.d.)
The wikidata SPARQL tutorial, rich with examples to learn with.
“Course: Querying SIB Resources with SPARQL” (n.d.)
Overview of different biological SPARQL endpoints.
Sima et al. (2020)
A guide on how to query for evolutionary relationships.

R programming language

A scientific progamming language oriented towards statistics and data visualisation. Installation guide here. An entry level guide on R is available here.

Resource Description Framework (RDF)

A file from the W3C organisation. This file format can store a large variety of information in a self describing manner. Information is stored in the form of subject, predicate, object relations (see example of Figure 0.1).

A RDF graph encoding the contact details of Erik Miller. The statement 'Erik is a doctor' is encoded as 'eric:me contact:personalTitle Dr.'

Figure 0.1: A RDF graph encoding the contact details of Erik Miller. The statement ‘Erik is a doctor’ is encoded as ‘eric:me contact:personalTitle Dr.’

An rdf file of Figure 0.1 is:

@prefix eric:    <http://www.w3.org/People/EM/contact#> .
@prefix contact: <http://www.w3.org/2000/10/swap/pim/contact#> .
@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

eric:me contact:fullName "Eric Miller" .
eric:me contact:mailbox <mailto:e.miller123(at)example> .
eric:me contact:personalTitle "Dr." .
eric:me rdf:type contact:Person .

This file begins with namespace definitions, indicating where more information about that group of variables can be found.

Further reading:

  • “RDF 1.2 Concepts and Abstract Syntax” (n.d.)

References

“Course: Querying SIB Resources with SPARQL.” n.d. Accessed September 19, 2023. https://edu.sib.swiss/course/view.php?id=440.
“RDF 1.2 Concepts and Abstract Syntax.” n.d. Accessed September 19, 2023. https://www.w3.org/TR/rdf12-concepts/.
Sima, Ana Claudia, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, and Tarcisio Mendes de Farias. 2020. “A Hands-on Introduction to Querying Evolutionary Relationships Across Multiple Data Sources Using SPARQL.” F1000Research 8 (July): 1822. https://doi.org/10.12688/f1000research.21027.2.
Studer, Rudi, V. Richard Benjamins, and Dieter Fensel. 1998. “Knowledge Engineering: Principles and Methods.” Data & Knowledge Engineering 25 (1): 161–97. https://doi.org/10.1016/S0169-023X(97)00056-6.
“Wikidata:SPARQL Tutorial - Wikidata.” n.d. Accessed September 19, 2023. https://www.wikidata.org/wiki/Wikidata:SPARQL_tutorial.