SubjectsSubjects(version: 943)
Course, academic year 2023/2024
Semantic web in chemistry and biology - AP143004
Title: Semantic web in chemistry and biology
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2019
Semester: both
Points: 0
E-Credits: 0
Examination process:
Hours per week, examination: 3/0, other [HT]
Capacity: winter:unlimited / unknown (unknown)
summer:unknown / unknown (unknown)Schedule is not published yet, this information might be misleading.
Min. number of students: unlimited
Language: English
Teaching methods: full-time
Teaching methods: full-time
For type: doctoral
Note: course is intended for doctoral students only
can be fulfilled in the future
you can enroll for the course in winter and in summer semester
Guarantor: Galgonek Jakub RNDr. Ph.D.
Interchangeability : P143004
Annotation -
Last update: Pátková Vlasta (08.06.2018)
A course introduces theoretical and practical aspects of Semantic Web technologies used in areas of chemical and biological databases. The Semantic Web was meant to address data interoperability. The interoperability is achieved by the conceptualization of data and storing them according to standardized rules. The key is the creation of ontologies that describe data organizations in various scientific domains. The theoretical part of the lecture is focused on Semantic Web technologies allowing storing, accessing, querying and processing of data. Whereas the practical part of the lecture is focused on ontologies used in chemical and biological databases build on these technologies.
Aim of the course -
Last update: Pátková Vlasta (08.06.2018)

Students will know:

  • Basics principles of semantic databases (in particular Resource Description Framework)
  • The SPARQL query language to select data from databases
  • Federated queries to combine data originating from different databases
  • RDFS and OWL languages to understand data ontologies
  • Selected chemical and biological databases and their ontologies

Literature -
Last update: Pátková Vlasta (08.06.2018)

R: R. Cyganiak, D. Wood, M. Lanthaler, RDF 1.1 Concepts and Abstract Syntax,

R: S. Harris, A. Seaborne, SPARQL 1.1 Query Language,

R: P. Hitzler, M. Krötzsch, B. Parsia, P. F. Patel-Schneider, S. Rudolph, OWL 2 Web Ontology Language Primer (Second Edition),

A: D Brickley, R.V. Guha, RDF Schema 1.1,

A: S. Das, S. Sundara, R. Cyganiak, R2RML: RDB to RDF Mapping Language,

A: B. DuCharme, Learning SPARQL: Querying and Updating with SPARQL 1.1, O'Reilly Media 2013, ISBN 1449371434. (book)

Learning resources -
Last update: Pátková Vlasta (08.06.2018)

Online course materials

Syllabus -
Last update: Pátková Vlasta (08.06.2018)

1. Basics of the Semantic Web (Resource Description Framework)

2. Basics of the SPARQL query language

3. Advanced language constructions of SPARQL

4. Mapping from relational databases to RDF (R2RML)

5. Existing implementations and frameworks (Jena, RDF4J, …)

6. Implementation of user extensions to SPARQL

7. Ontology languages (RDFS, OWL, …)

8. Syntaxes for writing ontologies (RDF, XML, functional and Manchester syntax)

9. Automatic derivation of new data (simple, RDF, RDFS and OWL entailment)

10. Common ontologies (DCMI, CiTO, …)

11. Cheminformatics ontologies (ChEBI, CHEMINF, …)

12. Bioinformatics ontologies (GO, BioPAX, BAO, …)

13. Global identification of database entities

14. Related issues of chemical and biological database interoperability

Registration requirements -
Last update: Pátková Vlasta (08.06.2018)


Course completion requirements -
Last update: Pátková Vlasta (08.06.2018)

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