Semantic web in chemistry and biology - P143004
Title: Sémantický web v chemii a biologii
Guaranteed by: Department of Informatics and Chemistry (143)
Actual: from 2019
Semester: summer
Points: summer s.:0
E-Credits: summer s.:0
Examination process: summer s.:
Hours per week, examination: summer s.:3/0 other [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: doctoral
Guarantor: Galgonek Jakub RNDr. Ph.D.
Is interchangeable with: AP143004
Examination dates   Schedule   
Annotation -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)
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: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

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: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

R: R. Cyganiak, D. Wood, M. Lanthaler, RDF 1.1 Concepts and Abstract Syntax, https://www.w3.org/TR/rdf11-concepts/.

R: S. Harris, A. Seaborne, SPARQL 1.1 Query Language, https://www.w3.org/TR/sparql11-query/.

R: P. Hitzler, M. Krötzsch, B. Parsia, P. F. Patel-Schneider, S. Rudolph, OWL 2 Web Ontology Language Primer (Second Edition), https://www.w3.org/TR/owl2-primer/.

A: D Brickley, R.V. Guha, RDF Schema 1.1, https://www.w3.org/TR/rdf-schema/.

A: S. Das, S. Sundara, R. Cyganiak, R2RML: RDB to RDF Mapping Language, https://www.w3.org/TR/r2rml/.

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

Learning resources -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

Online course materials

Syllabus -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

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: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

None

Course completion requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

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