Intern:Ontologies and Semantics

This is a work in progress page. This wiki page shall serve as an introduction into the topic of ontologies and semantics.

=Definition= to be continued

=Educational material=
 * Introduction and construction of ontologies
 * https://protegewiki.stanford.edu/wiki/Ontology101
 * https://protegewiki.stanford.edu/wiki/Protege4Pizzas10Minutes
 * http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/


 * Introduction into semantic web + data exchange formats
 * https://www.cambridgesemantics.com/blog/semantic-university/
 * https://open.hpi.de/courses/semanticweb2016

=Ontology databases and look-ups= (for life science domain)
 * https://bioportal.bioontology.org/
 * https://www.ebi.ac.uk/ols/index
 * https://terminologies.gfbio.org/
 * http://www.ontobee.org/ (data server for OBO ontologies http://obofoundry.org/)
 * http://aber-owl.net/#/

=Ontology editors and visualization tools=
 * Editor
 * https://protege.stanford.edu/ (ontology editor; desktop and web version)
 * Visualisation (Remark: only functions properly for small ontologies)
 * http://vowl.visualdataweb.org/ (for web or as protégé plugin)

=Important ontologies=
 * https://www.ebi.ac.uk/chebi/ (Chemical Entities of Biological Interest)
 * https://www.nlm.nih.gov/mesh/ (Medical Subject Headings, indexing of publications)
 * http://www.geneontology.org/ (Topic: cell biology, gene functions on molecular, cellular and tissue system level)
 * https://bioportal.bioontology.org/ontologies/ENVO (Environment Ontology)

=PANGAEA presentation= This presentation deals with the different use cases of ontologies within the PANGAEA database (improved search, disambiguation of terms
 * Without notes
 * https://drive.google.com/file/d/10p6LT5-yK1aTpzMP44d6sJ6nbafyBTzA/view?usp=sharing
 * With notes
 * https://drive.google.com/file/d/1NIw40KkY7eEzr42_qm27alXMg0ajHDjy/view?usp=sharing