Frequently Asked Questions

1. What is Ontobee?

Ontobee is a web linked dataa server that serves as linked data for ontology terms. For each ontology term, Ontobee also returns a source page in the RDF format, which supports the Semantic Web. In addition, Ontobee is a web-based browser of ontology terms. Ontobee provides query and visualization of ontology terms and ontology hierarchy.

2. What are the ontology sources used by Ontobee?

The primary ontology source comes from Neurocommons (http://neurocommons.org), a knowledgebase containing all ontologies in OBO foundry. Ontobee also supports ontologies from other data sources. For example, Ontobee maintains a local Virtuoso RDF store that contains several ontologies e.g., the Adverse Event Ontology (AEO).

3. What are the differences between the HTML page and the RDF source file for each ontology term, both generated by Ontobee?

This OWL (RDF/XML) format is the default page format for the term URI. The HTML file is embedded in a XSLT (Extensible Stylesheet Language Transformations) template which is linked to the OWL file. When the term URI was visited by using a web browser, both the OWL file and the HTML content will be retrieved but only the HTML content will be shown in the browser for easy reading. A user can easily access the OWL (RDF/XML) content by check the source code of the term page. Alternatively, the OWL output file can be retrieved by a web application program, or a Semantic Web system. This approach does not need a human visit to the HTML web page.

4. What are the design principles of the Ontobee program?

Ontobee has been developed by following specific design principles. Some specific requirements we are aiming to address with Ontobee are:

• Document and provide a consistent response for each OBO Library ontology.
• Linked Data Browsing
• Per term RDF-XML is valid OWL-DL.
• Includes an import of the full ontology, so the term is clearly defined. LOD browsers can choose whether or not to pay attention to the import.
• All necessary labels included.
• Attribution given, when available.
• No content negotiation - content negotiation confuses the identity of the resource. We prefer different URIs for different encodings.
• Conformance to httpRange-14 or chosen successor.
• Display of ontology developer html in addition, where developers have page-per-term resources.
• Links to or inclusion of additional html material, for example from sources like BioPortal, etc.
  

4. What is Ontobeep?

Ontobeep is an ontology comparison program that is developed based on the basic Ontobee function of serving and browsing linked data for ontology terms. Ontobeep retrieves selected ontologies using SPARQL and display them in a single ontological hierarchy structure. The terms are labeled with following parentheses with the names of specified ontologies that contain these terms. Shared and unique ontology terms among different ontologies are also calculated.