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Tutorial: Ontobeep for aligment and comparison of ontologies listed in Ontobee

The Ontobeep (http://www.ontobee.org/ontobeep) is a relatively independent tool in Ontobee. Ontobeep is targeted for ontology alignment and comparison of ontologies that are listed in Ontobee. Ontobee is able to display the similarities and differences among selected ontologies. Ontobeep also provides a page to summarize statistical numbers out of the ontologies' alignment and comparison.

Table of Contents

  1. Introduction of ontology alignment, matching, and comparison
  2. Ontobeep features
    1. Ontology alignment and comparison
    2. Display of ontology comparison statistics
  3. Ontology alignment tools, references, and web links
    1. Ontology alignment tools
    2. Books and review articles
    3. Additional web links

1. Introduction of Ontology alignment, matching, and comparison:

Ontology alignment, or ontology matching, is the process of determining correspondences between terms in ontologies. Usually two ontologies are used for alignment.

Historically, the need for ontology alignment originated from the requirement of integrating hetereogeneous databases that were developed independently with own data vocabulary. Ontology alignment tools are able to find ontological classes "semantically equivalent". These classes are not necessarily logically identical.

There are many algorithms and tools available to support ontology alignment and comparison. Each of these tools tend to have different focuses based on dfiferent settings. For example, PROMPT and AlViz are two Protege plugin programs related to ontology alignments, where PROMPT focuses on ontology merging and AlViz focuses on visual ontology alignments. BLOOMS is an ontology alignment system for linked open data (LOD) schema alignment based on the idea of bootstrapping information already present on the LOD cloud. Aligment-API is a Java API and implementation for expressing and sharing ontology alignments. More ontology alignment tools are listed in the section of "Ontology alignment tools" on this web page.

Ontobeep is developed with a different emphasis in mind. Instead of matching different ontology terms by assuming different ontologies naturally use different labels and axioms to represent the same entities (or concepts), Ontobeep is developed by first assuming different ontologies are integrated and reuse terms that already exist in reference ontologies. This assumption is consistent with the OBO Foundry principles, including "FP 005 delineated content" and "FP 010 collaboration". Based on this assumption, Ontobeep aims to support ontology term matching and reuse, compare hierarchical ontology structures, and identify possible redundancy and errors for future fixation.


2. Ontobeep features:

This section introduces individual features of Ontobeep:

(i) Ontology alignment and comparison:

On the cover page of Ontobeep, you will be able to select 2-3 ontologies using the Ontobeep comparison form. For example, here I compared three ontologies: BFO, CLO, and CL:

Ontobeep selection

After clicking the "Compare Selected", you will come to an Ontobeep page where you can click the "Expand One Level Down" or the "+"-containing square boxes to expand the ontology hierarchy. The next screenshot displays some comparison results (generated by Oliver He on 3/22/2014):

Ontobeep ex

As seen in the above screenshot, different ontologies are displayed with different colors, which help you to visualize the shared or unique terms among these ontologies.

In the above page, you can also click "Statistics". Once you do so, you will come to the statistics display as seen below.


(ii) Display of ontology comparison statistics:

The following web page shows you an example term statistics page in Ontobeep. This example compared the term statistics results among BFO, CLO, and CL.

Ontobee term stat

Note that the above screenshot (generated by Oliver He on 3/22/2014) suggests that some ontololgy improvements can possibly be done. For example, some terms have the same term labels and different term URIs. This can be solved by using only one URI and merging the usage of the other URI to this chosen URI.


3. Web links and References:

(i) Ontology alignment tools:

(ii) Selected books and articles:


Back to Ontobee Tutorial page

-- Prepared by Oliver He, 3/22-23/2014.