Ontology Alignment Evaluation Initiative - OAEI-2017.5 Campaign


General description

The Anatomy track consists of finding an alignment between the Adult Mouse Anatomy and a part of the NCI Thesaurus (describing the human anatomy). The task is placed in a domain where we find large, carefully designed ontologies that are described in technical terms. Besides their large size and a conceptualization that is only to a limited degree based on the use of natural language, they also differ from other ontologies with respect to the use of specific annotations and roles, e.g. the extensive use of the partOf relation. The manual harmonization of the ontologies leads to a situation, where we have a high number of rather trivial mappings that can be found by simple string comparison techniques. At the same time, we have a good share of non-trivial mappings that require a careful analysis and sometimes also medical background knowledge.

The anatomy track in OAEI 2017.5 consists of the default task to match the two ontologies of the anatomy track with the standard configuration of your matching system. We will use HOBBIT platform to evaluate systems.

In the past, we have evaluated matching systems with respect to their ability to exploit an input alignment (= partial reference alignment). We will include this modality of evaluation, in case it is requested prior to the final deadline by at least three participants. In case your tool offers such a functionality and you want it to be evaluated, please write a mail to the track organizers (mail see at the bottom of this page).

Data sets and HOBBIT Supporting Evaluation

It is highly recommended that you run local tests to see whether your matching system can cope with the dataset. There are two options:

(1) You can download the whole dataset and run your tests with this input data.

(2) However, finally you have to wrap your tool according to HOBBIT platform and run this client against the Anatomy Benchmark (See example of LogMap wrapping for HOBBIT). For running the Anatomy testsuite you will have to add the following Benchmark API parameter in your system's metadata description (system.ttl) when you create your system adapter. To run your system in anatomy track under HOBBIT platform, you can follow the tutorial here.

Related Links


This track is organized by Huanyu Li, and Patrick Lambrix. If you have any problems working with the ontologies, any questions related to tool wrapping, or any suggestions related to the anatomy track, feel free to write an email to oaei-anatomy [at] ida [.] liu [.] se.


[1] Oliver Bodenreider, Terry F. Hayamizu, Martin Ringwald, Sherri De Coronado, Songmao Zhang. Of mice and men: Aligning mouse and human anatomies. Proceedings of the American Medical Informatics Association (AIMA) Annual Symposium, 2005.

[2] Elena Beisswanger, Udo Hahn. Towards valid and reusable reference alignments - Ten basic quality checks for ontology alignments and their application to three different reference data sets. Journal of Biomedical Semantics, 2012.

[3] Jerome Euzenat, Christian Meilicke, Heiner Stuckenschmidt, Pavel Shvaiko, Cassia Trojahn. Ontology Alignment Evaluation Initiative: Six Years of Experience. Journal of Data Semantics, 2011.