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k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction

View ORCID ProfileChristopher J. Mungall, Sebastian Koehler, Peter Robinson, Ian Holmes, View ORCID ProfileMelissa Haendel
doi: https://doi.org/10.1101/048843
Christopher J. Mungall
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, MS977, 1 Cyclotron Road, Berkeley, CA 94720 USA
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  • ORCID record for Christopher J. Mungall
Sebastian Koehler
2Institute for Medical and Human Genetics, Charite-Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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Peter Robinson
2Institute for Medical and Human Genetics, Charite-Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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Ian Holmes
3Department of Bioengineering, University of California, Berkeley, CA, USA
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Melissa Haendel
4Department of Medical Informatics & Clinical Epidemiology, Oregon Health and Sciences University, Portland, Oregon, USA
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  • ORCID record for Melissa Haendel
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ABSTRACT

One strategy for building ontologies covering domains such as disease or anatomy is to weave together existing knowledge sources (databases, vocabularies and ontologies) into single cohesive whole. A first step in this process is to generate mappings between the elements of these different sources. There are a number of well-known techniques for generating mappings (also known as ontology alignemnt), both manual and automatic[7]. Sometimes mappings are seen as an end in themselves, with the sources remaining in a loosely connected state. However, if we want to take the next step and use the mappings to integrate the different sources into a cohesive reference ontology, then we need to translate the mappings into precise logical relationships. This will allow us to safely merge equivalent concepts, creating a unified ontology. This translation is a non-trivial step, as each mapping can be interpreted as multiple different logical relationships, with each interpretation affecting the likelihood of the others. There is a lack of automated methods to assist with this last step; this resolution is typically performed by expert ontologists.

Here we describe an ontology construction technique that takes two or more ontologies linked by hypothetical axioms, and estimates the most likely unified logical ontology. Hypothetical axioms can themselves be derived from semantically loose mappings. The method combines deductive reasoning and probabilistic inference and is called Bayesian OWL Ontology Merging (BOOM). We describe a special form k-BOOM that works by factorizing the probabilistic ontology into k submodules. We also briefly describe a supplemental lexical and knowledge-based technique for generating a set of hypothetical axioms from loose mappings.

We are currently using this technique to build a merged disease ontology (Monarch Disease Ontology; MonDO) that unifies a broad range of vocabularies into a consistent and coherent whole.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 29, 2019.
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k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction
Christopher J. Mungall, Sebastian Koehler, Peter Robinson, Ian Holmes, Melissa Haendel
bioRxiv 048843; doi: https://doi.org/10.1101/048843
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k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction
Christopher J. Mungall, Sebastian Koehler, Peter Robinson, Ian Holmes, Melissa Haendel
bioRxiv 048843; doi: https://doi.org/10.1101/048843

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