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arXiv · 2506.04286

OxO2 -- A SSSOM mapping browser for logically sound crosswalks

Henriette Harmse·Haider Iqbal·Helen Parkinson·James McLaughlin
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Abstract

EMBL-EBI created OxO to enable users to map between datasets that are annotated with different ontologies. Mappings identified by the first version of OxO were not necessarily logically sound, lacked important provenance information such as author and reviewer, and could timeout or crash for certain requests. In this paper we introduce OxO2 to address these concerns. Provenance is addressed by implementing SSSOM, a mapping standard that defines provenance for mappings. SSSOM defines the conditions under which logical sound mappings can be derived and is implemented in OxO2 using Nemo, a Datalog rule engine. To ensure reasoning is performant and memory efficient, Nemo implements a number of strategies that ensures OxO2 will be stable for all requests. Due to these changes, OxO2 users will be able to integrate between disparate datasets with greater confidence.

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Henriette Harmse, Haider Iqbal, Helen Parkinson, James McLaughlin. 2025-09-26. OxO2 -- A SSSOM mapping browser for logically sound crosswalks. https://arxiv.org/abs/2506.04286

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