@conference {ICBO_2018_22, title = {ICBO_2018_22: Reconciling ontology definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP framework}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

Many bio-ontologies use formal, logical definitions to automate multiple inheritance classification and drive cross-ontology inference. This requires the use of standardised design patterns: shared patterns of axiomatisation using common reference ontologies. Developing, managing and implementing a suitably consistent set of design patterns can be challenging. In many phenotype ontologies, for example, a large proportion of class terms have formal definitions following a general framework, known as entity/quality (EQ), with common relations and reference ontologies. Despite this, the formal definitions used are often too divergent to drive classification and cross-ontology inference. Here we present software tools for improving and managing formalisation using design patterns. The Ontology Pattern Reconciliation Workbench helps users prioritise patterns for reconciliation between two related ontologies based on the impact pattern reconciliation will have on cross-ontology mapping. An extension to the ontology starter kit provides a practical workflow for developing ontologies using formally specified design patterns.

}, keywords = {entity/quality definitions, logical definitions, ontology design patterns, pattern reconciliation, phenotype ontologies}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_22.pdf }, author = {Nicolas Matentzoglu and David Osumi-Sutherland} } @conference {ICBO_2018_40, title = {ICBO_2018_40: Human Cell Atlas Ontology}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

The Human Cell Atlas (HCA) project aims to build comprehensive reference maps of Human cells that will further our understanding of biological processes and diagnosing and treating disease. We present the Human Cell Atlas Ontology (HCAO), an application ontology that builds and extends from existing ontology standards to provide terminology standards with well-defined semantics for describing experimental data coming into the HCA to ensure the data is interoperable and amenable to integrative analysis.

}, keywords = {application ontology, data interoperability, Human Cell Atlas}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_40.pdf }, author = {Danielle Welter and Simon Jupp and David Osumi-Sutherland} }