论文信息 - Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns

Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns

The Human Phenotype Ontology (HP) and Mammalian Phenotype (MP) Ontology represent information about abnormal phenotypes encountered in human diseases and mammalian organisms, respectively. It is a goal to codevelop these ontologies and align the terminology and logical axioms to increase interoperability of the two ontologies. Towards this end, we have worked to develop consistent design patterns for commonly used types of classes, such as morphological phenotypes or abnormal anatomical structures. We are currently implementing ‘dead simple ontology design patterns’ (DOSDP), which are design patterns that can be specified in a YAML text file and can be used to generate new terms, documentation, retrofit old terms, and allows for reuse of patterns. This paper describes the development and implementation of the DOSDP in the HP and MP.

[1] Damian Smedley,et al. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. , 2013, F1000Research.

[2] Chris Mungall,et al. Dead simple OWL design patterns , 2017, J. Biomed. Semant..

[3] Cynthia L. Smith,et al. Integrating phenotype ontologies across multiple species , 2010, Genome Biology.

[4] Cynthia L. Smith,et al. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information , 2004, Genome Biology.