Semantic Linking of Phenotypes and Environments


One of the fundamental goals of biology is understanding the interactions of environment and phenotype, but this is a surprisingly difficult topic to study – not because of the concepts, but because of the data. Observations about environment and phenotype occur in separate data sets and the terms used are far too idiosyncratic for automated integration. Several biological domains, including conservation and phylogenetics could be advanced if these two data types could be easily merged on a large scale.

I led a recent paper, published in PeerJ, which suggests that the use of ontologies to standardize and link data about phenotypes and environments can enable scientific breakthroughs by increasing the scale and flexibility of research. This paper was a product of a workshop facilitated by the Phenotype RCN and supported by the National Science Foundation. My co-authors and I give several domain-specific use cases describing how an ontology can help advance science in four biological sciences. We then discuss the challenges to be addressed, present some proof-of-concept analyses, and discuss existing ontologies. The summary contains three suggestions for increasing interoperability between phenotype and environment data.

We hope this paper provides you with an overview of the landscape of ontologies available for integrating environmental data, and inspires you to use them in relation to your own data. For more information about ontologies and semantics, a good first read is Semantic Web for the Working Ontologist by Dean Allemang and Jim Hendler.