Linked Science is a practice of integrating and aggregating structured information in physical, chemical, biological, sociological, and other traditional fields of scientific study. Much of this data does not live in the cloud, but rather in organizational data centers that provide tools and add value by cleaning, validating, curating, disseminating, and analyzing the data. In this paper, we focus on the data in Earth and Climate Sciences and on the use of ontologies to facilitate search and integration of this data. Mercury is a distributed metadata harvesting, search and retrieval tool developed at Oak Ridge National Laboratory. It currently provides uniform access to more than 100,000 metadata records. We have augmented search in Mercury with ontologies, such as the ontologies in the Semantic Web for Earth and Environmental Terminology collection. BioPortal, developed at Stanford University, is used as an infrastructure to store and access ontologies. BioPortal REST services are used to enable faceted search based on the structure of the ontologies, and to improve the accuracy of user queries.