The Semantic Web enables the dissemination of data on the Internet through a common format in order to integrate or combine databases from different sources. The National Institute for Amazonian Research (INPA) has several collections of data, mainly scientific, that can be disclosed and used in the research and development of the Amazon as well as for the advancement of science. The objective of this study is to investigate how the use of Semantic Web technologies, among them the tool Rexplorator, can improve the research process by processing the semantics in collections of biological data. Use cases are developed with input from INPA researchers. Queries are constructed based on RDFS (Resource Description Framework Schema) created for INPAs existing collections. Use cases can be reused by other researchers, including researchers from different fields. In this process of reuse, the customization and collaborative development of use cases is possible. The result of this process is the generation of Web applications that abstract the RDF model on which data are represented. Consequently, other researchers unfamiliar with the RDF model are also able to access information. In addition to enabling semantic queries in databases by lay users in a given field of research, this ease of access enables researchers to make transdisciplinary queries enriching their vision of research development, as well as their power in political, economic and social decision-making, and hence better knowledge management.