Sustainable use of Brazilian biodiversity - Using Linked Data for natural product discovery

• Applicant: Professor Dr. Thomas Riechert
• Subject Area: Data Management, Data-Intensive Systems, Computer Science Methods in Business Informatics
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 459288952

The growth and evolution of our civilization have been based on the use of biodiversity. Human survival was much sustained using plant species, especially for nutrition and medicinal uses. Natural products are the most traditional source for the design and development of new drugs. Taking into account all drugs approved worldwide, 67% are either a natural product, semi-synthetic derivative, macromolecule isolated from an organism or have a pharmacophore group inspired by natural product. Natural products researchers have been studying the medicinal properties of plants and great advances regarding biosynthesis, ecology and biological properties were achieved in the last century. The biodiversity of tropical and equatorial environments is plentiful and could offer a particularly rich potential in the search for biologically active compounds to be used as models for drug discovery and medicinal chemistry. Brazil is a country with one of the greatest bio-diversities in the world, accounting for ca.10% of all living species. It comprises six terrestrial biomes, the Amazonian rainforest, Caatinga, Cerrado (Savanna), Atlantic forest, Pantanal and Pampas. This extraordinary biodiversity and its chemical diversity could be used for the development of bioproducts, including pharmaceuticals, cosmetics, food supplements, and agricultural pesticides. Many species from these biomes are endangered. The chemical diversity of the flora and fauna of the Brazilian Biomes is revealed by a diversity of compound classes and structural types of secondary metabolites from plants, fungi, insects, marine organisms and bacteria. The scientific information published in more than 50 years of studies on Brazilian biodiversity becomes easier to access when standardized, certified and organized in a knowledge graph. As an initial effort, the NuBBEDB was created as the database of compounds from Brazilian biodiversity with the objective of organizing its chemical, biological and pharmacological information. NuBBEDB presently contains data of 2218 compounds, an estimative of 5% of the published information on natural products isolated and identified from species collected in the Brazilian territory. Within this proposal, we would like to investigate the challenges imposed on building, managing, and consuming Biochemical Knowledge Graph (BKG) using Semantic Web Technologies with a focus on the research of new natural products using Brazilian biodiversity through NuBBEDB. We aim to increase the dataset quality by enriching its organization with taxonomies and ontologies through RDF standard, and enrich its information, using other datasets available in the Linked Open Data cloud. Additionally, we propose to increase the dataset management and distribution introducing versioning and licensing as well as apply machine learning on this high-quality information to create better AI models for natural product discovery.

• DFG Programme: Research Grants
• International Connection: Brazil
• Partner Organisation: Fundaçao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP
• Cooperation Partners: Professor Dr. Adriano Defini Andricopulo; Professorin Dr. Vanderlan da Silva Bolzani