Job Description *
The Department of Animal and Aquacultural Sciences seeks a bioinformatician with skills in ontological annotation, semantic interoperability and knowledge management (Researcher, 3 years with possibility of extension). The successful candidate will be central in establishing a knowledge base for the systems biology of farmed salmon, and will work within the Centre for Integrative Genetics (CIGENE).
The project “Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)” is part of Digital Life Norway, the first call dedicated to systems biology by the Research Council of Norway. Effective management of data and model resources is key in this endeavour, and DigiSal will initiate The Digital Salmon: a knowledge base of salmon genetics and physiology, interfacing closely with complementary databases, repositories, and research infrastructures such as ELIXIR. It will eventually encompass a coherent digital and mathematical representation of the salmon body, which can be adjusted to represent individuals with different genetic make-ups, populations, disease states, feeding regimes, or other scenarios of interest. A separate, but related part of the salmon knowledge base will address the metagenomics of the microbiota of the salmon gut. The use of standard formats and ontological annotation enables new knowledge to automatically connect to that which already exists, aiding discoverability and reuse of knowledge. This knowledge base will enable aquaculture industry to quickly address emerging challenges, quickly reanalysing existing data and identifying knowledge gaps to rapidly acquire required new data.
The successful applicant will help design the architecture of the Digital Salmon knowledge base, in close interaction with the researchers that will contribute to and benefit from the knowledge base, and with partners that provide technical solutions. The latter include FAIRDOM, who provide the SEEK commons as part of their knowledge management platform (http://fairdomhub.org), and will work with the DigiSal team to assist with adaptations required to support DigiSal Project; the ELIXIR node at NMBU, with focuses primarily on the salmon genome; the ELIXIR node for marine metagenomics in Tromsø; and the Digital Life Norway network. Users include bioinformaticians and wet-lab researchers who generate various omics data and microscopy images, and systems biologists who develop physiological models, in particular constraint-based models of salmon metabolism.
Further tasks include:
- Training project participants in use of The SEEK for a) extracting and analyzing information and b) entering new information
- Annotating resources for semantic interoperability: a) resources generated in DigiSal b) from literature etc
- Assisting researchers in establishing best practice structuring of data using community standards.