Data and model management needs for a knowledge base of salmon physiology: The Digital Salmon

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By Tina Graceline and Jon Olav Vik, Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences.

Systems biology for salmon farming is the topic of the Digital Salmon, a FAIRDOM partner and active user of FAIRDOMHub.org. Our use-case was highlighted at the first FAIRDOM user meeting in Barcelona, 15 Sept 2016. The Digital Salmon currently has two projects, DigiSal and GenoSysFat, which comprise a model-driven, tightly integrated theoretical-experimental study of mechanistic interactions among genetic and feed factors. By combining experiment and modelling we aim to deliver a predictive understanding of a whole range of possible diets, much more efficiently than by traditional feeding trials alone. From a data management perspective, we have a lot of data and models that can potentially be linked via common languages; genes code for enzymes, which catalyze biochemical reactions, which transform molecules whose concentrations we can manipulate, measure and model.

Atlantic salmon farming generates approximately 6 billion euro every year and is projected to generate 20 billion euro in 2050. To support this growth, many challenges must be addressed. Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, climate change, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal lays the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology along with genomics and experimental biology. We chose to begin with the challenges associated with novel feedstuffs.

Salmon are carnivores but today aquaculture provides more than half their fat and protein from plants, challenging the metabolic system and affecting fish health and nutritional value of salmon meat. The effects of the novel feed ingredients on the salmon body are complex and involve many organs. The newly sequenced salmon genome and related resources will enable a tightly integrated theoretical-experimental study of mechanistic interactions among genetic and feed factors. This brings us to systems biology: understanding the living body as a set of components that both affect each other and depend on each other. By combining experiment and modelling we aim to deliver a predictive understanding of a whole range of possible diets, much more efficiently than by traditional feeding trials alone.

In late 2015, the Digital Salmon became a FAIRDOM partner. We have been using the FAIRDOMHub, an online instance of the SEEK software, and it has proved very useful in contextualizing our research assets—data, operating procedures, and models—in an investigation-study-assay structure, adapted to our research. We have saved much time and explanation and avoided many misunderstandings by being able to point coworkers to a data file that automatically links to experimental protocols and the wider research motivation.

Members of the FAIRDOM team have provided training, help, and advice on planning how we should structure and manage our data within the FAIRDOMHub. We are currently seeking a dedicated biosemantician to improve the semantic interoperability of our data and ultimately our ability to query over related data. If this sounds like an attractive challenge to you, please contact project leader Jon Olav Vik.

The project also faces difficult design decisions in managing large, non-public data. The raw data make up a few TB per year, and we would prefer to catalogue rather than store this data in the FAIRDOMHub, perhaps linking to our homebrew, lightweight LIMS system which keeps track of our biological samples. We are also eagerly anticipating FAIRDOM development in interfacing the SEEK with Git version control of analysis reports and computer code, and programmatic access to data and models on the FAIRDOMHub.

Overall, FAIRDOM software and expertise has greatly improved our ability to implement data and model management protocol across our project. We see this being hugely valuable as our project matures. We’re looking forward to growing our relationship with the FAIRDOM team, in particular our contact persons Natalie Stanford and Stuart Owen.

DigiSal is funded by the Research Council of Norway grant 248792 as part of its Digital Life initiative. It is hosted by the Norwegian University of Life Sciences, with partners at universities in Trondheim, Bergen, Tromsø, Wageningen and Stirling, the Institute for Marine Research, and the industry companies AquaGen and EWOS. We also collaborate closely with the Foods of Norway centre for research-driven innovation.