Abstract:
Replication and corroboration of experimental results is an integral part of the scientific process, but in the biosciences, recent renewed scrutiny has revealed somewhat of a reproducibility crisis. The promise of eScience - the application of computer technology to improve research practice throughout all stages of the research cycle, including the ability to more easily share, understand, and reuse knowledge generated by others - is clearly falling short when it comes to supporting laboratory experiments. Typically, eScience solutions to problems of describing, sharing, and integrating scientific artefacts entail the use of ontologies and workflow management systems. These alone however, cannot always provide sufficient knowledge to support the human reasoning and situated comprehension needed to help us reuse such artefacts effectively. Wet-lab experiments are executed in non-computational, heterogeneous surroundings, and we need alternate ways to organise and represent laboratory knowledge in meaningful ways. In this thesis we undertake a thorough investigation into the nature of laboratory knowledge, contributing a clearer understanding and delineation of the kinds of knowledge that are important, uncovering what is missing from our record, and showing what we need to do in order to capture more of it. We introduce the notion of design patterns as an alternate knowledge representation framework, compare them to existing approaches such as ontologies, and show how they are better suited to capture the knowledge we require. We then extend design patterns into the domain of laboratory science, providing a method for knowledge elicitation, and a structured representation for them in the form of Linked Data. Finally, we demonstrate how design patterns can be used to restore aspects of laboratory knowledge currently missing from our record. This work provides us with an alternate and pragmatic solution to the problem of sharing, understanding, and reusing a laboratory experiment, and the inclusion of design patterns alongside other eScience approaches adds to our knowledge representation tools, and can improve the epistemological adequacy of our record. It is our hope that other domains and endeavours where complex design knowledge is intrinsic can also benefit from the new representations and ways of thinking introduced in this thesis.