title: On the formalization and reuse of scientific research.
abstract: The reuse of scientific knowledge obtained from one investigation in another investigation is basic to the advance of science. Scientific investigations should therefore be recorded in ways that promote the reuse of the knowledge they generate. The use of logical formalisms to describe scientific knowledge has potential advantages in facilitating such reuse. Here, we propose a formal framework for using logical formalisms to promote reuse. We demonstrate the utility of this framework by using it in a worked example from biology: demonstrating cycles of investigation formalization [F] and reuse [R] to generate new knowledge. We first used logic to formally describe a Robot scientist investigation into yeast (Saccharomyces cerevisiae) functional genomics [f(1)]. With Robot scientists, unlike human scientists, the production of comprehensive metadata about their investigations is a natural by-product of the way they work. We then demonstrated how this formalism enabled the reuse of the research in investigating yeast phenotypes [r(1) = R(f(1))]. This investigation found that the removal of non-essential enzymes generally resulted in enhanced growth. The phenotype investigation was then formally described using the same logical formalism as the functional genomics investigation [f(2) = F(r(1))]. We then demonstrated how this formalism enabled the reuse of the phenotype investigation to investigate yeast systems-biology modelling [r(2) = R(f(2))]. This investigation found that yeast flux-balance analysis models fail to predict the observed changes in growth. Finally, the systems biology investigation was formalized for reuse in future investigations [f(3) = F(r(2))]. These cycles of reuse are a model for the general reuse of scientific knowledge.
authors.affiliation: Department of Computer Science, Aberystwyth University, Wales SY23 3DB, UK. rdk@aber.ac.uk
authors.forename: Ross D
authors.initials: RD
authors.lastname: King
authors.forename: Maria
authors.initials: M
authors.lastname: Liakata
authors.forename: Chuan
authors.initials: C
authors.lastname: Lu
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
authors.forename: Larisa N
authors.initials: LN
authors.lastname: Soldatova
mesh_terms: D035843:Biomedical Research / Q000379:methods*; D003198:Computer Simulation; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal / Q000502:physiology; D023281:Genomics / Q000379:methods*; D033181:Information Dissemination / Q000379:methods*; D008962:Models, Theoretical; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D049490:Systems Biology / Q000379:methods
chemical_list: D005656:Fungal Proteins