EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

Uses of wonder in popular science : Cosmos: A Personal Voyage and the origin of life

This paper analyses the use of wonder in the TV-series Cosmos: A Personal Voyage (1980). Popular science has been studied extensively (e.g. Broks 2006; Leane 2007; Perrault 2013), and wonder has been studied moderately (e.g. Daston & Park 1998; Fuller 2006; Vasalou 2015). However, there are very few studies of wonder in popular science. This paper explores how and why wonder is used in Cosmos, with the wider aim of understanding uses of wonder in popular science. The studies that discuss wonder in popular science (Fahnestock 1986; Perrault 2013) argue that wonder is used to enthuse the audience about science, but they do not discuss why wonder has this ability, nor whether wonder has other functions. This paper argues that Fuller's (2006) psychological and evolutionary account of wonder can elucidate why wonder has the ability to enthuse; it discerns three senses of ‘wonder’ (related to objects, emotions and attitudes); and it discusses other functions of wonder (existential, aesthetic and ethical). Due to the centrality of astrobiological questions in Cosmos, this paper also highlights the relation of these questions to the senses and functions of wonder in Cosmos

Whose Mass is it Anyway? Particle Cosmology and the Objects of Theory

Physicists in different branches of the discipline were puzzled by the problem of mass during the 1950s and 1960s: why do objects have mass? Around the same time, yet working independently, specialists in gravitational studies and in particle theory proposed that mass might arise due to objects’ interactions with a new (and as yet undetected) field. Although the questions they posed and even the answers they provided shared several similarities - and even though both proposals quickly became ‘hot topics’ in their respective subfields - virtually no one discussed one proposal in the light of the other for nearly 20 years. Only after massive, unprecedented changes in pedagogical infrastructure rocked the discipline in the early 1970s did a new generation of physicists begin to see possible links between the Brans-Dicke field and the Higgs field. For the new researchers, trained in different ways than most of their predecessors, the two objects of theory were not only similar - some began to proclaim that they were exactly the same. Charting the histories of these two objects of theory illuminates the complicated institutional and pedagogical factors that helped to produce a new subfield, particle cosmology, which today ranks at the very forefront of modern physics