Encouraging and Facilitating Laboratory Scientists to Curate at Source

Computers and computation have become essential to scientific activity and significant amounts of data are now captured digitally or even “born digital”. Consequently, there is more and more incentive to capture the full experiment records using digital tools, such as Electronic Laboratory Notebooks (ELNs), to enable the effective linking and publication of experiment design and methods with the digital data that is generated as a result. Inclusion of metadata for experiment records helps with providing access, effective curation, improving search, and providing context, and further enables effective sharing, collaboration, and reuse. Regrettably, just providing researchers with the facility to add metadata to their experiment records does not mean that they will make use of it, or if they do, that the metadata they add will be relevant and useful. Our research has clearly indicated that researchers need support and tools to encourage them to create effective metadata. Tools, such as ELNs, provide an opportunity to encourage researchers to curate their records during their creation, but can also add extra value, by making use of the metadata that is generated to provide capabilities for research management and Open Science that extend far beyond what is possible with paper notebooks. The Southampton Chemical Information group, has, for over fifteen years, investigated the use of the Web and other tools for the collection, curation, dissemination, reuse, and exploitation of scientific data and information. As part of this activity we have developed a number of ELNs, but a primary concern has been how best to ensure that the future development of such tools is both usable and useful to researchers and their communities, with a focus on curation at source. In this paper, we describe a number of user research and user studies to help answer questions about how our community makes use of tools and how we can better facilitate the capture and curation of experiment records and the related resources

User-Defined Metadata: Using Cues and Changing Perspectives

User-defined metadata is useful for curating and helping to provide context for experiment records, but our previous investigations have demonstrated that simply providing the facility to add metadata is not enough to ensure that metadata is added, let alone to ensure that the metadata is of high quality. For metadata to be useful it first has to be present, but enforcing metadata generation is of no benefit if it is low quality, inconsistent, or irrelevant. Researchers need support. One strategy to encourage more effective metadata creation is to design user interfaces that invite users to add metadata by asking them questions. If we ask users specific questions about their experiments and other activities then we could capture more relevant or useful metadata, although there is a risk that asking the wrong questions may lead to loss of valuable metadata terms or the creation of irrelevant material. In this paper we report on a study to investigate how different questions could be used to generate metadata by eliciting information in three different conditions: free recall, changing perspective by thinking about search terms to help someone else, and providing cues by using a set of topic-based questions. We also investigate how responses varied with different information types. The results of the study show that different terms are created under the different conditions, as expected. The use of cues generates the highest numbers of terms and the most diverse range, including elements that are not captured in other conditions. However, important themes generated in other conditions are not produced because the cues to create them are missing. The study also generated a number of unexpected findings, including responses describing information that is not in the original material: personal opinions and experiences, and comments about the information text itself. These unexpected responses have both positive and negative consequences for the generation of metadata and the curation of scientific records. The results of studies using these techniques to capture metadata for chemistry experiments are also discussed

Using Metadata Actively

Almost all researchers collect and preserve metadata, although doing so is often seen as a burden. However, when that metadata can be, and is, used actively during an investigation or creative process, the benefits become apparent instantly. Active use can arise in various ways, several of which are being investigated by the Collaboration for Research Enhancement by Active use of Metadata (CREAM) project, which was funded by Jisc as part of their Research Data Spring initiative. The CREAM project is exploring the concept through understanding the active use of metadata by the partners in the collaboration. This paper explains what it means to use metadata actively and describes how the CREAM project characterises active use by developing use cases that involve documenting the key decision points during a process. Well-documented processes are accordingly more transparent, reproducible, and reusable.

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Recording science in the digital era: From paper to electronic notebooks and other digital tools

For most of the history of scientific endeavour, science has been recorded on paper. In this digital era, however, there is increasing pressure to abandon paper in favour of digital tools. Despite the benefits, there are barriers to the adoption of such tools, not least their usability. As the relentless development of technology changes the way we work, we need to ensure that the design of technology not only overcomes these barriers, but facilitates us as scientists and supports better practice within science. This book examines the importance of record-keeping in science, current record-keeping practices, and the role of technology for enabling the effective capture, reuse, sharing, and preservation of scientific data.Covering the essential areas of electronic laboratory notebooks (ELNs) and digital tools for recording scientific data, including an overview of the current data management technology available and the benefits and pitfalls of using these technologies, this book is a useful tool for those interested in implementing digital data solutions within their research groups or departments. This book also provides insight into important factors to consider in the design of digital tools such as ELNs for those interested in producing their own tools. Finally, it looks at the role of current technology and then considers how that technology might develop in the future to better support scientists in their work, and in capturing and sharing the scientific record

Asking the right questions: Designing digital tools to support researchers recording scientific experiments

The paper notebook is the trusty companion of the majority of those who engage in scientific research. In this digital era though, there is pressure to abandon paper in favour of the benefits of digital tools. For many researchers, particularly in academic environments, there are a number of barriers to adopting Electronic Laboratory Notebooks, not least of which are anxieties about their ease of use. Another concern is the impact using these tools may have on the quality of experiment records. In order to design digital tools that support researchers recording scientific experiments it is necessary to understand how researchers work with paper and digital tools, and the impacts different designs may have upon what they record. In this thesis, research is presented on the note-taking and experiment capture behaviour of a range of scientific researchers together with requirements for digital tools obtained from this research. A number of original studies are presented that explore how different techniques for eliciting information from the memories of researchers can be used to capture information of value to the experiment record, with both positive and negative consequences. This thesis also includes an overview of the development of a mobile ELN, designed for use by synthetic chemists, to explore the potential to bridge the gap between desktop ELNs and paper-notebooks. The conclusions of this thesis put forward suggestions as to how digital tools could be enhanced in the future to both support researchers recording scientific experiments and to facilitate the management of research projects

Effects of using structured templates for recalling chemistry experiments

BACKGROUND: The way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interface for the capture of experiment records through the use of forms and templates. These templates can be useful by providing cues to help researchers to remember to record particular aspects of their experiment, but they may also constrain the information that is recorded by encouraging them to record only what is asked for. It is therefore unknown whether using structured templates for capturing experiment records will have positive or negative effects on the quality and usefulness of the records for assessment and future use. In this paper we report on the results of a set of studies investigating the effects of different template designs on the recording of experiments by undergraduate students and academic researchers. RESULTS: The results indicate that using structured templates to write up experiments does make a significant difference to the information that is recalled and recorded. These differences have both positive and negative effects, with templates prompting the capture of specific information that is otherwise forgotten, but also apparently losing some of the personal elements of the experiment experience such as observations and explanations. Other unexpected effects were seen with templates that can change the information that is captured, but also interfere with the way an experiment is conducted. CONCLUSIONS: Our results showed that using structured templates can improve the completeness of the experiment context information captured but can also cause a loss of personal elements of the experiment experience when compared with allowing the researcher to structure their own record. The results suggest that interfaces for recording information about chemistry experiments, whether paper-based questionnaires or templates in Electronic Laboratory Notebooks, can be an effective way to improve the quality of experiment write-ups, but that care needs to be taken to ensure that the correct cues are provided. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-016-0118-6) contains supplementary material, which is available to authorized users

Knowledge and memory: a study of what students remember about chemistry experiments

The way we recall information is dependent upon the knowledge in our memories and the conditions under which we recall the information. In this study the knowledge that undergraduate students have about chemistry experiments and the impact that changing how they were asked to recall the experiment is examined. The motivation is to understand what students remember about experiments and whether the use of questionnaires improves or impairs the quality of information they capture. The students were second-year undergraduates taking part in a chemistry summer school. They were asked a set of questions before they completed the experiment to elicit their existing knowledge and then asked to produce a write-up of the experiment under two different conditions: using a blank piece of paper or a structured questionnaire. The data from the study was analyzed to determine what about chemistry experiments was more easily remembered, and whether significant differences existed in the write-ups produced under the different conditions. The results indicate that certain types of information about experiments are more prominent in the memories of the students and using a questionnaire to write up the experiment makes significant changes to the information that the students recalled. These differences have both positive and negative effects, with more background knowledge recorded using the questionnaire, but fewer details of the personal experience. Understanding what information about experiments students are more likely to remember and the effects of recall conditions enable questionnaires for recording experiments to be designed to support learning. For example cues can be provided for the parts of the experiment that the students are less likely to remember to include. Also care needs to be taken when using a formal structure to ensure that important personal experiences of their observations, actions, and reasoning are not omitted from their experiment records

Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciences

Egyptian evidence of scientific records dates back almost 50 centuries. In more recent times da Vinci and Faraday provide role models for scrupulous recording of ideas, observations, and conclusions. Their medium was paper, but despite the quality of their notebooks, we cannot turn the clock back. Our primary purpose is to review the influences of the digital era on scientific record keeping. We examine the foundations of the emerging opportunities for preserving and curating electronic records focussing on electronic laboratory notebooks (ELNs), with an emphasis on their characteristics and usability.<br/