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First steps towards semantic descriptions of electronic laboratory notebook records.

ABSTRACT: In order to exploit the vast body of currently inaccessible chemical information held in Electronic Laboratory Notebooks (ELNs) it is necessary not only to make it available but also to develop protocols for discovery, access and ultimately automatic processing. An aim of the Dial-a-Molecule Grand Challenge Network is to be able to draw on the body of accumulated chemical knowledge in order to predict or optimize the outcome of reactions. Accordingly the Network drew up a working group comprising informaticians, software developers and stakeholders from industry and academia to develop protocols and mechanisms to access and process ELN records. The work presented here constitutes the first stage of this process by proposing a tiered metadata system of knowledge, information and processing where each in turn addresses a) discovery, indexing and citation b) context and access to additional information and c) content access and manipulation. A compact set of metadata terms, called the elnItemManifest, has been derived and caters for the knowledge layer of this model. The elnItemManifest has been encoded as an XML schema and some use cases are presented to demonstrate the potential of this approach.

SUBMITTER: Coles SJ

PROVIDER: S-EPMC3878183 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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First steps towards semantic descriptions of electronic laboratory notebook records.

Coles Simon J SJ Frey Jeremy G JG Bird Colin L CL Whitby Richard J RJ Day Aileen E AE

Journal of cheminformatics 20131220 1

In order to exploit the vast body of currently inaccessible chemical information held in Electronic Laboratory Notebooks (ELNs) it is necessary not only to make it available but also to develop protocols for discovery, access and ultimately automatic processing. An aim of the Dial-a-Molecule Grand Challenge Network is to be able to draw on the body of accumulated chemical knowledge in order to predict or optimize the outcome of reactions. Accordingly the Network drew up a working group comprisin ...[more]

PMID: 24360292

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Project description:BackgroundAsthma severity is typically assessed through a retrospective assessment of the treatment required to control symptoms and to prevent exacerbations. The joint British Thoracic Society and Scottish Intercollegiate Guidelines Network (BTS/SIGN) guidelines encourage a stepwise approach to pharmacotherapy, and as such, current treatment step can be considered as a severity categorisation proxy. Briefly, the steps for adults can be summarised as: no controller therapy (Step 0), low-strength Inhaled Corticosteroids (ICS; Step 1), ICS plus Long-Acting Beta-2 Agonist (LABA; Step 2), medium-dose ICS + LABA (Step 3), and finally either an increase in strength or additional therapies (Step 4). This study aimed to investigate how BTS/SIGN Steps can be estimated from across a large cohort using electronic prescription records, and to describe the incidence of each BTS/SIGN Step in a general population.MethodsThere were 41,433,707 prescriptions, for 671,304 individuals, in the Asthma Learning Health System Scottish cohort, between 1/2009 and 3/2017. Days on which an individual had a prescription for at least one asthma controller (preventer) medication were labelled prescription events. A rule-based algorithm was developed for extracting the strength and volume of medication instructed to be taken daily from free-text data fields. Asthma treatment regimens were categorised by the combination of medications prescribed in the 120 days preceding any prescription event and categorised into BTS/SIGN treatment steps.ResultsAlmost 4.5 million ALHS prescriptions were for asthma controllers. 26% of prescription events had no inhaled corticosteroid prescriptions in the preceding 120 days (Step 0), 16% were assigned to BTS/SIGN Step 1, 7% to Step 2, 21% to Step 3, and 30% to Step 4. The median days spent on a treatment step before a step-down in treatment was 297 days, whereas a step-up only took a median of 134 days.ConclusionWe developed a reproducible methodology enabling researchers to estimate BTS/SIGN asthma treatment steps in population health studies, providing valuable insights into population and patient-specific trajectories, towards improving the management of asthma.

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First steps towards semantic descriptions of electronic laboratory notebook records.

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First steps towards semantic descriptions of electronic laboratory notebook records.

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