Dataset Information

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology.

ABSTRACT: Analysis of trends in nanotoxicology data and the development of data driven models for nanotoxicity is facilitated by the reporting of data using a standardised electronic format. ISA-TAB-Nano has been proposed as such a format. However, in order to build useful datasets according to this format, a variety of issues has to be addressed. These issues include questions regarding exactly which (meta)data to report and how to report them. The current article discusses some of the challenges associated with the use of ISA-TAB-Nano and presents a set of resources designed to facilitate the manual creation of ISA-TAB-Nano datasets from the nanotoxicology literature. These resources were developed within the context of the NanoPUZZLES EU project and include data collection templates, corresponding business rules that extend the generic ISA-TAB-Nano specification as well as Python code to facilitate parsing and integration of these datasets within other nanoinformatics resources. The use of these resources is illustrated by a "Toy Dataset" presented in the Supporting Information. The strengths and weaknesses of the resources are discussed along with possible future developments.

SUBMITTER: Marchese Robinson RL

PROVIDER: S-EPMC4660926 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology.

Marchese Robinson Richard L RL Cronin Mark T D MT Richarz Andrea-Nicole AN Rallo Robert R

Beilstein journal of nanotechnology 20151005

Analysis of trends in nanotoxicology data and the development of data driven models for nanotoxicity is facilitated by the reporting of data using a standardised electronic format. ISA-TAB-Nano has been proposed as such a format. However, in order to build useful datasets according to this format, a variety of issues has to be addressed. These issues include questions regarding exactly which (meta)data to report and how to report them. The current article discusses some of the challenges associa ...[more]

PMID: 26665069

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Project description:Background and motivationThe high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.ResultsWe have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.ConclusionThe ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.

Project description:BackgroundReporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that datasets are comprehensible and, in principle, reproducible, comparable and reusable. Furthermore, sharing datasets in formats designed for consumption by humans and machines will also maximize their use. The Investigation/Study/Assay (ISA) open source metadata tracking framework facilitates standards-compliant collection, curation, visualization, storage and sharing of datasets, leveraging on other platforms to enable analysis and publication. The ISA software suite includes several components used in increasingly diverse set of life science and biomedical domains; it is underpinned by a general-purpose format, ISA-Tab, and conversions exist into formats required by public repositories. While ISA-Tab works well mainly as a human readable format, we have also implemented a linked data approach to semantically define the ISA-Tab syntax.ResultsWe present a semantic web representation of the ISA-Tab syntax that complements ISA-Tab's syntactic interoperability with semantic interoperability. We introduce the linkedISA conversion tool from ISA-Tab to the Resource Description Framework (RDF), supporting mappings from the ISA syntax to multiple community-defined, open ontologies and capitalising on user-provided ontology annotations in the experimental metadata. We describe insights of the implementation and how annotations can be expanded driven by the metadata. We applied the conversion tool as part of Bio-GraphIIn, a web-based application supporting integration of the semantically-rich experimental descriptions. Designed in a user-friendly manner, the Bio-GraphIIn interface hides most of the complexities to the users, exposing a familiar tabular view of the experimental description to allow seamless interaction with the RDF representation, and visualising descriptors to drive the query over the semantic representation of the experimental design. In addition, we defined queries over the linkedISA RDF representation and demonstrated its use over the linkedISA conversion of datasets from Nature' Scientific Data online publication.ConclusionsOur linked data approach has allowed us to: 1) make the ISA-Tab semantics explicit and machine-processable, 2) exploit the existing ontology-based annotations in the ISA-Tab experimental descriptions, 3) augment the ISA-Tab syntax with new descriptive elements, 4) visualise and query elements related to the experimental design. Reasoning over ISA-Tab metadata and associated data will facilitate data integration and knowledge discovery.

Project description:BackgroundCurrent obstructive sleep apnea treatment relies on manual PAP titration, but it has limitations. Complex interactions during titration and variations in SpO2 data accuracy pose challenges. Patients with co-occurring chronic hypercapnia may require precise oxygen titration. To address these issues, we propose a Clinical Decision Support System using Markov decision processes.MethodsThis study, compliant with data protection laws, focused on adults with OSA-induced hypoxemia utilizing supplemental oxygen and CPAP/BiPAP therapy. PAP titration, conducted over one night, involved vigilant monitoring of vital signs and physiological parameters. Adjustments to CPAP pressure, potential BiLevel transitions, and supplemental oxygen were precisely guided by patient metrics. Markov decision processes outlined three treatment actions for disorder management, incorporating expert medical insights.ResultsIn our study involving 14 OSA patients (average age: 63 years, 27% females, BMI 41 kg m-2), significant improvements were observed in key health parameters after manual titration. The initial AHI of 61.8 events per hour significantly decreased to an average of 18.0 events per hour after PAP and oxygen titration (p < 0.0001), indicating a substantial reduction in sleep-disordered breathing severity. Concurrently, SpO2 levels increased significantly from an average of 79.7% before titration to 89.1% after titration (p < 0.0003). Pearson correlation coefficients demonstrated aggravation of hypercapnia in 50% of patients (N = 5) with initial pCO2 < 55 mmHg during the increase in CPAP pressure. However, transitioning to BiPAP exhibited a reduction in pCO2 levels, showcasing its efficacy in addressing hypercapnia. Simultaneously, BiPAP therapy correlated with a substantial increase in SpO2, underscoring its positive impact on oxygenation in OSA patients. Markov Decision Process analysis demonstrated realistic patient behavior during stable night conditions, emphasizing minimal apnea and good toleration to high CPAP pressure.ConclusionsThe development of a framework for Markov decision processes of PAP and oxygen titration algorithms holds promise for providing algorithms for improving pCO2 and SpO2 values. While challenges remain, including the need for high-quality data, the potential benefits in terms of patient management and care optimization are substantial, and this approach represents an exciting frontier in the realm of telemedicine and respiratory healthcare.

Project description:BackgroundStandardized collection of predictors of pediatric sepsis has enormous potential to increase data compatibility across research studies. The Pediatric Sepsis Predictor Standardization Working Group collaborated to define common data elements for pediatric sepsis predictors at the point of triage to serve as a standardized framework for data collection in resource-limited settings.MethodsA preliminary list of pediatric sepsis predictor variables was compiled through a systematic literature review and examination of global guideline documents. A 5-round modified Delphi that involved independent voting and active group discussions was conducted to select, standardize, and prioritize predictors. Considerations included the perceived predictive value of the candidate predictor at the point of triage, intra- and inter-rater measurement reliability, and the amount of time and material resources required to reliably collect the predictor in resource-limited settings.ResultsWe generated 116 common data elements for implementation in future studies. Each common data element includes a standardized prompt, suggested response values, and prioritization as tier 1 (essential), tier 2 (important), or tier 3 (exploratory). Branching logic was added to the predictors list to facilitate the design of efficient data collection methods, such as low-cost electronic case report forms on a mobile application. The set of common data elements are freely available on the Pediatric Sepsis CoLab Dataverse and a web-based feedback survey is available through the Pediatric Sepsis CoLab. Updated iterations will continuously be released based on feedback from the pediatric sepsis research community and emergence of new information.ConclusionRoutine use of the common data elements in future studies can allow data sharing between studies and contribute to development of powerful risk prediction algorithms. These algorithms may then be used to support clinical decision making at triage in resource-limited settings. Continued collaboration, engagement, and feedback from the pediatric sepsis research community will be important to ensure the common data elements remain applicable across a broad range of geographical and sociocultural settings.

Dataset Information

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology.

Publications

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology.

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