Dataset Information

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences.

ABSTRACT: Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a dataset. In this work, we propose a reproducible computational workflow to assess data FAIRness in the life sciences. Our implementation follows principles and guidelines recommended by the maturity indicator authoring group and integrates concepts from the literature. In addition, we propose a FAIR balloon plot to summarize and compare dataset FAIRness. We evaluated the feasibility of our method on three real use cases where researchers looked for six datasets to answer their scientific questions. We retrieved information from repositories (ArrayExpress, Gene Expression Omnibus, eNanoMapper, caNanoLab, NanoCommons and ChEMBL), a registry of repositories, and a searchable resource (Google Dataset Search) via application program interfaces (API) wherever possible. With our analysis, we found that the six datasets met the majority of the criteria defined by the maturity indicators, and we showed areas where improvements can easily be reached. We suggest that use of standard schema for metadata and the presence of specific attributes in registries of repositories could increase FAIRness of datasets.

SUBMITTER: Ammar A

PROVIDER: S-EPMC7594074 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences.

Ammar Ammar A Bonaretti Serena S Winckers Laurent L Quik Joris J Bakker Martine M Maier Dieter D Lynch Iseult I van Rijn Jeaphianne J Willighagen Egon E

Nanomaterials (Basel, Switzerland) 20201020 10

Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a datase ...[more]

PMID: 33092028

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Project description:BackgroundCurrent text mining tools supporting abstract screening in systematic reviews are not widely used, in part because they lack sensitivity and precision. We set out to develop an accessible, semi-automated "workflow" to conduct abstract screening for systematic reviews and other knowledge synthesis methods.MethodsWe adopt widely recommended text-mining and machine-learning methods to (1) process title-abstracts into numerical training data; and (2) train a classification model to predict eligible abstracts. The predicted abstracts are screened by human reviewers for ("true") eligibility, and the newly eligible abstracts are used to identify similar abstracts, using near-neighbor methods, which are also screened. These abstracts, as well as their eligibility results, are used to update the classification model, and the above steps are iterated until no new eligible abstracts are identified. The workflow was implemented in R and evaluated using a systematic review of insulin formulations for type-1 diabetes (14,314 abstracts) and a scoping review of knowledge-synthesis methods (17,200 abstracts). Workflow performance was evaluated against the recommended practice of screening abstracts by 2 reviewers, independently. Standard measures were examined: sensitivity (inclusion of all truly eligible abstracts), specificity (exclusion of all truly ineligible abstracts), precision (inclusion of all truly eligible abstracts among all abstracts screened as eligible), F1-score (harmonic average of sensitivity and precision), and accuracy (correctly predicted eligible or ineligible abstracts). Workload reduction was measured as the hours the workflow saved, given only a subset of abstracts needed human screening.ResultsWith respect to the systematic and scoping reviews respectively, the workflow attained 88%/89% sensitivity, 99%/99% specificity, 71%/72% precision, an F1-score of 79%/79%, 98%/97% accuracy, 63%/55% workload reduction, with 12%/11% fewer abstracts for full-text retrieval and screening, and 0%/1.5% missed studies in the completed reviews.ConclusionThe workflow was a sensitive, precise, and efficient alternative to the recommended practice of screening abstracts with 2 reviewers. All eligible studies were identified in the first case, while 6 studies (1.5%) were missed in the second that would likely not impact the review's conclusions. We have described the workflow in language accessible to reviewers with limited exposure to natural language processing and machine learning, and have made the code available to reviewers.

Project description:Capture and representation of scientific knowledge in a structured format are essential to improve the understanding of biological mechanisms involved in complex diseases. Biological knowledge and knowledge about standardized terminologies are difficult to capture from literature in a usable form. A semi-automated knowledge extraction workflow is presented that was developed to allow users to extract causal and correlative relationships from scientific literature and to transcribe them into the computable and human readable Biological Expression Language (BEL). The workflow combines state-of-the-art linguistic tools for recognition of various entities and extraction of knowledge from literature sources. Unlike most other approaches, the workflow outputs the results to a curation interface for manual curation and converts them into BEL documents that can be compiled to form biological networks. We developed a new semi-automated knowledge extraction workflow that was designed to capture and organize scientific knowledge and reduce the required curation skills and effort for this task. The workflow was used to build a network that represents the cellular and molecular mechanisms implicated in atherosclerotic plaque destabilization in an apolipoprotein-E-deficient (ApoE(-/-)) mouse model. The network was generated using knowledge extracted from the primary literature. The resultant atherosclerotic plaque destabilization network contains 304 nodes and 743 edges supported by 33 PubMed referenced articles. A comparison between the semi-automated and conventional curation processes showed similar results, but significantly reduced curation effort for the semi-automated process. Creating structured knowledge from unstructured text is an important step for the mechanistic interpretation and reusability of knowledge. Our new semi-automated knowledge extraction workflow reduced the curation skills and effort required to capture and organize scientific knowledge. The atherosclerotic plaque destabilization network that was generated is a causal network model for vascular disease demonstrating the usefulness of the workflow for knowledge extraction and construction of mechanistically meaningful biological networks.

Project description:IntroductionMicro-computed tomography (μCT) is a valuable imaging modality for longitudinal quantification of bone volumes to identify disease or treatment effects for a broad range of conditions that affect bone health. Complex structures, such as the hindpaw with up to 31 distinct bones in mice, have considerable analytic potential, but quantification is often limited to a single bone volume metric due to the intensive effort of manual segmentation. Herein, we introduce a high-throughput, user-friendly, and semi-automated method for segmentation of murine hindpaw μCT datasets.MethodsIn vivo μCT was performed on male (n = 4; 2-8-months) and female (n = 4; 2-5-months) C57BL/6 mice longitudinally each month. Additional 9.5-month-old male C57BL/6 hindpaws (n = 6 hindpaws) were imaged by ex vivo μCT to investigate the effects of resolution and integration time on analysis outcomes. The DICOMs were exported to Amira software for the watershed-based segmentation, and watershed markers were generated automatically at approximately 80% accuracy before user correction. The semi-automated segmentation method utilizes the original data, binary mask, and bone-specific markers that expand to the full volume of the bone using watershed algorithms.ResultsCompared to the conventional manual segmentation using Scanco software, the semi-automated approach produced similar raw bone volumes. The semi-automated segmentation also demonstrated a significant reduction in segmentation time for both experienced and novice users compared to standard manual segmentation. ICCs between experienced and novice users were >0.9 (excellent reliability) for all but 4 bones.DiscussionThe described semi-automated segmentation approach provides remarkable reliability and throughput advantages. Adoption of the semi-automated segmentation approach will provide standardization and reliability of bone volume measures across experienced and novice users and between institutions. The application of this model provides a considerable strategic advantage to accelerate various research opportunities in pre-clinical bone and joint analysis towards clinical translation.

Dataset Information

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences.

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A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences.

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