Keep It Simple: Using README Files to Advance Standardization in Chronobiology
Abstract
:- Extra effort: Implementing metadata standards and guidelines may be perceived as complex and time-consuming. Software tools can help researchers prepare standards-compliant metadata, but writing and updating such tools is a further effort;
- Lack of incentives and recognition: if adherence to metadata standards is not incentivized or recognized by the scientific community, researchers may consider them additional burdensome requirements;
- Technical challenges: adopting metadata standards may require modifications to existing data management systems and infrastructures;
- Resource constraints: researchers may lack the necessary resources, including funding, technical expertise, and training, to effectively implement metadata standards, let alone the associated software tools and repositories;
- Resistance to change: researchers may be comfortable with their current data management practices and reluctant to adopt new standards.
- Agile development: In order to ensure the relevance and applicability of our recommendations, we will adopt an agile development approach. This means that we will generate frequent and actionable recommendations that can be easily incorporated into existing workflows and software infrastructure. By adopting an iterative approach, we can avoid the issue of obsolescence and ensure that our guidelines remain up to date with evolving practices and technologies;
- Enhanced metadata descriptions: While existing minimal information guidelines focus on technical aspects of data measurement and reproducibility, we believe it is essential to emphasize the reporting of biological and environmental contexts for datasets. To achieve this, we will develop guidelines and provide examples for reporting important experimental factors such as light and temperature entrainment or drug interventions during experiments. By capturing these contextual details, we aim to facilitate data reuse and enable comprehensive interpretations by researchers;
- Utilization of README templates: To simplify the process of capturing metadata, we propose the use of simple README templates in a human-readable format, such as plain text. These templates will provide researchers with a clear structure for capturing the required metadata without requiring specialized technical knowledge or software tools. README templates can seamlessly integrate into existing data organization practices and repositories. This approach accommodates various needs and contextual information while promoting flexibility and ease of use. Additionally, README documents can be easily version-controlled, allowing for collaborative and iterative changes to the metadata. This adaptability ensures that the value of README files remains intact regardless of the target data repository, whether it is a generic, data-agnostic repository like Zenodo [33] and Figshare [34], or a domain-specific resource like BioDare2 [31];
- Tailored templates: Instead of developing a single comprehensive template, we recognize the need to create multiple templates tailored to specific organisms and experimental techniques. This approach simplifies template usage and resolves issues related to different terminologies used for describing humans compared to model organism data. For instance, human data are typically grouped in cohorts and described with demographics, while data from model organisms are often recorded as biological replicates and described with genotypes. By tailoring the templates, we can provide researchers with focused guidance that is relevant to their specific experimental contexts;
- Syntax for automatic parsing and validation: While simple README templates offer advantages, we acknowledge the importance of machine-readability and interoperability. To address this, we propose developing a syntax that enables at least automatic parsing and validation of the text documents. For example, we suggest using specific characters, such as #, to distinguish between keys and their values. By incorporating machine-readable syntax, we enhance the interoperability and compatibility of the metadata with data processing systems and repositories. This approach ensures compatibility with evolving guidelines and facilitates potential conversion to more formal formats (e.g., JSON) if necessary;
- Collaboration with Metadata4Wearables: To align our efforts and ensure compatibility and complementarity, we plan to collaborate with the Metadata4Wearables [35] community. This community focuses on standardizing actigraphy and light exposure data using JSON schemas. By collaborating with Metadata4Wearables, we can leverage their expertise and complement our ongoing initiatives to create a cohesive approach to metadata standardization in chronobiology;
- Dedicated GitHub repository: In order to disseminate our work and gather feedback from the scientific community, we have established a dedicated GitHub repository (https://github.com/circadianmentalhealth/circadian-data-standards) (accessed on 25 August 2023) [36]. We strongly encourage readers to contribute their thoughts, offer insights, and provide feedback on the proposed plan or draft templates using the issue tracking system within the repository. This collaborative approach ensures that the standards we develop reflect the needs and perspectives of the broader scientific community;
- Future steps: Our future work involves listing circadian variables for routine use and recommending analysis methods for their estimation. Additionally, we will focus on improved interoperability by suggesting suitable ontologies and closed vocabularies for formal data descriptions.
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Zieliński, T.; Hodge, J.J.L.; Millar, A.J. Keep It Simple: Using README Files to Advance Standardization in Chronobiology. Clocks & Sleep 2023, 5, 499-506. https://doi.org/10.3390/clockssleep5030033
Zieliński T, Hodge JJL, Millar AJ. Keep It Simple: Using README Files to Advance Standardization in Chronobiology. Clocks & Sleep. 2023; 5(3):499-506. https://doi.org/10.3390/clockssleep5030033
Chicago/Turabian StyleZieliński, Tomasz, James J. L. Hodge, and Andrew J. Millar. 2023. "Keep It Simple: Using README Files to Advance Standardization in Chronobiology" Clocks & Sleep 5, no. 3: 499-506. https://doi.org/10.3390/clockssleep5030033