Joss paper #651
Joss paper #651
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paper/paper.md
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| # Statement of need | ||
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| Scientific data across experimental physics and materials science remains largely non-FAIR (Findable, Accessible, Interoperable, and Reproducible) due to inconsistent implementation and documentation of standardized data formats. While NeXus provides comprehensive data specifications for structured scientific data storage, researchers typically struggle with its specification requirements, leading to incomplete implementations, non-compliant outputs, or abandonment of standardization efforts entirely. Existing tools (do some parts of what we offer, and then list what we provide) lack robust validation frameworks and provide insufficient guidance for proper NeXus adoption. pynxtools addresses this critical gap by providing an accessible framework that enforces complete NeXus application definition compliance through automated validation, detailed error reporting for missing required data points, and clear implementation pathways via configuration files and extensible plugins. This approach transforms NeXus from a complex specification into a practical solution, enabling researchers to achieve true data interoperability without deep technical expertise in the underlying standards. |
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The first sentence needs, irrespective how more positive we're gonna formulate it, references. Otherwise, it stays as an unsubstantiated hypothesis, which is an easy target for reviewers.
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The point I raised was, we can reformulate along these lines:
"The transitioning from paper to electronic lab notebooks paired with efforts to report research as structured data rather than prose (which is the summary of what everybody in the NFDI and across the globe is currently working on) (according to the FAIR principles as lead to an increased use of semantic modeling (including above-mentioned our target communities, i.e. condensed matter, materials science, as well as materials engineering). These essentially build domain-specific ontologies (adds refs) along the semantic web technology stack. Achieving true interoperability though, calls for work that enales semantic mapping of concepts. asserting if two concepts are equivalent or different (and in which regards). Different strategies exist to implement such mapping: Explicit mapping rules (e.g. SSSOM). A complementary alternative is standardization. That is the negotiating of a concensus across multiple research communities to define and use a shared and set of semantic concepts with on average fewer concepts. This (or the latter) strategy is used by NeXus."
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I think we can resolve this, right? This part has changed a lot anyway.
Co-authored-by: Sherjeel Shabih <shabihsherjeel@gmail.com>
paper/paper.bib
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Add author, year, doi, journal name if journal, url and urldate if online link to each if available
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| # Summary | ||
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| Scientific data across experimental physics and materials science often lacks adherence to FAIR principles [@Wilkinson:2016; @Jacobsen:2020; @Barker:2022] due to incompatible instrument-specific formats and diverse standardization practices. pynxtools is a Python software development framework with a CLI interface that standardizes data conversion for scientific experiments in materials characterization to the NeXus format [@Koennecke:2015] across diverse scientific domains. NeXus uses NeXus application definitions as their data storage specifications. pynxtools provides a fixed, versioned set of NeXus application definitions that ensures convergence and alignment in data specifications across photoemission spectroscopy, electron microscopy [@Prestat:2025], atom probe tomography, optical spectroscopy, scanning probe microscopy, and X-ray diffraction. Through its modular plugin architecture, pynxtools provides maps for instrument-specific raw data, and electronic lab notebook metadata, to these unified definitions, while performing validation to ensure data correctness and NeXus compliance. By simplifying the adoption of standardized application definitions, the framework enables true data interoperability and FAIR data management across multiple experimental techniques. |
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We should format all usage of software tools differently, maybe italics if readable?
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What of usage? And what software tools?
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From the Joss example paper, software tools like pint and elasticsearch are written with ``, we should do the same. So e.g.
powered by `Elasticsearch`For internal module names, shall we change them to italics? So instead of Metainfo, we write Metainfo?
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(Usage for humans easily explore, machines to use):
One sentence for each
--semantic use
--concept
--annotations
One sentence, further functionalities:
--documentation
--default plottable
Some guiding on improving the shorting
Co-authored-by: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com>
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Still open:
References:
Final checks:
Current word count (excl. author names, affiliations, etc.) is 993 words. |
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