Fixes and refs

Author: sherjeelshabih

paper/paper.bib

@@ -18,4 +18,113 @@ @article{Scheidgen:2023
   author = {Markus Scheidgen and Lauri Himanen and Alvin Noe Ladines and David Sikter and Mohammad Nakhaee and Ádám Fekete and Theodore Chang and Amir Golparvar and José A. Márquez and Sandor Brockhauser and Sebastian Brückner and Luca M. Ghiringhelli and Felix Dietrich and Daniel Lehmberg and Thea Denell and Andrea Albino and Hampus Näsström and Sherjeel Shabih and Florian Dobener and Markus Kühbach and Rubel Mozumder and Joseph F. Rudzinski and Nathan Daelman and José M. Pizarro and Martin Kuban and Cuauhtemoc Salazar and Pavel Ondračka and Hans-Joachim Bungartz and Claudia Draxl},
   title = {NOMAD: A distributed web-based platform for managing materials science research data},
   journal = {Journal of Open Source Software}
-}
+}
+
+@article{konnecke2015nexus,
+  title={The NeXus data format},
+  author={K{\"o}nnecke, Mark and Akeroyd, Frederick A and Bernstein, Herbert J and Brewster, Aaron S and Campbell, Stuart I and Clausen, Bj{\"o}rn and Cottrell, Stephen and Hoffmann, Jens Uwe and Jemian, Pete R and M{\"a}nnicke, David and others},
+  journal={Applied Crystallography},
+  volume={48},
+  number={1},
+  pages={301--305},
+  year={2015},
+  publisher={International Union of Crystallography}
+}
+
+@software{eric_prestat_2025_15548174,
+  author       = {Eric Prestat and
+                  Francisco de la Peña and
+                  Jonas Lähnemann and
+                  Petras Jokubauskas and
+                  Carter Francis and
+                  Vidar Tonaas Fauske and
+                  pietsjoh and
+                  Tomas Ostasevicius and
+                  T. Nemoto and
+                  Tom Furnival and
+                  Duncan N. Johnstone and
+                  Niels Cautaerts and
+                  Suhas Somnath and
+                  pquinn-dls and
+                  Jan Caron and
+                  Katherine E. MacArthur and
+                  Magnus Nord and
+                  Pierre Burdet and
+                  Nicolas Tappy and
+                  Thomas Aarholt and
+                  Timothy Poon and
+                  Joshua Taillon and
+                  actions-user and
+                  Stephanie Ribet and
+                  Attolight-NTappy and
+                  Tom Slater and
+                  Vadim Migunov and
+                  DENSmerijn},
+  title        = {hyperspy/rosettasciio: v0.9.0},
+  month        = may,
+  year         = 2025,
+  publisher    = {Zenodo},
+  version      = {v0.9.0},
+  doi          = {10.5281/zenodo.15548174},
+  url          = {https://doi.org/10.5281/zenodo.15548174},
+  swhid        = {swh:1:dir:dca5e6b5c0268b38a8c20c7ac2f2b8563ebec3e8
+                   ;origin=https://doi.org/10.5281/zenodo.8011666;vis
+                   it=swh:1:snp:81d7db282a096b8dad625da0b79b451c9cb84
+                   400;anchor=swh:1:rel:6b6e8cef8b3b352f67409e82fecf4
+                   c1c0203c784;path=hyperspy-rosettasciio-5454676
+                  },
+}
+
+@article{wilkinson2016fair,
+  title={The FAIR Guiding Principles for scientific data management and stewardship},
+  author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others},
+  journal={Scientific data},
+  volume={3},
+  number={1},
+  pages={1--9},
+  year={2016},
+  publisher={Nature Publishing Group}
+}
+
+@misc{jacobsen2020fair,
+  title={FAIR principles: interpretations and implementation considerations},
+  author={Jacobsen, Annika and de Miranda Azevedo, Ricardo and Juty, Nick and Batista, Dominique and Coles, Simon and Cornet, Ronald and Courtot, M{\'e}lanie and Crosas, Merc{\`e} and Dumontier, Michel and Evelo, Chris T and others},
+  journal={Data intelligence},
+  volume={2},
+  number={1-2},
+  pages={10--29},
+  year={2020},
+  publisher={MIT Press One Rogers Street, Cambridge, MA 02142-1209, USA journals-info~…}
+}
+
+@article{barker2022introducing,
+  title={Introducing the FAIR Principles for research software},
+  author={Barker, Michelle and Chue Hong, Neil P and Katz, Daniel S and Lamprecht, Anna-Lena and Martinez-Ortiz, Carlos and Psomopoulos, Fotis and Harrow, Jennifer and Castro, Leyla Jael and Gruenpeter, Morane and Martinez, Paula Andrea and others},
+  journal={Scientific Data},
+  volume={9},
+  number={1},
+  pages={622},
+  year={2022},
+  publisher={Nature Publishing Group UK London}
+}
+
+@book{mkoennecke2024nexusformat,
+	title = {nexusformat/cnxvalidate},
+	url = {https://github.com/nexusformat/cnxvalidate},
+	author = {mkoennecke and Bernstein, Herbert J. and Richter, Tobias and Caswell, Thomas A and Jemian, Pete R and Levinsen, Yngve},
+	date = {2024-10-08},
+	year = {2024},
+	month = {10},
+	day = {8},
+}
+
+@book{Jemian2025prjemian,
+	title = {prjemian/punx},
+	url = {https://github.com/prjemian/punx},
+	author = {Jemian, Pete R and Ching, Daniel and dependabot[bot] and De Nolf, Wout and Stöckli, Peter},
+	date = {2025-03-04},
+	year = {2025},
+	month = {3},
+	day = {4},
+}
+

paper/paper.md

@@ -36,22 +36,11 @@ bibliography: paper.bib
 
 # Summary
 
-(Add statement like sentence for the start like the Nomad JOSS). pynxtools is a Python framework that standardizes data conversion for scientific experiments (materials characterization, something like This standardized approach addresses the historical problem of incompatible formats across research communities.) to NeXus HDF5 format across diverse scientific domains. pynxtools provides a fixed set of NeXus application definitions (reference needed here) that ensures convergence and alignment in data specifications across photoemission spectroscopy, electron microscopy(Check if there is a review paper, or just cite rosettasciIO), atom probe tomography, optical spectroscopy, scanning probe microscopy, and X-ray diffraction (Ref: CIFF, IUPAC). 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.
-(Missing what NeXus is. Add a bit of context.)
-(Add it's a CLI tool. And code framework)
-(Nexus Reference, https://doi.org/10.1107/S1600576714027575)
-(Compromise for Nomad: We have a standalone tool that is also integrated in Nomad as an example.)
-(https://github.com/ess-dmsc/nexus-constructor)
-(Cite some FAIR papers, one from Jacobson, FAIR4RS, FAIR4Workflows-thisnotsoimp)
-
-
+Scientific data across experimental physics and materials science remains largely fragmented 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 NeXus HDF5 format [@konnecke2015nexus] across diverse scientific domains. pynxtools provides a fixed set of NeXus application definitions that ensures convergence and alignment in data specifications across photoemission spectroscopy, electron microscopy [@eric_prestat_2025_15548174], 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 [@wilkinson2016fair] [@jacobsen2020fair] [@barker2022introducing] data management across multiple experimental techniques.
 
 # Statement of need
 
-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.
-(Can we tone down the first sentence to not offend readers/people who worked before. Don't dwell on stuff not working. How to make this sound less negative?)
-(Second sentence: We base everything on NeXus. We don't wanna say it's too complicated. Make it nicer. We make it more easier to handle it.)
-(Third: refer to cnxvalidate and such)
+Achieving FAIR (Findable, Accessible, Interoperable, and Reproducible) data principles in experimental physics and materials science requires consistent implementation of standardized data formats. While NeXus provides comprehensive data specifications for structured scientific data storage, pynxtools simplifies the implementation process for developers and researchers by providing guided workflows and automated validation to ensure complete compliance. Existing tools [@mkoennecke2024nexusformat] [@Jemian2025prjemian] 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.
 
 # Dataconverter and validation (Sherjeel)