Merge pull request #663 from FAIRmat-NFDI/joss_paper_dataconverter_edit

Author: lukaspie

paper/paper.bib

@@ -20,17 +20,90 @@ @article{Scheidgen:2023
   journal = {Journal of Open Source Software}
 }
 
+@article{Draxl:2019,
+  title={The NOMAD laboratory: from data sharing to artificial intelligence},
+  author={Draxl, Claudia and Scheffler, Matthias},
+  journal={Journal of Physics: Materials},
+  volume={2},
+  number={3},
+  pages={036001},
+  year={2019},
+  publisher={IOP Publishing}
+}
+
+@article{Ghiringhelli:2017,
+  title={Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats},
+  author={Ghiringhelli, Luca M and Carbogno, Christian and Levchenko, Sergey and Mohamed, Fawzi and Huhs, Georg and L{\"u}ders, Martin and Oliveira, Micael and Scheffler, Matthias},
+  journal={npj computational materials},
+  volume={3},
+  number={1},
+  pages={46},
+  year={2017},
+  publisher={Nature Publishing Group UK London}
+}
+
+
 @article{Koennecke:2015,
   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},
+  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 et. al.},
   journal={Applied Crystallography},
   volume={48},
   number={1},
   pages={301--305},
   year={2015},
+  doi={10.1107/S1600576714027575},
   publisher={International Union of Crystallography}
 }
 
+@article{Klosowski:1997,
+title = {NeXus: A common format for the exchange of neutron and synchroton data},
+journal = {Physica B: Condensed Matter},
+volume = {241-243},
+pages = {151-153},
+year = {1997},
+note = {Proceedings of the International Conference on Neutron Scattering},
+issn = {0921-4526},
+doi = {https://doi.org/10.1016/S0921-4526(97)00865-X},
+url = {https://www.sciencedirect.com/science/article/pii/S092145269700865X},
+author = {P Klosowski and M Koennecke and J.Z Tischler and R Osborn},
+keywords = {Data format, Data analysis, Data visualization, Computing},
+abstract = {NeXus is a data format for the exchange of neutron and synchrotron scattering data between facilities and user institutions. It has been developed by an international team of scientists and computer programmers from neutron and X-ray facilities around the world. The NeXus format uses the hierarchical data format (HDF) which is portable, binary, extensible and self-describing. The NeXus format defines the structure and contents of these HDF files in order to facilitate the visualization and analysis of neutron and X-ray data. In addition, an application program interface (API) is being produced in order to simplify the reading and writing of NeXus files. The details of the format are available at 〈http://www.neutron.anl.gov/NeXus/〉.}
+}
+
+@article{Koennecke:2006,
+title = {The state of the NeXus data format},
+journal = {Physica B: Condensed Matter},
+volume = {385-386},
+pages = {1343-1345},
+year = {2006},
+issn = {0921-4526},
+doi = {10.1016/j.physb.2006.06.106},
+url = {https://www.sciencedirect.com/science/article/pii/S0921452606013779},
+author = {Mark Könnecke},
+keywords = {Data format, Data analysis, Data management},
+abstract = {NeXus is an effort by an international group of scientists to define a common data exchange format for neutron, muon and X-ray scattering. NeXus has six levels: a physical file format, a file structure, rules for storing individual data items in a file, a dictionary of names, instrument definitions and an application programming interface (API) to NeXus files. The authors will present the large steps forward which have been made both with instrument definitions and the NeXus-API.}
+}
+
+@article{Wilkinson:2025,
+  title    = "Applying the {FAIR} Principles to computational workflows",
+  author   = "Wilkinson, Sean R and Aloqalaa, Meznah and Belhajjame, Khalid and
+              Crusoe, Michael R and de Paula Kinoshita, Bruno and Gadelha, Luiz
+              and Garijo, Daniel and Gustafsson, Ove Johan Ragnar and Juty,
+              Nick and Kanwal, Sehrish and Khan, Farah Zaib and K{\"o}ster,
+              Johannes and Peters-von Gehlen, Karsten and Pouchard, Line and
+              Rannow, Randy K and Soiland-Reyes, Stian and Soranzo, Nicola and
+              Sufi, Shoaib and Sun, Ziheng and Vilne, Baiba and Wouters,
+              Merridee A and Yuen, Denis and Goble, Carole",
+  journal  = "Sci. Data",
+  volume   =  12,
+  number   =  1,
+  pages    = "328",
+  month    =  feb,
+  year     =  2025,
+  doi = {10.1038/s41597-025-04451-9},
+  language = "en"
+}
+
 @software{Prestat:2025,
   author       = {Eric Prestat and
                   Francisco de la Peña and
@@ -76,34 +149,37 @@ @software{Prestat:2025
 
 @article{Wilkinson:2016,
   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},
+  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 et. al.},
   journal={Scientific data},
   volume={3},
   number={1},
   pages={1--9},
   year={2016},
+  doi={10.1038/sdata.2016.18},
   publisher={Nature Publishing Group}
 }
 
 @article{Jacobsen:2020,
   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},
+  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 et. al.},
   journal={Data intelligence},
   volume={2},
   number={1-2},
   pages={10--29},
   year={2020},
+  doi={10.1162/dint_r_00024},
   publisher={MIT Press One Rogers Street, Cambridge, MA 02142-1209, USA journals-info~…}
 }
 
 @article{Barker:2022,
   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},
+  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 et. al.},
   journal={Scientific Data},
   volume={9},
   number={1},
   pages={622},
   year={2022},
+  doi={10.1038/s41597-022-01710-x},
   publisher={Nature Publishing Group UK London}
 }
 
@@ -138,7 +214,7 @@ @software{Druskat:2021
 @article{Hoyer:2017,
   title   = {xarray: {N-D} labeled arrays and datasets in {Python}},
   author  = {Hoyer, S. and J. Hamman},
-  journal = {In revision, J. Open Res. Software},
+  journal = {J. Open Res. Software},
   year    = {2017}
 }
 
@@ -218,7 +294,6 @@ @software{Pandas:2020
     month        = feb,
     year         = 2020,
     publisher    = {Zenodo},
-    version      = {latest},
     doi          = {10.5281/zenodo.3509134},
     url          = {https://doi.org/10.5281/zenodo.3509134}
 }
@@ -234,10 +309,9 @@ @InProceedings{ McKinney:2010
 }
 
 @misc{Behnel:2005,
-  title={lxml: XML and HTML with Python},
+  title={ {l}xml: XML and HTML with Python},
   author={Behnel, Stefan and Faassen, Martijn and Bicking, Ian},
-  year={2005},
-  publisher={Lxml}
+  year={2005}
 }
 
 @article{Hjorth:2017,
@@ -252,7 +326,7 @@ @article{Hjorth:2017
   volume={29},
   number={27},
   pages={273002},
-  url={http://stacks.iop.org/0953-8984/29/i=27/a=273002},
+  doi={10.1088/1361-648X/aa680e},
   year={2017},
   abstract={The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.}
 }
@@ -267,28 +341,25 @@ @software{Pint:2012
 }
 
 @software{Click:2014,
-    author       = {The click development team},
-    title        = {Command Line Interface Creation Kit},
+    author       = {The Pallets development team},
+    title        = {click: Command Line Interface Creation Kit},
     month        = apr,
     year         = 2014,
-    version      = {latest},
     url          = {https://github.com/pallets/click}
 }
 
 @software{Clarke:2019,
     author       = {Travis Clarke},
-    title        = {A deep merge function for Python},
+    title        = {mergedeep: A deep merge function for Python},
     month        = feb,
     year         = 2019,
-    version      = {latest},
     url          = {https://github.com/clarketm/mergedeep}
 }
 
 @software{H5py:2008,
-    author       = {The h5py development team},
-    title        = {HDF5 for Python},
+    author       = {Andrew Collette et al.},
+    title        = {h5py: HDF5 for Python},
     month        = may,
     year         = 2008,
-    version      = {latest},
     url          = {https://github.com/h5py/h5py}
 }