JOSS paper: cut wordcount for NOMAD part #661
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paper/paper.md
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| While pynxtools works as a standalone tool using the command line, it can also be integrated directly into Research Data Management Systems (RDMS). Out of the box, the package functions as a plugin within the NOMAD platform, converting and parsing data from experiments. This enables experimental data in the NeXus format to be integrated into NOMAD's metadata model, making it searchable and interoperable with other data from theory and experiment. The plugin consists of several key components (so called entry points): | ||
| While pynxtools works as a standalone tool using the command line, it can also be integrated directly into Research Data Management Systems (RDMS). Out of the box, the package functions as a plugin within the NOMAD platform, converting and parsing data from experiments. This enables data in the NeXus format to be integrated into NOMAD's metadata model, making it searchable and interoperable with other data from theory and experiment. |
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"converting ... from experiment" > "where it is used for parsing and normalizing to NeXus and subsequent mapping onto the NOMAD's Metainfo [@Ghiringhelli] model, which makes these data"
paper/paper.md
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| - Schema Package: The NeXus (meta)data definitions are expressed in XML using the NeXus Definition Language (NXDL), which in turn is defined using XSD. pynxtools converts this representation and extends NOMAD's internal data schema (called __Metainfo__) with these domain-specific quantities. pynxtools also connects the NeXus vocabulary to existing base sections in NOMAD — reusable, standardized building blocks used to represent common scientific concepts. This connection enables interoperability between NeXus-defined concepts and other standardized representations in NOMAD, such as those for sample synthesis or theoretical calculations. | ||
| The __DataConverter__ as described above is available in NOMAD, allowing users to convert their experimental data to NeXus through NOMAD's graphical interface. The __DataConverter__ class also handles NOMAD's electronic lab notebooks (ELNs), converting manual input data to NeXus. |
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I would keep the sentence on "The plugin ... (so called entry points)."
paper/paper.md
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| - Schema Package: The NeXus (meta)data definitions are expressed in XML using the NeXus Definition Language (NXDL), which in turn is defined using XSD. pynxtools converts this representation and extends NOMAD's internal data schema (called __Metainfo__) with these domain-specific quantities. pynxtools also connects the NeXus vocabulary to existing base sections in NOMAD — reusable, standardized building blocks used t 8000 o represent common scientific concepts. This connection enables interoperability between NeXus-defined concepts and other standardized representations in NOMAD, such as those for sample synthesis or theoretical calculations. | ||
| The __DataConverter__ as described above is available in NOMAD, allowing users to convert their experimental data to NeXus through NOMAD's graphical interface. The __DataConverter__ class also handles NOMAD's electronic lab notebooks (ELNs), converting manual input data to NeXus. |
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"The ... allowing users" > "This DataConverter functionality of pynxtools in NOMAD allows users"
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The point that the manually inputted data are also part of the conversion does not come across but is important as one can therefore also search for these.
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"The ... allowing users" > "This DataConverter functionality of pynxtools in NOMAD allows users"
I think it's fine as it is, adding another full stop plus new sentence start introduces too many words.
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The point that the manually inputted data are also part of the conversion does not come across but is important as one can therefore also search for these.
Added another half-sentence to address this.
paper/paper.md
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| While pynxtools works as a standalone tool using the command line, it can also be integrated directly into Research Data Management Systems (RDMS). Out of the box, the package functions as a plugin within the NOMAD platform, converting and parsing data from experiments. This enables experimental data in the NeXus format to be integrated into NOMAD's metadata model, making it searchable and interoperable with other data from theory and experiment. The plugin consists of several key components (so called entry points): | ||
| While pynxtools works as a standalone tool using the command line, it can also be integrated directly into Research Data Management Systems (RDMS). Out of the box, the package functions as a plugin within the NOMAD platform, converting and parsing data from experiments. This enables data in the NeXus format to be integrated into NOMAD's metadata model, making it searchable and interoperable with other data from theory and experiment. |
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maybe we stop after "platform, " with a full-stop and rewrite the converting and parsing sentence such that we mention that this parsing is realized via the "DataConverter" functionality. I still like the idea that we give each functionality at least one sentence.
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moved this part to the DataConverter part
paper/paper.md
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| - Data Converter: The __DataConverter__ as described above is also available in NOMAD. Thus, NOMAD users can directly convert their experimental data to NeXus using NOMAD's graphical interface. In addition to the capabilities already described, the internal __DataConverter__ class also handles NOMAD's electronic lab notebooks (ELNs) and converts these such that the manually inputted data can be converted to NeXus as well. | ||
| The NeXus (meta)data definitions are expressed in XML using the NeXus Definition Language (NXDL), which is defined using XML Schema Definition (XSD). pynxtools converts this representation and extends NOMAD's internal data schema (called __Metainfo__) with these NeXus-specific quantities. It also connects the NeXus vocabulary to existing base sections in NOMAD — reusable, standardized building blocks for representing common scientific concepts. This connection enables interoperability between NeXus-defined concepts and other standardized representations in NOMAD, such as those for sample synthesis or theoretical calculations. The NOMAD parser module in pynxtools (__NexusParser__) extracts structured data from NeXus HDF5 files to populate NOMAD with __Metainfo__ object instances as defined by the pynxtools schema package. This enables direct ingestion of NeXus data into NOMAD. Parsed data is post-processed using NOMAD's normalization pipeline. This includes automatic handling of units, linking references (including sample and instrument identifiers defined elsewhere in NOMAD), and populating derived quantities needed for advanced search and visualization. The entire pynxtools workflow (conversion, parsing, and normalization) is exemplified in a representative NOMAD upload shipped with the package. This example helps new users understand the workflow and serves as a template to adapt the plugin to new NeXus applications. |
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Why at all to mention that NeXus is XML and XSD, important is there is a DataConverter functionality that can be used command-line or in NOMAD. In the case of "in NOMAD" the DataConverter is called internally plus other functionalities, like reported here.
Everything after "This connection enables" is fine.
I somewhat feel that this connection is also where to mention that ELN data are processed as well into Metainfo.
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The last sentence about the example I would personally move to the bottom, like use the old structure and sequence of functionalities provided.
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Why at all to mention that NeXus is XML and XSD,
Makes sense, just removed it.
I somewhat feel that this connection is also where to mention that ELN data are processed as well into Metainfo.
added a half-sentence about this
paper/paper.md
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| - App: pynxtools contains an integrated search application for NeXus data within NOMAD. This application, powered by Elasticsearch [@elasticsearch:2025], enables users to efficiently filter uploaded data based on various parameters, such as experiment type, upload timestamp, and other relevant quantities. | ||
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| - Example Upload: The plugin includes a representative NOMAD upload (based on the NeXus application definition __NX_iv_temp__ describing temperature-dependent IV curve measurements), which exemplifies the entire workflow of pynxtools as a NOMAD package. This example upload details the conversion of data from experiments into NeXus files using the __DataConverter__, along with parsing them into the NOMAD archive. This example upload is designed for new users to understand the pynxtools workflow in NOMAD and serves as templates to adapt the plugin to new NeXus applications. | ||
| Finally, pynxtools contains an integrated search application for NeXus data within NOMAD, powered by Elasticsearch [@elasticsearch:2025]. This enables users to efficiently filter uploaded data based on parameters like experiment type, upload timestamp, and other relevant quantities. |
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we should mention that this search application from the user perspective is currently "providing a dashboard"
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I overall like the shortening, came to me though with a slightly too strong refactoring. Would appreciate, if still the named individual functionalities SchemaPackage, DataConverter, NeXusParserAndNormalizer, App, and Example remain identifiable, maybe should I edit in place ?
This shrinks the wordcount for this part by ~120 words, down to ~ 330 words. Maybe we can cut even a bit more.