ifes-apt-tc-data-modeling 0.0.1

Foster exchange about data models and work towards clear specifications of file formats and data models in the research field of atom probe microscopy.

atomprobe-data-modeling

Mission:

Foster exchange about data models and work towards specifications of file formats from the research field of atom probe microscopy.

Documentation of file formats and data models in atom probe status quo

Detailed technical specifications of the file formats and data models are not available for all formats in the field of atom probe microscopy. A practical solution to address this limitation has been so far to collect examples in respective format, so-called instances, and share and inspect these. Based on this individuals the community has contributed collect knowledge about what is likely a sort of specification for many file formats.

Pieces of information about file formats are reported in the literature in e.g. books by D. Larson et al. and B. Gault et al. Individuals such as D. Haley have contributed much to make the community aware of existent limitations. AMETEK/Cameca as the key technology partner in atom probe has created an open file format called APT which improves the accessibility of specific numerical data and some metadata. Individuals like M. Kühbach have driven the implementation and communication of parsers for this APT file format.

Nowadays there is an increased interest and demand expressed by funding agencies that researchers should and have to make their research data management and data stewardship better matching and brought into accordance with the FAIR principles. In fact it turns out useful to exchange more details about data models and file formats as otherwise it is not foreseeable how atom probe data can be made really interoperable with electronic lab notebooks, research data management systems, and software tools.

In light of these challenges, the idea of understanding formats just by examples, showed to be a slow and error prone route as e.g. source code and workflows used to write such files, input, workflow, provenance information might not or has not been captured or/and the specific software tool(s) used might not be shared or made accessible for reviewing and analyzing their functions.

Benefit and Next Steps

You can easily imagine that the more people will support us with this work the more complete our understanding and knowledge about the available file formats in atom probe microscopy can and will become. This can help all of us in the long run to build software tools which are more reliably and robustly capable of parsing research data - irrespective from which tools they come or which tools you would like to used them further when digitalizing your atom probe research.

The Python parsers in this repository are meant as a motivation to offer immediate benefit to users. The collection of examples and technical discussions via issues serves the more long-term aim which is to arrive at a detailed technical specification rather than more robust parsers so that atom probe data can be exchanged across tools irrespective their formatting.

Support us with this work

Thank you very much for supporting this activity and your time.

Feedback, questions

Feel free to drop us a message via setting up or commenting on an issue and feel free to use the resources in this repository.

Where to place your examples?

There is a examples_with_provenance and examples_without_provenance sub-directory for each file format.

When you do know with which software and measured dataset you have created a file, you should share the file and these pieces of information (software version). Do so by naming at least the respective raw files. Ideally you share the examples via offering a link to an external data repository such as Zenodo or other providers. This not only avoids that this repository would get too much filled up with binary data. Also it enables you to share clearly under which license you would like make your example(s) accessible.

Provenance if possible, plain examples if in doubt

Use the examples_with_provenance sub-directory. With this it is at least possible to reproduce the file creation. A practical solution is to share (by uploading) the screenshot of the complete IVAS/APSuite version info screen, including the APSuite version, the CernRoot version, the CamecaRoot version, and the versions of libraries used by APSuite. This can help other atom probers and AMETEK/Cameca to improve their software as it enables them to identify inconsistencies or bugs eventually easier.

Atom probers should be aware that file formats like POS, ePOS, or APT are neither raw data nor follow a clear technical documentation. Therefore, all current file formats are not meeting the FAIR principles.ey specified. Instead, refer to RRAW, STR, RHIT and/or HITS files. Ideally, you add unique identifiers (such as SHA256 checksums) for each raw file. A documentation how you can do this was issued by your IFES APT TC colleagues (How to hash your data).

If you cannot provide such detailed pieces of information to your work you can still participate and support us a lot if you share your knowledge by adding at least a link to a repository or file share with content in the relevant atom-probe -specific file formats. In this case, please use the examples_without_provenance directory. While these examples are stripped of the context in which they were created and used (provenance information), these examples can still be very useful to run the file formats parsers against to make the parsers more robust.

Background information

File formats, data models, in (almost every) research field may not be fully documented. A checklist of the necessary pieces of information and documentation required to call a data model, data schema, and/or file format fully documented in accordance with the FAIR data and research software stewardship principles is given below:

1. Each piece of information (bit/byte) is documented.
2. This documentation fulfills the FAIR principles, i.e. Wilkinson et al., 2016 and Barker et al., 2022 For binary files, tools like kaitai struct offer a solution to describe the exact binary information content in a data item. This can be a file but also the storage of a database entry or the response of a call to an API. Let alone the binary structure is insufficient, tough.
3. To each piece of information there has to exist also a parameterized description, what this piece of information conceptually means. One way to arrive at such description is to use a data schema or ontology. It is important to mention that the concepts in this schema/ontology have unique identifier so that each data item/piece of information is identifiable as an instance of an entry in a database or a knowledge graph. This holds independently of which research data management system or electronic lab notebook is used.
4. In addition, it is very useful that timestamps are associated with each data item (ISO8061 with time zone information) so that it is possible to create a timeline of the context in which and when the e.g. file was created.

The first and second point is known as a specification, while the third and fourth point emphasize that the contextualization and provenance is key to make a specification complete and useful.