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SBP Review Neuromorphological File Format V SBP Review Neuromorphological File Format v 4.0 Reviewers: Samir Das and Trygve Leergaard Authors: Susan Tappan, Maci Heal, Aidan Sullivan, INCF Standards and Best Pracices Committee, and Jyl Boline Basic metadata Title: Neuromorphological File Format v 4.0 Brief description: MBF Bioscience’s Neuromorphological file format provides an openly documented and broadly utilized digital reconstruction and modeling structure for microscopic anatomies. The Extensible Markup Language (XML) based file structure has been driven for over 30 years by the ever-advancing science, technology, and input of neuroscientists throughout the world. It balances structure with flexibility by storing each geometrically modeled object as unique data elements and providing mechanisms for grouping any number and type of data elements. This accommodates a number of analytical possibilities such as detailed morphometric analyses, simulations, and electrotonic modeling of the neurons. File-level metadata is retained to provide detail on the origin of the sample, ensuring that the provenance of derivative data is tracked and that important source information is not separated from the corresponding data. URL: http://www.mbfbioscience.com/filespecification Steward: Aidan Sullivan, Susan Tappan Relevant publication: Sullivan, A. E., Tappan, S. J., Angstman, P. J., Rodriguez, A., Thomas, G. C., Hoppes, D. M., Abdul-Karim, M. A., Heal, M. L., Glaser, J. R. (2020). A comprehensive, FAIR file format for neuroanatomical structure modeling. bioRxiv, 306670. https://doi.org/10.1101/2020.09.22.306670 This publication has been submitted to Neuroinformatics and is currently under review. Nomination Information: Neuromorphological File Format v 4.0 was nominated for consideration by Susan Tappan on November 25, 2020. Summary of discussion: Neuromorphological File Format v 4.0 is the first standard created and maintained by a for-profit corporation to be submitted to INCF for endorsement. The SBP Committee feels it is important to encourage companies to keep SBPs as open as possible, but understands this needs to be balanced with the interest of the business. These types of companies can play an important role in promoting the use of standards in the neuroscience community, as a standard is often easier to employ, and thus more likely to be adopted, when a researcher can generate data directly into the standard format with the aid of tools they commonly use to generate or handle the data. This is such an instance, as the Neuromorphological File Format is the underlying standard of tools offered by MBF. The reviewers feel that the Neuromorphological File Format v 4.0 meets the criteria for INCF endorsement of a standard and should be put forward for community review. It is actively maintained, and widely disseminated through the MBF tools. It is freely available for use, well documented, and currently being used in multiple data-sharing projects. Moreover, in response to recommendations during the review process, MBF has created a transparent and balanced mechanism for community feedback. Open criteria: 1. Is the SBP covered under an open license so that it is free to implement and reuse by all interested parties (including commercial)? (List of open source licenses) Under the originally proposed license CC-BY-NC-ND, it would not be open for commercial use. After discussions with members of the SBP Committee and further consideration, MBF Bioscience proposes moving to the CC-BY-ND license, which would make it open to implement and reuse by all interested parties.The license in conjunction with their governance policy allows for anyone to submit modification requests, but these must be approved by the Neuromorphological File Format’s Editorial Board. The CC-BY-ND license would allow for other commercial entities to export digital models of microscopic anatomies in the neuromorphological file format. 2. What license is used? The Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC- BY-NC-ND) was originally proposed, but following discussions with members of the SBP Committee and further consideration, MBF Bioscience proposes moving to the CC-BY-ND license. 3. Does the SBP follow open development practices? The governance policy allows for anyone to request changes to the file format, however, the request must be approved by the Neuromorphological File Format’s Editorial Board. 4. Where and how are the code/documents managed? Neuromorphological file format documentation and examples are available on http://www.mbfbioscience.com/filespecification and https://github.com/MBFBioscience/nmf- schema. A web forum specific to the files specification facilitates community contributions and support for tool developers implementing the file format: https://forums.mbfbioscience.com/c/neuromorphological-file-specification. 5. Any additional comments on the openness of the SBP? MBF Bioscience is a commercial company, and as this standard is an output of their proprietary software, they put a great deal of effort into balancing their needs as a corporation but still offering a mechanism for the community (even commercial) to use and suggest modifications. Currently, reconstructions in the neuromorphological file format are only generated within MBF Bioscience proprietary software. In an effort to broaden the use of the neuromorphological file format and integrate other reconstruction formats into the open ecosystem, MBF Bioscience plans to develop a tool for reading and writing the neuromorphological format. This tool will be developed in Python and made available to the community via GitHub to allow users to adapt it for their specific needs. We predict that this tool will help to make the neuromorphological file format more accessible to the neuroscience community easing integration with software tools. Tool builders can use the neuromorphological reader/writer to develop tools that: convert alternative digital neuroanatomical reconstruction file formats to the open, and FAIR neuromorphological file format, convert the neuromorphological data files to a format that can be read by their unique software, and/or extract valuable metadata stored within neuromorphological data files. Simple examples of neuromorphological data files will be hosted on the GitHub repository. FAIR criteria Considers the SBP from the point of view of some (not all) of the FAIR criteria (Wilkinson et al. 2016). Is the SBP itself FAIR? Does it result in the production of FAIR research objects? Note that many of these may not apply. If so, leave blank or mark N/A. 1. SBP uses/permits persistent identifiers where appropriate (F1) Yes ● Research Resource Identifier (RRID) for the digital reconstruction software application and institution that produce that software are reported. These RRIDs are generated when the application is registered in the SciCrunch knowledge base. ● Unique identifiers are reported using an API connection with the SciCrunch InterLex Terminology Portal for subject and annotation of anatomical regions. 2. SBP allows addition of rich metadata to research objects (F2) Yes. The Neuromorphological file format stores: ● Metadata regarding the software application used to generate the digital reconstruction file to ensure the data generated is reproducible, reusable, and citable. This includes the expected file structure, the software application unique identifier, institution unique identifier, and version number of the neuromorphological file structure. ● Subject and annotation metadata for each data file including fields for subject species, identifier, sex, and age of the sample. ● The file path, name, X, Y, and Z scaling, location, size, order, and color channel information from the source microscopy image conveying the provenance of the data as it relates to the images in which it was derived. The lineage of the derivative data is recorded in the file, regardless of complexity. ● Essential information regarding the software application includes the application name, application version, application Research Resource Identifier (RRID), and institution RRID. 3. SBP uses/permits addition of appropriate PIDs to metadata (F3) N/A. Metadata is embedded within the Neuromorphological file format. 4. The protocol allows for an authentication and authorization when reQuired (A1.2) Not directly applicable to the file format. 5. SBP uses or allows the use of vocabularies that follow the FAIR principles (I2) Yes. RRIDs for software applications and institutions registered with the Resource Identification Portal are reported. This Portal collates many community repositories to provide unique resource identifiers that promote identification, discovery and reuse of the tools and data. Unique identifiers are reported using an API connection with the SciCrunch InterLex Terminology Portal for subject and annotation of anatomical regions. The terminology portal aims to collate existing terminologies, lexicons, and ontologies to provide unique identifiers that help scientists communicate about their data. Term relationships included are described by the SciCrunch Portal. 6. SBP includes/allows Qualified links to other identifiers (I3) N/A 7. Does the standard interoperate with other relevant standards in the same domain? (I1) This data standard employs mechanisms that facilitate interoperability such as using RRIDs and ontologies. 8. Does the SBP provide citation metadata so its use can be documented and tracked? (R1.2) N/A 9. Any additional comments on aspects of FAIR? Encoded
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