MetaCook: The Metadata Cookbook
The importance of metadata when sharing FAIR data cannot be overstated. The MetaCook project was initially envisioned as a cookbook-like set of instructions for developing high-quality vocabularies and subsequently metadata. However, we decided to turn the cookbook into an interactive software called VocPopuli, which includes the collaborative development of controlled vocabularies. In this way, instead of reading lists of instructions, users from any background and level of experience can easily navigate VocPopuli and receive interactive guidance. Using VocPopuli ensures that the developed vocabularies will be FAIR themselves.
VocPopuli offers the capability to immediately apply the vocabulary to datasets stored in electronic lab notebooks. As an example, an integration with Kadi4Mat is already established, and we are currently implementing the same for Herbie.
Functionally, VocPopuli has a few main features:
GitLab login is used to associate user contributions with term versions and vocabularies
Each term’s provenance can be tracked both via VocPopuli’s user interface and GitLab’s commit history and branches
Every term contains: label, synonyms, translations, expected data type, broader terms, related internal/external terms, up/downvotes, collaborative discussion board, visual history graph
Each vocabulary contains: metadata about its contents, a hierarchical structure of terms, a set of allowed named relationships, a git repository
In the backend VocPopuli’s data is stored in a graph database
SKOS and PROV (in progress) are optional exports
Any resource can be digitalized: Lab Procedure; Lab Specimen, ELN, ELN Export, Data Analysis
FAIR vocabularies hold enough information which enables their transformation into ontologies. We verify this with a prototype of a second piece of software called OntoFAIRCook. At the time of writing, OntoFAIRCook is available as a command line tool, and is being transformed into a web interface which is easy to use.
MetaCook is a joint project between the Helmholtz Centres KIT and Hereon funded within the HMC Project Cohorte 2021.
https://helmholtz-metadaten.de/storage/1027/2022-03-30_Metadata-Coockbook_HMC-Welcome.pdf
Publications:
Flachmann, M., Biesinger, J., Gorenflo, M., Bagov, I., Greiner, C. and Garabedian, N. (2023) „Copper Tribology FAIR Data Experiments - Sapphire Counterbody“. Available at: https://doi.org/10.5281/zenodo.8024881 (Accessed: 08.04.2024).
Bagov, I., Flachmann, M., Garabedian, N., Tiezema, T., Li, Y., Rau, J., Blatter, I., Dollmann, A., Seitz, M. and Greiner, C. (2023) „Vocabulary of Materials Tribology Lab at KIT“. Available at: https://doi.org/10.5281/zenodo.7923148 (Accessed: 08.04.2024).
Bagov, I., Garabedian, N., Ye, N., Meller, M. and Bresser, F. (2023) „VocPopuli“. Available at: https://gitlab.com/metacook/vocpopuli (Accessed: 08.04.2024).
Dembska, M., Held, M. and Schindler, S. (2024) “PolyMat - bringing semantics to polymer membrane research”, in Valdestilhas, A. et al. (eds.) Proceedings of the First International Workshop on Semantic Materials Science: Harnessing the Power of Semantic Web Technologies in Materials Science. (CEUR Workshop Proceedings). Aachen. URL: https://ceur-ws.org/Vol-3760/paper6.pdf
Martin Held; Talk ”Electronic Lab Notebooks Compiling Big Datasets for Machine Learning Analysis”, Microscopy Conference, 26.02 – 02.03.2023.
Ilia Bagov, Nick Garabedian, Floriane Bresser, Malte Flachmann, Christian Greiner, Milosz Meller, Nuoyao Ye; Workshop “An End-to-End Framework for FAIR Data in Experimental Materials Tribology”, NFDI-MatWerk Conference, 27.-29.06.2023.
Nick Garabedian, Ilia Bagov, Malte Flachmann, Nuoyao Ye, Miłosz Meller, Floriane Bresser, Christian Greiner; Poster “(Do) We Produce FAIR Data”, 1st Conference on Research Data Infrastructure, 12.-14.09.2023.
Nick Garabedian, Ilia Bagov, Malte Flachmann, Nuoyao Ye, Miłosz Meller, Floriane Bresser and Christian Greiner; Poster “Generate, Store, and Publish FAIR Data in Experimental Sciences“, 19th International Conference on Semantic Systems, 20.-22.09.2023.
Nick Garabedian; Tutorial “VocPopuli and Kadi4Mat for FAIR Data Collection in Experimental Sciences”, 2023 NFDI4Ing Conference, 27.-.28.09.2023.
Nick Garabedian, Martin Held, Ilia Bagov, Fabian Kirchner; Workshop “An End-to-End Framework for FAIR Data in Experimental Materials Science”, HMC Conference 2023, 10.-12.10.2023.
Malte Flachmann, Jakob Biesinger, Max Gorenflo, Ilia Bagov, Christian Greiner, Nikolay Garabedian; Research data “Copper Tribology FAIR Data Experiments - Sapphire Counterbody”, https://doi.org/10.5281/zenodo.8024881.
Fabian Kirchner; Invited Talk ”From ontologies to knowledge graphs with the ELN Herbie (short)”, MSE Day, 14.11.2023.
Fabian Kirchner; Talk ”From ontologies to knowledge graphs with the ELN Herbie (extended)”, HMC dialogue, 08.12.2023.
Ilia Bagov, Malte Flachmann, Nikolay Garabedian, Torben Tiezema, Yulong Li, Julia Rau, Ines Blatter, Antje Dollmann, Michael Seitz, Christian Greiner; Controlled vocabulary ”Vocabulary of Materials Tribology Lab at KIT”, https://doi.org/10.5281/zenodo.7923148.
Ilia Bagov, Nick Garabedian, Nuoyao Ye, Miłosz Meller, Floriane Bresser; Software ”VocPopuli”, https://gitlab.com/metacook/vocpopuli.
Garabedian, N., et al., Poster “MetaCook: FAIR Vocabularies Cookbook”, HMC Conference 2022, https://doi.org/10.5281/zenodo.7125644.
Bagov, I., et al., Poster abstract, “Collaborative Metadata Definition using Controlled Vocabularies, and Ontologies”, First International Conference on FAIR Digital Objects 2022, https://doi.org/10.3897/rio.8.e94931.
Garabedian, et al., Presentation, “Collaborative Metadata Definition using Controlled Vocabularies, and Ontologies - FAIR Data Showcase in Experimental Tribology”, NFDI4Ing Conference 2022, https://doi.org/10.5281/zenodo.7362038 (Contribution 844).
Garabedian, N., et al., Video “Big (Open) Data in Tribology. Big (Open) Data in Experimental Science.” https://www.youtube.com/watch?v=ts1LeM2hVpQ.
Garabedian, N., et al., Video, “Give Tribological Data a Meaning: VocPopuli and PIDs”, https://www.youtube.com/watch?v=ts1LeM2hVpQ.
Garabedian, N., Video, “HMC Project MetaCook – start your FAIR journey with VocPopuli”, https://doi.org/10.5446/60349.