Digitisation / Cataloguing of non-textual objects: Towards an integrative and comprehensive standard for meta-omics data of collection objects (MOD-CO)
Microbial Ecology and Applied Microbiology
Final Report Abstract
With the advent of advanced molecular meta‘omics techniques and methods, a new era came up for analysing and characterizing historic collection specimens, as well as recently collected environmental samples. Nucleic acid and protein sequencing-based analyses are increasingly applied to determine provenance, identity, and traits of environmental (biological) objects and organisms. In this context, the need for new data structures became evident and former approaches for data processing need to be expanded according to the new meta’omics techniques and operational standards. The MOD-CO project addressed these issues. A cooperative Semantic Wiki working environment was created for the project partners. It allows them to collect general information on schema organisation in an access-restricted internal part and facilitates the organisation of publication of less structured as well as Linked-Open-Data-structured information in the public part. In parallel, the concrete data management on schema design, descriptor definition, descriptor grouping and descriptor mapping could be done in an installation of the SQL database DiversityDescriptions (DD). Existing schemata and community standards in the biodiversity and molecular domain concentrate on (minimum) sets of terms important for data exchange and publication. Detailed operational aspects of provenance and laboratory as well as object and data management issues are often neglected. The MOD-CO (= Meta’Omics Data and Collection Objects) schema has therefore been set up as a new schema for meta’omics research, with a hierarchical organisation of the descriptors describing collection samples, as well as products and data objects generated during subsequent processing. MOD-CO schema is comprehensive and focussed on operational aspects. It is thereby suitable to support database modelling for R & D laboratory management systems (LIMS) with functions of an Electronic Laboratory Notebook (ELN). The schema in its current version 1.0 includes 653 descriptors and 1,810 predefined descriptor states. It is published in several representations, one being a TDWG terminology Wiki compliant Semantic Media Wiki publication with 2,463 interlinked wiki pages for the ‘concepts’, being equivalent to the descriptors and descriptor states and being grouped in 37 ‘concept (sub-)collections’. The SQL database application DiversityDescriptions is the generic tool for MOD-CO schema development and applied for descriptor mapping issues concerning external data exchange schemata. DD was expanded for the prototypic implementation of core functions of a LIMS and ELN with real life use cases from meta’omics research. The MOD-CO partners organised workshops for domain experts, training courses and participated on several national and international conferences. The MOD-CO wiki under www.mod-co.net gives open and free access to the schema publications, use cases and downloads of xml data files as well as to the generic software tool appropriate for schema development, i.e. DiversityDescriptions.
Publications
- 2016. Linking external SQL databases and the Semantic Web: A Pipeline for dynamic web publication with stable URI identifiers for database structural information and content schemes – In TDWG 2016 Annual Conference. Santa Clara de San Carlos, Costa Rica. 5.–9. December 2016
Triebel, D., Link, A., Hagedorn, G., Plank, A., Weiss, M., Fichtmueller, D., Weibulat, T. & Rambold, G.
- 2016. Management and publication of an integrative and comprehensive scheme for meta-omics data of collection objects (MOD-CO). – In TDWG 2016 Annual Conference. Santa Clara de San Carlos, Costa Rica. 5.–9. December 2016
Yilmaz, P., Link, A., Weibulat, T., Glöckner, F.O., Triebel, D. & Rambold, G.
- 2016. Towards an integrative and comprehensive standard for meta-omics data of collection objects (MOD-CO). – In 17th Annual Meeting of the Gesellschaft für Biologische Systematik. 21.–24. February 2016. – Zitteliana 88: 55. München
Yilmaz, P., Klaster, S., Link, A., Weibulat, T., Glöckner, F. O., Triebel, D. & Rambold, G.
- 2017. Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects. – Database, 2017, 1–9
Güntsch, A., Hyam, R., Hagedorn, G., Chagnoux, S., Röpert, D., Casino A., Droege, G., Glöckler, F., Gödderz, K., Groom, Q., Hoffmann, J., Holleman, A., Kempa, M., Koivula, H., Marhold, K., Nicolson, N., Smith, V. S. & Triebel, D.
(See online at https://doi.org/10.1093/database/bax003) - 2017. Citation of a taxon name identifier issued by the ICN-recognized registration repositories instead of taxon name author citation. – Taxon 66(5): 1200–1203
Rambold, G., Bensch, K., Kirk, P. M., Yao, Y.-J., Robert, V., Sanz, V. & Triebel, D.
(See online at https://doi.org/10.12705/665.12) - 2018. (F-007) Proposal to recommend the use of an identifier as an alternative to the citation of the authors of fungal names. In: Proposals for consideration at IMC11 to modify provisions related solely to fungi in the International Code of Nomenclature for algae, fungi, and plants. – IMA Fungus 9(1): vi–vii
Rambold, G., Bensch, K., Kirk, P. M., Yao, Y.-J., Robert, V. & Triebel, D.
- 2018. A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing. – Database, 2018, 1–10
Triebel, D., Reichert, W., Bosert, S., Feulner, M., Osieko Okach, D., Slimani, A. & Rambold, G.
(See online at https://doi.org/10.1093/database/bax096)
