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. 2019 Jan 1:2019:baz002.
doi: 10.1093/database/baz002.

Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research

Gerhard Rambold  1 , Pelin Yilmaz  2 , Janno Harjes  1 , Sabrina Klaster  1 , Veronica Sanz  1   3 , Anton Link  3 , Frank Oliver Glöckner  2   4 , Dagmar Triebel  3
Affiliations

Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research

Gerhard Rambold et al. Database (Oxford). .

Abstract

With the advent of advanced molecular meta-omics techniques and methods, a new era commenced 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 the origin, identity and traits of environmental (biological) objects and organisms. In this context, the need for new data structures is evident and former approaches for data processing need to be expanded according to the new meta-omics techniques and operational standards. Existing schemas and community standards in the biodiversity and molecular domain concentrate on terms important for data exchange and publication. Detailed operational aspects of origin and laboratory as well as object and data management issues are frequently neglected. Meta-omics Data and Collection Objects (MOD-CO) has therefore been set up as a new schema for meta-omics research, with a hierarchical organization of the concepts describing collection samples, as well as products and data objects being generated during operational workflows. It is focussed on object trait descriptions as well as on operational aspects and thereby may serve as a backbone for R&D laboratory information management systems with functions of an electronic laboratory notebook. The schema in its current version 1.0 includes 653 concepts and 1810 predefined concept values, being equivalent to descriptors and descriptor states, respectively. It is published in several representations, like a Semantic Media Wiki publication with 2463 interlinked Wiki pages for concepts and concept values, being grouped in 37 concept collections and subcollections. The SQL database application DiversityDescriptions, a generic tool for maintaining descriptive data and schemas, has been applied for setting up and testing MOD-CO and for concept mapping on elements of corresponding schemas.

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Figures

Figure 1
Figure 1
Workflow segments concatenated to a workflow. A workflow segment comprises the elementary operations transformation, measurement and transaction being applied once or twice (due to preceding subsampling or aliquotation) to a physical object in focus, and the generation of data (measurement) and its subsequent transformation, measurement and transaction within the segment.
Figure 2
Figure 2
Naming of MOD-CO concepts according a multipartite approach.
Figure 3
Figure 3
Excerpt of MOD-CO Schema Reference (versioned MOD-CO namespace scheme publication) with one concept showing concept name and concept details: the first elements of the multipartite name refer to the core element of the concept, the second to last (i.e. ‘referencing algorithm’) to its property and the last (i.e. ‘category’ equal to ‘categorical’) to the data type.
Figure 4
Figure 4
Excerpt of MOD-CO LOD-compliant namespace scheme publication with two concept collections and access to single Wiki pages, which provide stable URIs for each concept and concept collection.
See this image and copyright information in PMC

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