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nmrXiv aims to provide the data, present it unambiguously, and make it FAIRer (Findable, Accessible, Interoperable, Reusable). It focuses on making the data not only human-readable, but machine-readable as well, so that researchers can leverage advanced Machine Learning, Named Entity Recognition, and other language processing techniques to re-analyze the data. This can be facilitated by using ontologies.

Ontologies usage in nmrXiv

nmrXiv will use ontologies to annotate as many fields as possible, along with requesting some fields' values to be ontology-driven, including all units. In addition to being ontologies-consumers, being an NMR data repository, nmrXiv is suited for gathering missing terms via user submission and contributing them to ontologies relevant to NMR data, or repositories data in general (in other words, to domain-specific and domain-independent ontologies). This will be achieved through collaboration with the NFDI4Chem Terminology Service from Task Area 6 in NFDI4Chem.

Ontology Component

The ontology component will be provided as an open-source, platform-agnostic tool compatible with JavaScript interfaces. This component will ensure a user-friendly experience in finding ontology values from any terminology service supported by the platform using the component (NFDI4Chem Terminology Service in the case of nmrXiv). It will simplifiy the search for terms by providing auto-complete functionality, while enabling the platform to restrict the suggested terms to selected ontologies that are relavent to the field in hand. The development of the component is currently going on this branch of nmrXiv repository.

nmrXiv will make use of the available APIs in the Terminology Service, which, along with more general possibilities such as retrieving an entire ontology, enable retrieving a specific term and restricting the search to a list of ontologies. Additionally, they support the suggestion of new terms. For a detailed description of the available endpoints and parameters, please check the API Documentation.

Schemas Export with Ontologies

Metadata describing the submitted projects/studies/datasets can be exported in nmrXiv as files complying with a schema chosen by the user from the schemas supported in nmrXiv. Many of those schemas support ontologies usage such as ISA and Bioschemas, which will efficiently reflect the use of ontology terms in the exported files by providing links and identifiers to the intended terms.

Ontologies of Interest in nmrXiv

Several factors have been considered to pick the ontologies to use in nmrXiv,:

  • Flexibility: A flexible workflow of new terms submission has a high priority for nmrXiv as it will contribute to ontologies curation.
  • Usage in the NMR domain: Ontologies frequently used by other NMR repositories and already known to the chemists have been considred.
  • Specialisation: Specialised ontologies usually provide more extensive coverage of the field with more accurate definitions of terms.

Domain-Independent Ontologies:

The following ontologies provide identifiers, references, formats, and possible operations to define experiments:

Domain-Specific Ontologies: