USE CASE

Context of use:

With nanopublications, researchers can express their most important scientific findings in the form of individual “elementary snippets of knowledge” (or assertions) that are simultaneously human-readable and machine-actionable. These consist of a subject, object, and predicate triple structure, complete with provenance and publication information. Nanopublications can also be used to annotate, contribute to, update, and/or provide constructive feedback to existing data and publications. Nanopublications make it possible for simple scientific statements to be made FAIR: findable, available, identifiable, citable, machine-actionable, and reusable to both humans, computers, and AI tools.

Need:

Research output is exponentially growing, and so are the capabilities of AI-powered tools designed to assist scientists in navigating through the available publications and the latest scientific consensus. Adding standardized semantic meaning to entities and relations within them by community-accepted standards, controlled vocabularies, and ontologies along with precise information on the provenance and publication make the nanopublications a first-class method for scholarly semantic data publishing, annotation, and reuse.

Added Value:

Nanopublications convert human-created narratives of scientific knowledge into elementary, machine-actionable, simple, and straightforward scientific statements that prompt sharing, finding, accessibility, citability, and interoperability. By making it easier to trace individual findings back to their origin and/or follow-up updates, it also helps to better understand the provenance of biodiversity data.

Competitive Advantage:

In contrast to existing search engines and AI tools, the nanopublications follow a rather strict and pre-defined semantic structure, to minimize the risk of misinterpretation and ambiguity, which are both much more likely with human text or by purely AI-provided text and data interpretations.

A qualitative upgrade on the current use of biodiversity data:

The nanopublication format addresses the gap made by limited interoperability and provenance of biodiversity data, which is a major impediment in biodiversity science and research work. They can also be used for data exchange between research infrastructures and especially for annotations and curation of FAIR data.

Exemplary Use of the Service:

Nanopublications can be created and published through specialized tools, such as Nanodash (https://nanodash.petapico.org/) and nanopublication templates, for example, Associations between two organisms, or Associations between organisms and environments, or Organisms and nucleotide sequences.

For example, biotic relationships between organisms, e.g. feeding behavior (e.g. Species X feeds on Species Y) may be sought out from various publications to give a comprehensive view of the interactions within a certain ecosystem and its populations. Other examples of nanopublications in human-readable form are:

* The nucleotide sequence AH009955.2 (https://www.ncbi.nlm.nih.gov/nuccore/AH009955.2) was found in an organism of the species Meles meles (Linnaeus, 1758) (https://www.catalogueoflife.org/data/taxon/3ZDRX).

* The nucleotide sequence ABMC174-05 (https://v4.boldsystems.org/index.php/Public_RecordView?processid=ABMC174-05) can be used to identify the species Canis lupus Linnaeus, 1758) (https://www.catalogueoflife.org/data/taxon/QLXL).

Competencies and Skills that are needed to use the Service:

The collaboration between the Biodiversity Data Journal and Nanodash is designed by both biodiversity scientists and specialists in semantics to be accessible and usable by anyone with no specialized IT skills and competencies. To create nanopublications, authors need to click on the Nanopublications interface at the Biodiversity Data Journal and log into Nanodash with their ORCiD account.

Challenges for the Users:

Users may need time to familiarise themselves with the specifics of the formal structure of nanopublications and the use of ontologies and controlled vocabularies through the Nanodash platform and the range of available options to choose from (e.g. types of contributions, and associations).

Users Role in the Service Development

Users are encouraged to share their feedback about the platform and especially about the convenience and user-friendliness of the proposed nanopublication templates. The team needs to incorporate any user experience and constructive criticism given that the nanopublication format and workflows are quite novel and still in their very early development stage. We are also very keen to receive suggestions and proposals for new nanopublication templates for biodiversity.