Nanopublications for Biodiversity Go Live

Abstract

A nanopublication is the smallest unit of publishable information: a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author(s) and serve to communicate a single statement, its original source (provenance) and citation record (publication info) (Mons and Velterop 2009, Kuhn et al. 2021). Nanopublications are fully expressed in both human-readable and machine-interpretable formats and can be cited thorugh their unique URI identifiers (IDs). The development of the concept, formats and use cases of biodiversity-specific nanopublications started back in 2016 (Penev et al. 2016). Recently, Pensoft and Knowledge Pixels created a workflow to publish nanopublications related to a published article (Fig. 1). At its core, the generic biodiversity nanopublication consists of a triple structure with a Subject element, a Relation element, and an Object element. The Subject element refers to a specific organism identified by an Organism ID, or groups of organisms (Taxa, identified by Taxon Concept IDs). Universal Unique Identifiers (UUIDs) are minted for both in all cases, although if the given organism already has an identifier, e.g., from digitised collections or observations, then this identifier can be specified too. The Organism is linked via class membership (rdf:type) to a Taxon Concept, which is identified with another UUID that is minted upon nanopublication creation. The need to mint IDs is due to the fact that Organism or Taxon Concept IDs (which refer to taxon names but also details about their interpretation and use) are not currently available in any comprehensive vocabulary or database. The minted Taxon Concept IDs are further defined by linking them to a Taxon Name ID from Catalogue of Life / ChecklistBank (via a relation called "has Taxon Name") and by linking to Taxon Name's concept (interpretation of the name) by a publication's Digital Object Identifier (DOI) or TreatmentBank entry (via a relation called "used as defined in"). Apart from assigning a Taxon Concept, the subject organism can optionally be linked to a life cycle stage (based on the Uber-anatomy (UBERON) Ontology) and to occurrence data via Occurrence ID. The Relation element expresses the association between Subject and Object, according to a particular ontology (e.g., Relation Ontology). The Object element may have different formats. In the template “Association between organisms" the Object has the same structure as the Subject; while in the template “Association between an organism and environment”, the Object is a type of habitat available from the Environment Ontolog (ENVO). In addition to an assertion, a nanopublication has a provenance record (e.g., DOI of the article where the assertion has been published) and the type of evidence entered in the BasisOfRecord field. The publication info always contains the ORCID (Open Researcher and Contributor ID) of the nanopublication's creator, and the timestamp of creation. Another type of nanopublication template annotates an entire article or selected text from it by using the ORCID of the creator as the Subject, the article's DOI as the Object, and the Citation Typing Ontology (CiTO) to express evaluation of the article (e.g., “supports”, “agrees with”, “discusses”). These templates are complemented by free text comments and are available under the Nanopub tab on the article webpages at several Pensoft journals (see example and blog). Nanopublications can also prompt other types of publications, e.g., hypotheses, to become more machine-interpretable, as discussed for invasion biology (Heger et al. 2023).