Use Cases Help to Identify Primary Concepts in Biodiversity Information Modeling

“Use cases” are “a methodology used in system analysis to identify, clarify and organize system requirements” (Brush 2022). They provide context and purpose for data concepts. The Darwin Core (Wieczorek et al. 2012) was initially designed to serve two purposes: 1) to gather data for documenting species distributions, particularly through species distribution modeling, and 2) to support the discovery of specimens in biological collections. The occurrence concept, the "existence of a dwc:Organism at a particular place at a particular time" (Darwin Core Maintenance Group 2009), was established so that both observations and specimens could be combined into a single tabular data set and used to document the distribution of a species. By 2008, the TDWG Technical Architecture Group began recommending that TDWG develop its standards in the framework of the semantic web (SW); i.e., RDF. Two efforts have contributed significantly to casting the terms of Darwin Core in RDF. Baskauf and Webb (2015) distilled nearly a decade of online discussions into the Darwin-SW. In a separate effort, but involving many of the same people, a series of workshops were convened to coordinate standards between the genomics and biodiversity communities and produced the BioCollections Ontology (BCO; Walls et al. 2014), which placed Darwin Core terms in the context of the "OBO foundry" (Smith et al. 2007) and the Basic Formal Ontology (BFO; Arp et al. 2015, but also see videos by Smith). Darwin-SW included explicit recognition of IndividualOrganism, Occurrence, Event, and Token (i.e., evidence of a dwc:MaterialSample or an observation). The simplest use case, in which an organism is collected or observed once, doesn't require that Organism, Occurrence and MaterialSample/Observation be recognized as separate entities. The relationships are one-to-one-to-one. They can be joined into a single entity with only one identifier (e.g., materialSampleID) without loss of information. Note that a specimen or observation infers the existence of an organism and its occurrence in nature. The use cases that require separating Organism and possibly Occurrence from the MaterialSample or Observation are the ones where an organism is sampled or observed, remains in nature, and is subsequently sampled or observed again; i.e., the organism is the target of more than one dwc:Event. These cases require that the organism can be reliably identified as the same organism encountered earlier; e.g., by tag, identifyin