Scientific names serve to label biodiversity information: information related to species. Names, and their underlying taxonomic definitions, however, are unstable and ambiguous. This negatively impacts the utility of names as identifiers and as effective indexing tools in biological informatics where names are commonly utilized for searching, retrieving and integrating information about species. Semiotics provides a general model for describing the relationship between taxon names and taxon concepts. It distinguishes syntactics, which governs relationships among names, from semantics, which represents the relations between those labels and the taxa to which they refer. In the semiotic context, changes in semantics (i.e., taxonomic circumscription) do not consistently result in a corresponding and reflective change in syntax. Further, when syntactic changes do occur, they may be in response to semantic changes or in response to syntactic rules. This lack of consistency in the cardinal relationship between names and taxa places limits on how scientific names may be used in biological informatics in initially anchoring, and in the subsequent retrieval and integration, of relevant biodiversity information. Precision and recall are two measures of relevance. In biological taxonomy, recall is negatively impacted by changes or ambiguity in syntax while precision is negatively impacted when there are changes or ambiguity in semantics. Because changes in syntax are not correlated with changes in semantics, scientific names may be used, singly or conflated into synonymous sets, to improve recall in pattern recognition or search and retrieval. Names cannot be used, however, to improve precision. This is because changes in syntax do not uniquely identify changes in circumscription.

These observations place limits on the utility of scientific names within biological informatics applications that rely on names as identifiers for taxa. Taxonomic systems and services used to organize and integrate information about taxa must accommodate the inherent semantic ambiguity of scientific names. The capture and articulation of circumscription differences (i.e., multiple taxon concepts) within such systems must be accompanied with distinct concept identifiers that can be employed in association with, or in replacement of, traditional scientific names.

Taxonomic name services, taxon concepts, identifiers, relevance, search and retrieval

Scientific names are labels for taxa that are governed by formalized rules of nomenclature. These rules were introduced to establish clarity, stability, economy and uniqueness to the fragmented landscape of pre-Linnaean nomenclature (Mayr 1991). Sherborn’s Index Animalium(IA) represents a monumental attempt to capture key data elements regarding the source and orthography of (nearly) all zoological names for species from the beginning of formalized Linnaean zoological nomenclature in 1758 through 1850. An index, in the sense of Index Animalium, is a list of terms linked to, or pointing to, a greater volume of values, data, information or knowledge that pertain to the term. Index Animalium links zoological names to their originating bibliographic citation. (Pilsk et al. 2016) It also links two separate records when a species described with one name was subsequently moved to a new genus and established a new binomial name. The primary function, of the more than 9,000 pages, however, is as an authoritative reference that provides the correct spelling of a name and pointer to its original description (CWR 1903, Alonso-Zarazaga et al. 2016). Much of the value and respect that IA has received is derived from the enormous amount of work required to compile and verify the names and associated publications. Biologists rely on this reference when they need to consult the original work (Evenhuis 2016).

The use and value of IA, however, extends beyond its referential value and, in an age of increasingly vast amounts of digitized biodiversity information being accessible online, serves as an immensely valuable resource in establishing order within a substantially larger index of biodiversity information: the entire corpus of recorded biodiversity knowledge.

Throughout the past 250 years, nearly all information about taxonomic groups such as species has been linked through a name, nearly always a scientific name. (Grimaldi and Engel 2005). Scientific names are not the sole means to label species information. Informal and provisional names also play supporting roles (Murray and Stackebrandt 1995) but only when their use can be unambiguously linked to a species through a scientific name. Practically speaking, scientific names form the basis for referring to species and they label biodiversity information across the entire spectrum of biodiversity knowledge (Thompson and Pape 2016).

Names label voucher specimens in natural history museums, for instance, and are used to identify biological observations at all scales, from molecules to ecosystems, providing the key biological context to associated metacontent such as the observation locality and date Figure 1. Scientific names are used in all manner of publications and communications be they scientific, agricultural, commercial, medical, legislative or social. Increasingly, these communications are taking place online and in digital environments and legacy information is being retrospectively digitized and also placed in online data stores (Patterson et al. 2010). Without a name associated with an information or data object, the taxonomic link is effectively lost.

Figure 1. 

Scientific names label information about species.

Given the ubiquitous linkage between biodiversity information and scientific names, there must exist an enormous and virtual super-index of names tied to the world’s species information. Such an index, assembled and presented within a Sherborn-like data store, would, in principle, link to all, or nearly all, information related to all described species. This implies a far more important and central role for names as mediators to biodiversity information. As more and more retrospective and prospective information is placed in online data stores, such an index is becoming increasingly realistic (Pyle 2016).

Indexing and search engines like Google and Yahoo generate billions of dollars in revenue by processing countless electronic data stores and producing searchable indexes (Varian 2007). An index of names, such as provided through Index Animalium, combined with similar technologies could, in principal, provide access to whatever online information is associated with the names in the index. Broaden the list through the consolidation of similar indexes within the zoological, microbial and botanical domains, and it’s not inconceivable that a comprehensive list of names could be assembled. Such a collection would provide the means to discover and access the complete wealth of recorded biodiversity knowledge (Patterson et al. 2010). The legacy of Linneaus and Sherborn appear to have provided the framework for the systematic organization and delivery of biodiversity knowledge in the digital age (Patterson et al. 2006).

There are limits to this utility however, and these limits are inherent within biological nomenclature and its relationship to the taxa they label. Index Animalium and other similar compilations represent a list of names, not lists of species. This distinction has ramifications that place limits on helping us utilize their ubiquity in labeling biodiversity information. Semiotics refers to the study of how we use signs or symbols, such as names, to confer meaning to objects in the real world and provides a broader framework to this understanding. Semiotics is divided into several sub-domains that include:

• Semantics, which refers to the relationship between signs and the things to which they refer; their meaning.

• Syntactics, which refers to the relationships among signs or symbols within formal structures.

These two terms have analogs in taxonomy. Nomenclature, particularly formalized scientific nomenclature governs much of the syntax domain while semantics is the realm of taxonomy, which links names with taxon definitions or circumscriptions (Witteveen 2014, Dubois 2005, Franz et al. 2008).

The triangle of reference, or semiotic triangle (Ogden and Richards 1923), is a model of how syntax and semantics are related to the objects they represent (van Rijsbergen 1979).

In the model (Figure 3), there is no direct relationship (dotted line) between symbols (i.e., names) and the real-world objects (the referent) they represent (A). Meaning, or the relationship between the name and the object, is conveyed only through a concept that exists in the mind of the user of the name. In taxonomy, a biologist (B) determines a specimen is sufficiently distinct to constitute a new species and documents the concept or idea of this novelty to a publication and assigns a name to it. Another person (C) subsequently reading the name, perhaps as a label on a specimen, evokes the concept originally described by the biologist, to refer to the specimen. Accurate communication occurs when there is congruence between both concepts among the writer and the reader.

Figure 2. 

All information of a species is linked by a name.

Figure 3. 

The semiotic triangle describes how names communicate meaning.

In biological taxonomy, a species name refers to a concept anchored by a specimen but created in the mind of a biologist. The function of the name is to facilitate communication. Communication is facilitated, however, only when the concepts (not the objects) are approximately congruent. Success is not black and white, but can be partial – whether partial is good enough is contingent on context-specific inference needs that the reciprocal concept alignment must fulfill. Thus, two persons look at the same avocado and one declares it a fruit, because it is derived from floral ovaries, while another declares it is not a fruit because it is not sweet. This conflict occurs when there is no congruency in the concepts invoked through the use of the name. Similar issues occur within taxonomy. In the simple case above, the term ‘fruit’ is associated with two definitions, or, more formally, the cardinality between syntax and semantics is one-to-two, or more generally, one-to-many (1:N). The same object evokes the same name but refers to two concepts according to two individuals. It is the relationship between the name and the concept that is important. Cardinality between syntax and semantics has a direct impact on the use and limits of scientific names as identifiers in biological informatics (Franz NM 2014).

Identifiers such as names have utility in information discovery and retrieval that is directly proportional to the degree of correlation between the term and the associated meaning or, in the semiotic context, in the correlation between syntax and semantics. Laypersons may think of scientific names as stable and unique, where a single Latin binomial name refers to one species and remains that way for all time. In other words, that there is a stable one-to-one relationship between a name (syntax) and the taxon (semantics) that it labels (Stringer 2002). This is an important informatics pre-condition if we are to rely on names as a means to search for and retrieve relevant information related to taxa (Thau et al. 2010).

Relevance in information retrieval is measured as a combination of two factors: precision and recall (van Rijsbergen 1979). Precision refers to the exactness, or quality in an information retrieval instance. Recall is a measure of quantity or completeness. For example, in Figure 4, below, a search for articles on ants misses some relevant articles but also accidentally returns articles on plants.

Figure 4. 

Precision vs. recall in search results.

A search result, therefore, can produce two kinds of relevance errors.

• A false positive error occurs when the system returns a result that is non-relevant. This is an error of precision.

• A false negative error occurs when the system fails to return a relevant result. This is an error of recall.

Mitigation of homonyms

There are two ways to improve precision when a name is too ambiguous; syntactic and pragmatic. The syntactic approach is to change the cardinality between the names and taxa from one-to-many to one-to-one. This is achieved by changing the syntax to two distinct forms. In the case of Aotus for example, the legume may be formally referred to as Aotus Smith, 1805 while the primate is Aotus Illiger, 1811. While the name components remain identical, the appended authorship information renders them distinct. The usage of this form of the name improves precision, effectively moving the burden of relevance to recall. The use of the more precise term supports the distinction of the two taxa but results in the minting of a synonym. The result would be fewer false positive but a potential increase in false negatives as the use of the more refined name would miss relevant results labeled only with the homonym. In general, improvements in precision result in a decrease in recall and vice-versa; Resolving this would require changing all the retrospective ambiguous use of the name Aotus with the more precise amended form (Rees 2012).

The pragmatic approach relies on analytic techniques that try to identify context to disambiguate the term. For example, the term “monkey” or “pea” in the vicinity of the use of the name Aotus, could help disambiguate the usage and improve precision (Boulis and Ostendorf 2005).

One-to-Many

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One-to-Many	Cardinality		Impacts	Result
	Syntax	Semantics	Precision	False positives
	One name	Multiple meanings

Polysemy (literally “many meanings”) is a condition similar to homonymy and refers to a single name that refers to two taxa. Instead of consisting of entirely distinct taxa, however, the circumscriptions overlap. This occurs when taxa are lumped and split and result in two or more taxon concepts (Remsen and Patterson 2010) (Franz and Cardona-Duque 2013). A polyseme impacts relevance in a manner similar to a homonym but is much more common. Impacts on relevance are as follows:

• Recall – Recall is not impacted. Syntactic ambiguity is not a factor here as there is only a single name.

• Precision – Polysemes impact precision because a single taxon name refers to two or more different circumscriptions for a taxon.

Pneumocystis carinii Delanoe & Delanoe, 1912, is a fungal pathogen responsible for a deadly pneumonia (PCP) in HIV-infected patients. It was originally described in dogs and rats and later found to occur in humans. In 2002 genetic analysis determined that the human pathogen was distinct from the one that infects dogs. A new name, Pneumocystis jiroveci, was applied to the human pathogen (Stringer 2002). The result was a taxonomic split where the original name, Pneumocystis carinii subsequently referred to just part of the original circumscription and the new name Pneumocystis jiroveci, to the remaining part. Figure 5 illustrates this split.

Figure 5. 

A polyseme is a single name referring to more than one overlapping or included concept.

The name, Pneumocystis carinii, now refers to two different circumscriptions; one that contains dog and human pathogens and one that contains only dog pathogens. A search using the name can return results that may refer to either use of the name, corresponding to false positives that impact precision.

Scientific names link nearly all information related to a species but the relationship between nomenclatural syntax and taxonomic semantics is inherently ambiguous. Informatics processes that rely on data-gathering methods linked to taxon names are susceptible to this ambiguity and run the risk of providing imprecise or incomplete sets of data to subsequent downstream processes.

Sets of related scientific names may be used, as in today’s array of taxonomic name servers, to improve recall in search and retrieval for information tied to a taxon. The ambiguity of scientific names that occurs when the same name refers to two distinct, or overlapping taxa, however means that, in many cases, a single name returns an imprecise result and this is something that cannot be rectified through the use of name services.

Comprehensive taxonomic thesauri are required to model the relationships between names and taxa. Nomenclatural databases that currently capture the objective syntactic properties of names could improve their relevance by cataloging nomenclatural synonyms, as attempted in Index Animalium. Effectively modeling semantics requires a clean division between these syntactic aspects of taxonomy and the subsequent subjective processes that result in changes in circumscription (Lepage et al. 2014). An ideal system enables the identification, modeling and exposure of a complete array of circumscription changes for any and all taxa and are coupled with services that allow these to be embedded within informatics processes (Chem et al. 2014, Tuominen et al. 2011).

The author would like to extend his thanks and graditude to reviewers, Nico M Franz, Ph.D., Associate Professor and Curator of Insects, Arizona State University, and John Todd, Ph.D., Curator of Molluscs, Natural History Museum, London. An additional thanks to Dr. Ellinor Michel, ICZN Executive Secretary, for serving as general editor and expediting the whole Sherborn publication process.