Biological Taxonomies Research Articles

Guidance for creating individual and batch latinized binomial virus species names.

The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.

Attention and platypuses.

This perspective piece discusses a set of attentional phenomena that are not easily accommodated within current theories of attentional selection. We call these phenomena attentional platypuses, as they allude to an observation that within biological taxonomies the platypus does not fit into either mammal or bird categories. Similarly, attentional phenomena that do not fit neatly within current attentional models suggest that current models are in need of a revision. We list a few instances of the "attentional platypuses" and then offer a new approach, that we term dynamically weighted prioritization, stipulating that multiple factors impinge onto the attentional priority map, each with a corresponding weight. The interaction between factors and their corresponding weights determines the current state of the priority map which subsequently constrains/guides attentional allocation. We propose that this new approach should be considered as a supplement to existing models of attention, especially those that emphasize categorical organizations. This article is categorized under: Psychology > Attention Psychology > Perception and Psychophysics Neuroscience > Cognition.

TaxoTracker: A collaborative platform for taxonomic resource maintenance

Taxonomy is foundational to all biological sciences. Names allow us to organize and communicate information about biological groups. This process is critical for understanding and preserving the biodiversity of our planet. There are an estimated 8.7 million extant eukaryotes (Mora et al. 2011) and possibly as many as 1 trillion microbial species (Locey and Lennon 2016), with untold numbers of extinct taxa yet to be discovered in the fossil record. Accounting for all these taxa and maintaining their nomenclatural resources is one of the great challenges in biology. A few major hurdles in overcoming this challenge are the inability to find, share, and update taxonomic resources efficiently in real time. Efforts to standardize and continually update taxonomic names in a sustainable way have been limited. The problem is complex, and solutions must deal with the large backlog of names, a constant stream of new names, the confusing merging and splitting of taxonomic synonyms, the subjective nature of taxonomic concepts, and the fundamental limitations on available expertise and curators' time to prepare and maintain such resources. Hyperdiverse groups such as arthropods are especially challenging as there are relatively few experts on any given lineage and changes in taxonomy can be rapid as new species are continually being discovered and described. After struggling to wrangle taxonomic resources in support of specimen digitization efforts, I began development of TaxoTracker as a proof-of-concept, web-based platform for facilitating expert curation and dissemination of biological taxonomies. TaxoTracker is still in development, but its current and planned functionalities will be shown through a combination of demonstration and discussion. TaxoTracker identifies and implements features that attempt to simplify the production and maintenance of expert-curated resources, while also limiting the responsibilities that are placed on individual experts who are often already overburdened and underfunded. These features include: Centralized, searchable, and easily obtained resources in useful formats Community-driven, citation-based curatorial suggestions Expert-reviewed curatorial recommendations Consensus-driven curatorial decisions Effort tracking and credit for suggestions and reviews Centralized, searchable, and easily obtained resources in useful formats Community-driven, citation-based curatorial suggestions Expert-reviewed curatorial recommendations Consensus-driven curatorial decisions Effort tracking and credit for suggestions and reviews

Multi-Level Area Balancing of Clustered Graphs.

We present a multi-level area balancing technique for laying out clustered graphs to facilitate a comprehensive understanding of the complex relationships that exist in various fields, such as life sciences and sociology. Clustered graphs are often used to model relationships that are accompanied by attribute-based grouping information. Such information is essential for robust data analysis, such as for the study of biological taxonomies or educational backgrounds. Hence, the ability to smartly arrange textual labels and packing graphs within a certain screen space is therefore desired to successfully convey the attribute data . Here we propose to hierarchically partition the input screen space using Voronoi tessellations in multiple levels of detail. In our method, the position of textual labels is guided by the blending of constrained forces and the forces derived from centroidal Voronoi cells. The proposed algorithm considers three main factors: (1) area balancing, (2) schematized space partitioning, and (3) hairball management. We primarily focus on area balancing, which aims to allocate a uniform area for each textual label in the diagram. We achieve this by first untangling a general graph to a clustered graph through textual label duplication, and then coupling with spanning-tree-like visual integration. We illustrate the feasibility of our approach with examples and then evaluate our method by comparing it with well-known conventional approaches and collecting feedback from domain experts.

An expert study on hierarchy comparison methods applied to biological taxonomies curation.

Comparison of hierarchies aims at identifying differences and similarities between two or more hierarchical structures. In the biological taxonomy domain, comparison is indispensable for the reconciliation of alternative versions of a taxonomic classification. Biological taxonomies are knowledge structures that may include large amounts of nodes (taxa), which are typically maintained manually. We present the results of a user study with taxonomy experts that evaluates four well-known methods for the comparison of two hierarchies, namely, edge drawing, matrix representation, animation and agglomeration. Each of these methods is evaluated with respect to seven typical biological taxonomy curation tasks. To this end, we designed an interactive software environment through which expert taxonomists performed exercises representative of the considered tasks. We evaluated participants’ effectiveness and level of satisfaction from both quantitative and qualitative perspectives. Overall quantitative results evidence that participants were less effective with agglomeration whereas they were more satisfied with edge drawing. Qualitative findings reveal a greater preference among participants for the edge drawing method. In addition, from the qualitative analysis, we obtained insights that contribute to explain the differences between the methods and provide directions for future research.

SEMANTICALLY ORGANIZED BULGARIAN-CHINESE DICTIONARY OF ZHAN SONGFEN (SOFIA, 1969) – A RESEARCH BASE FOR LINGUISTIC STUDIES

han Songfen (张荪芬女士) was a co-founder of the teachings of Modern Chinese and the founder of the teachings of wenyan in Sofia University. In 1969 she published a semantically organized Bulgarian-Chinese Dictionary 、保汉分类词典。This dictionary can serve as a very useful base for linguistic studies. Some words for domestic birds are examined in the paper as an example of a possible analysis. As is known, natural objects are presented through linguistic taxonomies differently in different languages. With the designation of poultry, the Bulgarian language offers separate names for birds of the same species, specialized by sex and age. This is also a characteristic of the linguistic taxonomy of domestic animals and of animals in general as well. For example, in the Chinese language, there is a general term 鸡 jī which has the meaning `hen` as a biological species. There are no gender difference in this concept (i.e., the narrower term 'cock' is included here), nor age differences (i.e., the narrower term 'chicken' is included here). However, if a more specialized term is needed, it is expressed via composition：妈鸡 mā jī - `hen`, literally `mother hen`; 公鸡 gōng jī 'cock', literally `male hen`; .小鸡 xiǎo jī `chicken`, literally `little hen`. The formations with the main word-designation of the duck鸭yā and of the goose 鹅é as a biological species are parallel. These differences in the presentation of biological taxonomies in the language distinguish Chinese from Indo-European languages and not only from them.

“Every Living Beast Being a Word, Every Kind Being a Sentence”: Animals and Religion in Reformation Europe

The ability of animals to convey meaning, either sacred or profane, features prominently in the dialectic of natural knowledge and sacred histories. Animals, particularly those that exhibited irregularities of nature, symbolised and revealed God’s wrath and favour, fulfilling a polemical and pastoral purpose in the communication of God’s anger and assiduous care for humanity. The language of readable nature ran through the ancient natural histories of Pliny and Aristotle, the words and images of the medieval bestiaries, and the natural histories and popular discourses of Reformation Europe. In the history of the natural world, ‘God’s great book in folio’, ideas about connections between the written word and human observation, miracles, wonders and providences, were interleaved with theological and biological taxonomies. In so doing, discussions of irregularities and portents in nature expose the conceptualisation of human relationships with the world, with the past, with the present, and with the divine. This article explores the connections between real and symbolic animals, religious, and the plasticity of God’s creation in the natural histories and polemical literature of the Reformation. It explores the multivalent positioning of particular sea creatures as providential signs of God’s continued presence in the world, natural phenomena, and man-made objects, and the ongoing syncretism between natural history, religion, ancient texts and human observation in the dialectic of this period.

Vocabularies of Values: Tackling the Heterogeneity Problem

In the process of sharing information, it is of highest importance that we utilize common codes and signifiers, so that communication is effective. This process presents a series of complexities that are related to capturing and transmitting the meaning of the information despite homonymy, polysemy and synonymy. Biodiversity data sharing is not exempt from these challenges and understanding the meaning often requires expert knowledge. For communication to be effective, and therefore for data to be of maximal re-use, we need common vocabularies that unequivocally refer us to the same concepts. The community has agreed upon some vocabularies to structure shared information, i.e., biodiversity data standards such as the Darwin Core standard (Wieczorek et al. 2012). The bterms in Darwin Core can be thought of as the names of the columns in a spreadsheet. For example, there are terms such as genus, stateProvince, sex, etc. This allows us to capture and share information which we agree belongs under one of those terms. However, we have not yet reached an agreement on how to express the permitted values under all those terms, that is, vocabularies of values. As a simple example, we agree that if we have a record of an organism that is a female, we will share the fact that it is a female under the “sex” term, but we could represent female with the values “female”, “fem.”, “f.”, and other possible abbreviation and language variants. Other more complex examples, bound to expert knowledge, include biological taxonomies and how we name distinct species and species concepts. While many vocabularies exist in the community, we currently do not possess a full suite of vocabularies of values that apply uniformly across the biodiversity data community and there is no single repository to explore the available resources. While some of the available vocabularies are discipline-specific, many that could be applied more broadly remain independent and scattered. Additionally, similar lists of terms that refer to the same concepts can be found in different languages, but disconnected from one another. The lack of or non-adherence to vocabularies of values constitutes a data quality issue, as the heterogeneity in the data renders data less discoverable and difficult to use. Capturing information in myriad ways risks being incomplete and inaccurate in our transmission of information. If we cannot be certain that a particular value unambiguously refers to a particular concept, we cannot assert that a record containing that value could reliably be used for a particular purpose. In this context, the construction and use of vocabularies of values, including the explicit declaration of usage, is a data quality issue. From the TDWG Data Quality Interest Group we have begun to tackle this problem, with the aim of creating a suitable environment for thought and development of vocabularies of values. Accordingly, a new task group has been constituted, whose main goals are to: prepare a scoping document in which we will determine the types of vocabularies needed (including multi-lingual approaches) and the strategy for organizing the construction and/or management of new/existing vocabularies; develop a common repository to store vocabularies and/or link to existing ones; develop best practices for building TDWG vocabularies; and develop an exemplary vocabulary following the standard format. This will provide the community with a framework to work on and build upon vocabularies of values in a way that would allow better understanding and maximal interoperability.

Task-based assessment of visualization tools for the comparison of biological taxonomies

Maintenance and curation of large-sized biological taxonomies are complex and laborious activities. Information visualization systems use interactive visual interfaces to facilitate analytical reasoning on complex information. Several approaches such as treemaps, indented lists, cone trees, radial trees, and many others have been used to visualize and analyze a single taxonomy. In addition, methods such as edge drawing, animation, and matrix representations have been used for comparing trees. Visualizing similarities and differences between two or more large taxonomies is harder than the visualization of a single taxonomy. On one hand, less space is available on the screen to display each tree; on the other hand, differences should be highlighted. The comparison of two alternative taxonomies and the analysis of a taxonomy as it evolves over time provide fundamental information to taxonomists and global initiatives that promote standardization and integration of taxonomic databases to better document biodiversity and support its conservation. In this work we assess how ten user visualization tasks for the curation of biological taxonomies are supported by several visualization tools. Tasks include the identification of conditions such as congruent taxa, splits, merges, and new species added to a taxonomy. We consider tools that have gone beyond the prototype stage, that have been described in peer-reviewed publications, or are in current use. We conclude with the identification of challenges for future development of taxonomy comparison tools.

Names are not good enough: Reasoning over taxonomic change in the Andropogon complex1

We present a novel, logic-based solution to the challenge of reconciling the meanings of taxonomic names across multiple biological taxonomies. The challenge arises due to limitations inherent in using type-anchored taxonomic names as identifiers of granular semantic similarities and differences being expressed in original and revised taxonomic classifications. We address this challenge through: (1) the use of taxonomic concept labels - thereby individuating name usages according to particular sources and allowing each taxonomy to be recognized separately; (2) sets of user-provided Region Connection Calculus articulations among concepts (RCC-5: congruence, proper inclusion, inverse proper inclusion, overlap, exclusion); and (3) the use of an Answer Set Programming-based reasoning toolkit that ingests these constraints to infer and visualize consistent multi-taxonomy alignments. The feasibility of this approach is demonstrated with a use case involving pairwise alignments of 11 non-congruent classifications of Eastern United States grass entities variously assigned to the Andropogon glomeratus- virginicus 'complex' over an interval of 126 years. Analyses of name:meaning identity reveal that, on average, taxonomic names are reliable identifiers of taxonomic non-/congruence for approximately 60% of the 127 merge regions obtained in 12 pairwise alignments. The name:meaning cardinality over the entire time interval ranges from 1:6 to 4:1, with only 1:36 names attaining the semantically ideal 1:1 ratio. We discuss the applicability of the RCC-5 alignment approach in the context of achieving logic-based integration of non-/congruent taxonomic concept hierarchies in dynamic biodiversity data environments.

A mammoth undertaking: harnessing insight from functional ecology to shape de‐extinction priority setting

Summary De‐extinction, or the process of resurrecting extinct species, has been advanced as a promising new tool in conservation biology. Most scientific discussion of de‐extinction has thus far focused on the methodology and ethics of bringing once‐extinct species back to life. We ask: How can de‐extinction be strategically shaped into a service that maximally benefits ecological communities and ecosystems? Ecologists often indicate that the worst facet of extinction is the associated loss of ecological function. Several decades of research on defining, classifying and tracking changes in portfolios of ecological function have generated a rich repository of information that should be mined to help guide de‐extinction towards a future where its products can meaningfully restore extinction‐induced loss of function. Classifications of ecological function remain more subjective than other biological taxonomies. Yet, there is a clear consensus among ecologists that the functions of certain species are less ecologically redundant than others. The loss of such functionally unique species can have proximate and cascading effects on community and ecosystem functioning. We review, from an ecologist's vantage point, efforts underway to use de‐extinction to resurrect the woolly mammoth and the passenger pigeon. These iconic case studies illustrate the opportunities and challenges ahead for restoring ecological function using de‐extinction. There is great risk that de‐extinction could limit itself to the fabrication of products that mimic the biology of extinct species, but fail to resurrect their ecology. We suggest three ways that de‐extinction may more meaningfully restore the functioning of once‐extinct species: (i) select target species from guilds with low functional redundancy; (ii) concentrate on species that went extinct recently rather than older extinctions; and (iii) only work with species that can be restored to levels of abundance that meaningfully restore ecological function. A lay summary is available for this article.

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized ‘Given X, find all associated Ys’ query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: ‘Find all diseases associated with Bisphenol A’. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation.

Automated gene function prediction through gene multifunctionality in biological networks

As the number of sequenced genomes rapidly grows, Automated Prediction of gene Function (AFP) is now a challenging problem. Despite significant progresses in the last several years, the accuracy of gene function prediction still needs to be improved in order to be used effectively in practice. Two of the main issues of AFP problem are the imbalance of gene functional annotations and the ‘multifunctional properties’ of genes. While the former is a well studied problem in machine learning, the latter has recently emerged in bioinformatics and few studies have been carried out about it. Here we propose a method for AFP which appropriately handles the label imbalance characterizing biological taxonomies, and embeds in the model the property of some genes of being ‘multifunctional’. We tested the method in predicting the functions of the Gene Ontology functional hierarchy for genes of yeast and fly model organisms, in a genome-wide approach. The achieved results show that cost-sensitive strategies and ‘gene multifunctionality’ can be combined to achieve significantly better results than the compared state-of-the-art algorithms for AFP.

GPU‐UPGMA: high‐performance computing for UPGMA algorithm based on graphics processing units

SummaryConstructing phylogenetic trees is of priority concern in computational biology, especially for developing biological taxonomies. As a conventional means of constructing phylogenetic trees, unweighted pair group method with arithmetic (UPGMA) is also an extensively adopted heuristic algorithm for constructing ultrametric trees (UT). Although the UT constructed by UPGMA is often not a true tree unless the molecular clock assumption holds, UT is still useful for the clocklike data. Moreover, UT has been successfully adopted in other problems, including orthologous‐domain classification and multiple sequence alignment. However, previous implementations of the UPGMA method have a limited ability to handle large taxa sets efficiently. This work describes a novel graphics processing unit (GPU)‐UPGMA approach, capable of providing rapid construction of extremely large datasets for biologists. Experimental results indicate that the proposed GPU‐UPGMA approach achieves an approximately 95× speedup ratio on NVIDIA Tesla C2050 GPU over the implementation with 2.13 GHz CPU. The developed techniques in GPU‐UPGMA also can be applied to solve the classification problem for large data set with more than tens of thousands items in the future.Copyright © 2014 John Wiley & Sons, Ltd.

Bleeding over Species Lines: Writing against Cartographies of the Human in Queer of Color Fiction

With the rise of the genomic revolution, the human appears to be undergoing a radical retailoring in the cultural and scientific imagination. When read together, Sherman Alexie’s short stories in The Toughest Indian in the World (2000) and Monique Truong’s novel The Book of Salt (2003) suggest that this is not so. Both authors show how colonialist anxieties around bloodlines, miscegenation, and the human/animal border circulating early-twentieth-century eugenics remain ensconced in twenty-first-century gains in genetic science. This essay takes the literal bleeding over species lines that Alexie’s and Truong’s queer of color characters enact as an invitation to probe the limits of biological taxonomies. On a general level, the article asks: How do the distinctions made between human and nonhuman animals produce racialized and sexualized subjects? More specifically, it examines how literary representations of interspecies intimacies might reshape how we perceive biological difference in the twenty-first century.

When languages die: The extinction of the world's languages and the erosion of human knowledge (review)

Reviewed by: When languages die: The extinction of the world's languages and the erosion of human knowledge Andrew Nevins and Adam Roth Singerman When languages die: The extinction of the world's languages and the erosion of human knowledge. By K. David Harrison. Oxford: Oxford University Press, 2008. Pp. 304. ISBN 9780195372069. $17.95. A linguist dedicated to documenting languages in the field and to raising awareness of language endangerment, K. David Harrison offers in When languages die (WLD) an exploration of how 'traditional' or 'indigenous' (terms we introduce in quotes, recognizing their fragility) languages encode vast ecological, astronomical, topological, and mathematical information. Neither a how-to-save-languages guide nor a treatise on technical linguistic theory, this book aims to synthesize diverse academic fields through the prism of language structure and vocabulary, echoing [End Page 398] Sapir's (1921) view of language as 'the most massive and inclusive art we know, a mountainous and unconscious work of anonymous generations' (220). Examining how languages encode knowledge of taxonomy, geography, and calendrics via linguistically and culturally specific terminology, H asks, 'is it unique, irreplaceable knowledge, or merely common sense knowledge uniquely packaged? Could such knowledge ever be adequately captured in books and video recordings in the absence of any speakers? Once vanished, can such knowledge be re-created, will it re-emerge spontaneously after a while, or is it forever unrecoverable?' (9–10). Whereas much linguistics research examines languages so as to understand typology and constraints on grammatical structure, WLD focuses on the useful, practical knowledge of environment, of local species and technologies, and of numerical cognition that languages may encode. The dual interest in cultural knowledge and individual indigenous peoples leads to an intercalary structure for the book, with chapters and paired case studies organized by kinds of knowledge. The case studies, which focus on individual communities and speakers, highlight the very human side of language loss, though they sometimes have only a tenuous relationship with the chapters that they accompany. Both chapters and case studies provide many human-centered anecdotes and examples, with a sizeable number from H's extensive fieldwork. The first chapter sets the scene with an introduction to language death, examining correlations and divergences between language extinction and biological extinction. It provides a useful demonstration of 'language hotspots'—those areas with the highest indices of language diversity and extinction—and discusses how just a handful of languages have an enormous number of speakers, whereas an enormous number of languages have only a handful of speakers. Ch. 2, 'An extinction of (ideas about) species', which focuses on biological taxonomies and ethnobiology, asks an intriguing question: even though any 'ideas can be expressed in any language' (24), how do some languages efficiently organize such ideas so as to optimize the packaging of information? Drawing on his own fieldwork in Siberia, H shows how the Tofa utilize highly precise vocabulary that specify age, sex, fertility, and domestic usefulness to identify individual reindeer in large herds (27). While the concept 'five-year-old male castrated rideable reindeer' requires a loaded noun phrase in both Russian and English, the Tofa chary transmits the same information in a morphologically opaque but highly efficiently manner. Some endangered languages describe natural phenomena via very transparent etymologies, as shown in the following contrast between the Solomon Islands and England: 'Only 30 percent of West Nggela fish names are opaque, or lexically unanalyzable, meaning that for speakers of Nggela they convey no information about a fish's appearance, behavior or habitat. By contrast, a full 55 percent of English names for native Thames River fish are opaque, packaging no ecological information' (42). The Nggela, like other peoples who live in close proximity to their natural environment, store significant, readily available information about flora and fauna in their lexicon. H discusses research that shows how diminished use of an indigenous language correlates with reduced ethnobotanical knowledge, as in the case of the Barí of Venezuela (53), and reiterates the significance of 'folk taxonomies', such as that held by the Wayampi of Brazil: although independent from the Linnaean classification scheme, the Wayampi categorization of birds makes fine-tuned, useful distinctions between species. Ch. 3, 'Many moons ago...

BIOLOGICAL TAXONOMY AND ONTOLOGY DEVELOPMENT: SCOPE AND LIMITATIONS

The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are critically reviewed. The common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy is contrasted with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. It is suggested that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies.

Biological taxonomy and ontology development: scope and limitations

AbstractThe prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. We briefly such how such integration may proceed based on an initial expert alignment of concept relationship and subsequent use of first-order logic algorithms to maximize consistency, reveal implied relationships, and ultimately merge taxonomies. In light of the aforementioned obstacles, we suggest that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies. We furthermore suggest that the prospects of developing successful ontologies for taxonomy will largely depend on the ability of the taxonomic expert community to present their phylogenies and classifications in a way that is more compatible with ontological reasoning than concurrent practice. Minimally, this means (1) adopting rigorous standards for linking new core taxonomies to relevant peripheral taxonomies through comprehensive alignments so that their ontological/taxonomic connections are transparent; (2) using lineage-specific ontological standards for phenotype-based accounts of taxa while taking into account the phylogenetic contextuality of phenotypic descriptors; (3) presenting all nomenclatural and taxonomic novelties in an explicit, ontology-compatible format, including intensional and ostensive definitions; and (4) offering comprehensive intensional/ostensive alignments to entities in relevant preceding taxonomies.

A Lab of Their Own: Genomic sovereignty as postcolonial science policy

This paper analyzes the emergence of ‘genomic sovereignty’ policies as a newly popular way for postcolonial countries to frame their investment in genomics. It identifies three strands in the genealogy of this policy arena—the International Haplotype Mapping Project as a model and foil for postcolonial genomics; an emerging public health genomics field which stands in contrast to Western pursuits of personalized medicine; and North American drug companies increased focus on ethnic drug markets. I conceptualize postcolonial genomics as a nationalist project with contradictory tendencies—unifying and differentiating a diverse body politic, cultivating national scientific and commercial autonomy and dependence upon global knowledge networks and foreign capital. It argues that the ‘strategic calibration’ of socio-political versus biological taxonomies in postcolonial genomics creates two primary challenges for this arena, which I refer to heuristically as dilemmas of mapping and marketing.

Merging Taxonomies under RCC-5 Algebraic Articulations

Taxonomies are widely used to classify information, and multiple (possibly competing) taxonomies often exist for the same domain. Given a set of correspondences between two taxonomies, it is often necessary to “merge” the taxonomies, thereby creating a unied taxonomy (e.g., that can then be used by data integration and discovery applications). We present an algorithm for merging taxonomies that have been related using articulations given as RCC-5 constraints. Two taxa N and M can be related using (disjunctions of) the ve base relations in RCC-5: N≡M; N ? M; N ?; N ? M (partial overlap of N and M); and N ! M (disjointness: N ∩ M = ?). RCC-5 is increasingly being adopted by scientists to specify mappings between large biological taxonomies. We discuss the properties of the proposed merge algorithm and evaluate our approach using real-world taxonomies.