John Wieczorek

Darwin Core: an evolving community-developed biodiversity data standard.

Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.

The point-radius method for georeferencing locality descriptions and calculating associated uncertainty

Natural history museums store millions of specimens of geological, biological, and cultural entities. Data related to these objects are in increasing demand for investigations of biodiversity and its relationship to the environment and anthropogenic disturbance. A major barrier to the use of these data in GIS is that collecting localities have typically been recorded as textual descriptions, without geographic coordinates. We describe a method for georeferencing locality descriptions that accounts for the idiosyncrasies, sources of uncertainty, and practical maintenance requirements encountered when working with natural history collections. Each locality is described as a circle, with a point to mark the position most closely described by the locality description, and a radius to describe the maximum distance from that point within which the locality is expected to occur. The calculation of the radius takes into account aspects of the precision and specificity of the locality description, as well as the map scale, datum, precision and accuracy of the sources used to determine coordinates. This method minimizes the subjectivity involved in the georeferencing process. The resulting georeferences are consistent, reproducible, and allow for the use of uncertainty in analyses that use these data.

ECOLOGY OF SOCIALITY IN RODENTS: A CTENOMYID PERSPECTIVE

Abstract Group living is an important component of the social biology of numerous rodent species. For the past 2 decades, efforts to understand the ecological factors associated with group living in rodents have focused on subterranean taxa, in particular African mole-rats of the family Bathyergidae. Comparative analyses of the habitats occupied by solitary and social bathyergids suggest that group living occurs when the combined effects of sporadic rainfall, hard soils, and patchily distributed food resources render energetic costs of burrow excavation prohibitive for lone individuals. To determine whether these variables were associated with group living in other subterranean taxa, we characterized ecological differences between a solitary and a social member of a phylogenetically independent lineage of subterranean rodents, the Ctenomyidae. Specifically, we quantified soil conditions and spatial distributions of food resources for 1 population each of the solitary Patagonian tuco-tuco (Ctenomys haigi) and the group-living colonial tuco-tuco (C. sociabilis), both of which occur in the Limay Valley of southwestern Argentina. Our analyses revealed that while members of both species occurred in relatively mesic mallin habitats, only C. haigi also occurred in arid steppe habitat. No differences in spatial distributions of food resources were found between study sites. Significant differences in soil conditions, however, were detected; soils from steppe habitat were significantly harder to penetrate than soils from mallin areas, suggesting that costs of burrow excavation may be higher for the solitary C. haigi. Thus, data from ctenomyids in the Limay Valley are not consistent with explanations for group living developed for bathyergid mole-rats. Although ecological comparisons of ctenomyids over larger spatial scales are required, our data suggest that interactions between ecology and group living in subterranean rodents may be more diverse than previously realized.

VertNet: A New Model for Biodiversity Data Sharing

Responding to the urgent need to make biodiversity records broadly accessible, the natural history community turned to “the cloud.”

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.

The planet is experiencing an ongoing global biodiversity crisis. Measuring the magnitude and rate of change more effectively requires access to organized, easily discoverable, and digitally-formatted biodiversity data, both legacy and new, from across the globe. Assembling this coherent digital representation of biodiversity requires the integration of data that have historically been analog, dispersed, and heterogeneous. The Integrated Publishing Toolkit (IPT) is a software package developed to support biodiversity dataset publication in a common format. The IPT’s two primary functions are to 1) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and 2) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. Here we discuss the key need for the IPT, how it has developed in response to community input, and how it continues to evolve to streamline and enhance the interoperability, discoverability, and mobilization of new data types beyond basic Darwin Core records. We close with a discussion how IPT has impacted the biodiversity research community, how it enhances data publishing in more traditional journal venues, along with new features implemented in the latest version of the IPT, and future plans for more enhancements.

Georeferencing locality descriptions and computing associated uncertainty using a probabilistic approach

Locality information for specimens of geological, biological, and cultural objects is traditionally stored as textual descriptions. With an increasing demand for natural and cultural information, the lack of spatially explicit descriptions has become a major barrier to the management and analysis of these data using geographic information systems. In this paper, we propose a method to georeference descriptive data, using an uncertainty field model to represent the distribution of a locality based on two types of uncertainties: uncertainty of reference objects, and the uncertainty of spatial relationships. We propose probability distributions for each known form of these two types of uncertainties and present a probabilistic method to georeference localities based on the integration of different uncertainty sources.

Solitary Burrow Use by Adult Patagonian Tuco-tucos (Ctenomys haigi)

Although >100 Patagonian tuco-tucos ( Ctenomys haigi ) were live-trapped in the Limay River Valley, Rio Negro Province, Argentina, during January 1994, December 1994, and January 1996, no more than one adult was captured per burrow system. Radiotelemetry studies of nine adults revealed that areas occupied by different individuals did not overlap. This pattern of burrow use differed markedly from that reported for the colonial tuco-tuco ( C. sociabilis ), which also occurs in the Limay Valley. We suggest that comparative studies of C. haigi and C. sociabilis will yield important new insights into factors associated with interspecific differences in the social systems of subterranean rodents.

Positioning localities based on spatial assertions

In practice, descriptive localities are often communicated using named places and spatial relationships. Uncertainty associated with such descriptions of localities is inevitable, and knowledge of such uncertainty is normally not explicit. When translating descriptive localities into spatially explicit ones, it is critical to circumscribe locations and to estimate the associated uncertainty based on a set of appropriate spatial relationships. In conventional research on qualitative spatial reasoning (QSR), spatial relationships are modeled using formal logic. Unfortunately, QSR cannot deal with the uncertainty of a position. In this paper, based on the conceptual model of spatial assertions, we introduce the uncertainty field model to represent the probability distribution of a point locality. Using probability operations, we can combine a set of assertions to position a locality. Conflicts among assertions for a single locality can be detected based on the resulting field. Since spatial relationships play an important role in the uncertainty of target objects, we investigate conceptually the uncertainty fields associated with various types of spatial relationships (for example, topological, directional and metric). In a concrete application, these uncertainty fields can be customized and used without altering the proposed framework.

Community next steps for making globally unique identifiers work for biocollections data

Abstract Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.