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.

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science.

New information technologies have enabled the scientific collections community and its stakeholders to adapt, adopt, and leverage novel approaches for a nearly 300 years old scientific discipline. Now, few can credibly question the transformational impact of technology on efforts to digitize scientific collections, as IT now reaches into almost every nook and cranny of society. Five to ten years ago this was not the case.

TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics.

The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users.

Angiosperm phylogeny: 17 genes, 640 taxa.

Premise Of The Study: Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses.

Methods: We conducted two primary analyses based on 640 species representing 330 families.

Location, location, location: utilizing pipelines and services to more effectively georeference the world's biodiversity data.

Background: Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic locality descriptions associated with biodiversity records that are often heterogeneous and not in a map-ready format. The biodiversity informatics community has developed best practices and tools that provide the means to do retrospective georeferencing (e.

BioGeomancer: automated georeferencing to map the world's biodiversity data.

The BioGeomancer Project provides a toolkit to georeference data and specimens collected for natural history collections, a crucial task if the potential of these specimens is to be fully realized.