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Darwin-SW (DSW) is an RDF vocabulary designed to complement the Biodiversity Information Standards (TDWG) Darwin Core Standard. DSW is based on a model derived from a community discussion about the relationships among the main Darwin Core classes. DSW creates a new class to accommodate an important aspect of its model that is not currently part of Darwin Core: a class of Tokens, which are forms of evidence. DSW uses Web Ontology Language (OWL) to make assertions about the classes in its model and to define object properties that are used to link instances of those classes. A goal in the creation of DSW was to facilitate consistent markup of biodiversity data so that RDF graphs created by different providers could be easily merged. Accordingly, DSW provides a mechanism for testing whether its terms are being used in a manner consistent with its model. Two transitive object properties enable the creation of simple SPARQL queries that can be used to discover new information about linked resources whose metadata are generated by different providers. The Organism class enables semantic linking of biodiversity resources to vocabularies outside of TDWG that deal with observations and ecological phenomena.

The Darwin Core vocabulary is widely used to transmit biodiversity data in the form of simple text files. In order to support expression of biodiversity data in the Resource Description Framework (RDF), a guide was created as a non-normative addition to the Darwin Core standard. This paper describes the major issues that were addressed in the creation of the guide, particularly problems related to adapting terms designed to have literal values for use with IRI references. By making it possible to express millions of existing records as RDF, the guide is an important step towards enabling the biodiversity informatics community to participate in broader Linked Data and Semantic Web efforts.

Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.