ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.

Unlabelled: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses.

The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth.

The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.

Knowledge extraction and semantic annotation of text from the encyclopedia of life.

Numerous digitization and ontological initiatives have focused on translating biological knowledge from narrative text to machine-readable formats. In this paper, we describe two workflows for knowledge extraction and semantic annotation of text data objects featured in an online biodiversity aggregator, the Encyclopedia of Life. One workflow tags text with DBpedia URIs based on keywords.

Evolutionary informatics: unifying knowledge about the diversity of life.

The accelerating growth of data and knowledge in evolutionary biology is indisputable. Despite this rapid progress, information remains scattered, poorly documented and in formats that impede discovery and integration. A grand challenge is the creation of a linked system of all evolutionary data, information and knowledge organized around Darwin's ever-growing Tree of Life.

TreePlus: interactive exploration of networks with enhanced tree layouts.

Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food webs, ontologies, and social networks difficult to understand and interact with. We propose a new interactive Visual Analytics component called TreePlus that is based on a tree-style layout.

Visualizations for taxonomic and phylogenetic trees.

Motivation: Despite substantial efforts to develop and populate the back-ends of biological databases, front-ends to these systems often rely on taxonomic expertise. This research applies techniques from human-computer interaction research to the biodiversity domain.

Results: We developed an interactive node-link tool, TaxonTree, illustrating the value of a carefully designed interaction model, animation, and integrated searching and browsing towards retrieval of biological names and other information.

Phylogeny of magpies (genus Pica) inferred from mtDNA data.

We investigated the phylogenetic relationships of species and subspecies of the cosmopolitan genus Pica using 813 bp of the mitochondrial genome (including portions of 16s rDNA, tRNA-Leu, and ND1). The phylogenetic relationships within the genus Pica revealed in our molecular analyses can be summarized as follows: (1). the Korean magpie (Pica pica sericea) appears basal within the genus Pica; (2).