The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0560-6) contains supplementary material, which is available to authorized users.

BodyParts3D is a dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a 3D whole-body model for an adult human male. It encompasses morphological and geometrical knowledge in anatomy and complements ontological representation. Moreover, BodyParts3D introduces a universal coordinate system in human anatomy, which may facilitate management of samples and data in biomedical research and clinical practice. As of today, 382 anatomical concepts, sufficient for mapping materials in most molecular medicine experiments, have been specified. Expansion of the dictionary by adding further segments and details to the whole-body model will continue in collaboration with clinical researchers until sufficient resolution and accuracy for most clinical application are achieved. BodyParts3D is accessible at: http://lifesciencedb.jp/ag/bp3d/.

The processes of capillarization and venularization of sinusoids after porcine serum-induced rat liver fibrosis were studied by light and electron microscopy. Accompanying the development of fibrosis in the walls of central veins, most of the sinusoidal outlets collapsed, resulting in the formation of hepatic limiting plates around central veins. A few remaining sinusoids underwent capillarization (the development of a basal lamina and the defenestration of the sinusoidal endothelial cell), followed by venularization (the transformation into venules of sinusoids, characterized by the enlargement of the diameters with the lumina being lined with several endothelial cells, which lose fenestrae and develop a basal lamina). These newly formed venules served to maintain blood flow from sinusoids into central veins and thus have been designated the "outlet venules." Diameters of these venules could reach about 25 microns. They were classified into two types: (a) the septal outlet venules, which developed inside the septa; and (b) the angular outlet venules, which drained blood directly from the parenchyma into the fibrotic central veins at the angles between two septa. Associated with venularization, perisinusoidal stellate cells (fat-storing cells or Ito cells) differentiated to myofibroblasts.

The ongoing development of world wide web technologies has facilitated a change in health communication, which has now become bi-directional and encompasses people with diverse backgrounds. To enable an even greater role for medical illustrations, a data set, BodyParts3D, has been generated and its data set can be used by anyone to create and exchange customised three-dimensional (3D) anatomical images. BP3D comprises more than 3000 3D object files created by segmenting a digital mannequin in accordance with anatomical naming conventions. This paper describes the methodologies and features used to generate an anatomically correct male mannequin.