D60 Nucleic Acids Research, 2012, Vol. 40, Database issue microbes occurring in a hypersaline lake; (ii) PRJNA20401 and PRJNA13630, organism-speciﬁc gen- ome sequencing and transcriptome projects, respectively, for the primate Callithrix jacchus (white-tufted-ear marmoset); or (iii) PRJNA43021, a top level organization- al project which groups together subprojects of the NIH Human Microbiome Project. Several other resources are collecting and presenting bio-molecular projects but all of them are limited in scope either by speciﬁc organism group [MicrobesOnline (9), IMG (10), GDR (11)] or by project type [GOLD (12)]. BioProject supports a wider scope of projects in terms of type and complexity than any of these resources as it is not limited by organism or data type, i.e. genome, metagenome, expression. BioProject reports BioProject full reports present collected project metadata including the project data type (e.g. genome sequencing, transcriptome or gene expression); attributes concerning the sample scope and target, method, and project goals, submitting group, title, organism name or environmental sample label and brief description. If a project is linked to other projects hierarchically, then information about related projects is provided on the page, displayed as links ‘up’ to a higher umbrella project, links ‘down’ from an umbrella to sub-projects or links ‘across’ to sibling projects which share a common umbrella or have other types of relationships. Organism-speciﬁc links to the Genome Overview may also be displayed to provide navi- gation to Entrez Genome. Statistics on data availability are provided based on inclusion of the BioProject identi- ﬁer on the primary data. If data for a project are available in an archival database and includes the BioProject iden- tiﬁer, then a data table report is included in the BioProject record summarizing those databases with a count of either number of submissions to, or number of records in, the database. For example, SRA reports its content as the number of experiments submitted, whereas the nucleotide database reports its content as the number of accessions. Some projects are registered in the database in advance of data submission and thus do not yet point to any experi- mental data. A simple tabular report (http://www.ncbi.nlm.nih.gov/ bioproject/browse/) is also available from the home page; this report supports browsing the entire database content as well as ﬁltering to display subsets by project data type, locus_tag preﬁx or organism. BioProject data are also available for ftp (ftp://ftp.ncbi.nlm.nih.gov/bioproject/) in XML format and a subset of the data is reported as a tab-delimited text ﬁle. Current status At the time of writing, the BioProject database is populated with almost 12 000 projects derived from more than 3000 organisms. Many of these projects originated from NCBI’s Genome Project resource which was repurposed and redesigned to create this BioProject database. A breakdown of data by project data type is provided in Table 1. Table 1. Types of projects in BioProject 5 October 2011 Project data type Umbrella Primary submission Assembly Clone ends Epigenomics Exome Genome sequencing Map Metagenome Metagenomic assembly Other Phenotype or genotype Proteome Random survey Targeted locus (loci) Transcriptome or gene expression Variation RefSeq Number 216 10 712 6 65 9 33 9265 134 400 40 12 3 1 5 90 588 61 3418 As the intra-NCBI database cross-connections are established and enhanced, the number of some project types is expected to increase. For example, the number of ‘Phenotype or genotype’ projects will greatly increase when BioProject is populated with the studies from dbGaP. BIOSAMPLE DATABASE OVERVIEW NCBI’s BioSample database stores descriptions of the bio- logical materials under examination in a project. Given the huge diversity of sample types handled by NCBI’s archival databases, and the fact that appropriate sample descriptions are often dependent on the context of the study, the deﬁnition of what a BioSample represents is deliberately ﬂexible. Typical examples of a BioSample include a cell line, a primary tissue biopsy, an individual organism or an environmental isolate. Despite sample heterogeneity, the BioSample database presents new opportunities for improved capture and harmonization of sample descriptions across NCBI databases. It provides a dedicated environment in which to: . capture sample metadata in a structured way by promoting use of controlled vocabularies for sample attribute ﬁeld names; . link sample information to corresponding experimental data across multiple archival databases; . reduce submitter burden by enabling one-time upload of a sample description, then referencing that sample as appropriate when making data deposits to other archives; and . support cross-database queries by sample description. Attribute name dictionaries A major component of a BioSample record is the sample attributes section. Attributes deﬁne the material under in- vestigation and can include sample characteristics such as cell type, collection site and phenotypic information like disease state. Since a single sample can be used in multiple experiments and be subjected to different technologies and treatments, information regarding such methodology