D58 Nucleic Acids Research, 2012, Vol. 40, Database issue and consistent sample attribute descriptions. BioProject and BioSample objects can be reciprocally linked with each other and to corresponding experimental data within any of the archival databases. Neither database is limited by taxonomy and as such includes information spanning eukaryotes, prokaryotes and environmental samples. To support these databases and the primary data archives at NCBI, a new NCBI Submission Portal is being developed to guide and encourage submitters to provide rich project and sample metadata along with their experimental data. Together, the BioProject and BioSample databases and Submission Portal represent a proactive approach by NCBI to organize and integrate data across interdisciplin- ary resources and to obtain a rich set of contextual metadata from data producers. These databases allow users to query across many NCBI archives at either the project or sample level to retrieve experimental data sets relevant to their interests. Improved data organization and metadata increase the value of data, promoting more extensive reuse and reanalysis, allowing data to be more easily aggregated and examined from different perspec- tives, ultimately facilitating novel insights and discoveries across a broad range of biological ﬁelds including biomedicine, ecology and evolution. BIOPROJECT DATABASE OVERVIEW NCBI’s BioProject database represents a higher order organization of biological research projects and availabil- ity of the resulting data in several archival databases which are maintained by members of the INSDC. The BioProject database organizes metadata for research projects for which a large volume of data is anticipated and provides a central portal to access the data once it is deposited into an archival database. A BioProject encompasses biological data related to a single initiative, originating from a single organization or from a consor- tium of coordinating organizations. Records are primarily deﬁned by submitters using the Submission Portal described below but may also be deﬁned by funding source or NCBI staff. A unique BioProject accession number is assigned to each submitted project. Submitters reference this accession when depositing corresponding BioSample records or experimental data into the archival databases. Indeed, a BioProject accession is now a prerequisite for submission of several data types including dbVar structural variation data and whole genome assemblies. BioProject is an INSDC (1) database and, as such, project data are exchanged regu- larly between the international partners. The BioProject database provides a dedicated environ- ment in which to: . ﬁnd distinct data types for a registered project . ﬁnd projects that are related by a number of different metrics including organism, submitter, data type, collaboration . link project information to experimental data across multiple resources . access information about data availability for a project (sub-project or umbrella collaboration) . support cross-database queries by project identiﬁer BioProject types, metadata and hierarchies The resource supports a variety of projects in terms of type and complexity, ranging from a focused genome sequencing project to a large collaboration with multiple data types and subprojects such as genome sequencing, gene expression and epigenetics. The metadata collected includes structured information about the type of research investigation (e.g. genome sequencing, gene expression), project title and goals, the submitting group, environmen- tal sample label or organism and some project data type attributes regarding the sample scope, target and method. This resource also supports registration for a distinct locus_tag preﬁx, to be used to uniquely identify the genes for genome sequencing projects that will be assembled and annotated.To ﬂexibly describe different types of investigations, information about the sample scope, material used, information captured and method- ology are collected (see http://www.ncbi.nlm.nih.gov/ books/NBK54364/ for deﬁnitions). The combination of these attributes is used to calculate the project data type. For instance, a sequencing project may be from a single individual (monoisolate), multiple individuals of the same species (multi-isolate) or multiple individuals from differ- ent species (multispecies). The material being sequenced may be genomic or transcriptomic. The information being captured may be the entire genome or transcrip- tome, exome or a targeted locus. The method would be sequencing. The BioProject framework includes hierarchical linking to represent the complexity inherent in large collaborative research initiatives; in this way, distinct subprojects of a larger initiative (e.g. that apply different methods and yield different types of data) are grouped together by linking to an umbrella project which describes the wider Figure 1. Schematic depicting how BioProject, BioSample and data objects can be organized and linked. This example is composed of one umbrella project that encompasses three subprojects, each of which generated data derived from two BioSample records. Users can query either the BioProject or the BioSample database to retrieve the relevant records, and then navigate through links to the corresponding experimental data which continue to be stored in NCBI’s primary data archives, including GenBank, SRA, dbGaP and GEO. This schematic depicts direct links that can be applied between objects; it does not depict links to corresponding records in other NCBI databases, including PubMed, Gene, Genome and Taxonomy.