D62 Nucleic Acids Research, 2012, Vol. 40, Database issue user-friendly interfaces that balance the need for efﬁ- cient data input while promoting provision of rich and consistent descriptions. Depositing data through the Submission Portal ensures that submissions are syntactic- ally accurate, promotes capture of metadata using controlled vocabularies and enables linking and aggrega- tion of related objects. However, the BioProject and BioSample databases are submitter-driven primary data archives and submitters are responsible for the quality and content of their deposits. Database staff respond to queries and report errors but, as with other primary data archives, submitted data are not subject to extensive curation. Use of the Submission Portal requires authentication. Several login options are supported including various National Institutes of Health accounts and a general NCBI PDA (Primary Data Archives) account. Once logged in, the submitter can deposit BioProject and/or BioSample information via the relevant submission wizard, each of which is composed of a series of forms guiding input of descriptive metadata and object relations. Each portal provides a list of the submitter’s previously created submissions with some status information and a button to initiate a new submission. A submission may be started, set aside and completed at a later time by signing back into the Submission Portal and selecting the incom- plete submission. In the BioProject portal, submitters describe their ini- tiative and the types of data that they intend to submit. Fields are provided to capture project data type, as well as sample scope, material, capture method and methodology and ﬁnally the objectives of the study. Information about the organism or organisms being studied is also collected. One can also input relevant URLs, funding information, consortium information and links and other information. The submitter is asked to provide a description of their project that will be displayed in Entrez BioProject. Once the project is accepted, the submitter receives a BioProject accession and locus_tag preﬁx, if the project objectives include annotated genome submissions, both of which should be referenced when submitting corresponding experimental data to the archival databases. In the BioSample portal, submitters describe the bio- logical material under investigation in their project. After specifying the sample type, the user is presented with a list of required and optional attribute ﬁelds to ﬁll in, as well as the opportunity to supply any number of custom-descriptive attributes. For example, if a submitter speciﬁes that their sample is a pathogen, they are required to input information about collection locality and date, host, if applicable and isolation source (food, faeces, etc.). In addition, submitters are prompted with additional ﬁelds describing the host, disease state, etc. A batch input mechanism using spreadsheets tailored for the sample type is also supported. Authenticated users can provide associations between samples and registered projects, as well as relevant URLs and publications. Once the sample is accepted, the submitter receives a BioSample accession number which should be referenced when submitting corresponding experimental data to the archival databases. SEARCH AND RETRIEVE DATA Effective searches may be accomplished using the search box on the BioProject and BioSample home pages at http://www.ncbi.nlm.nih.gov/bioproject and http://www .ncbi.nlm.nih.gov/biosample, respectively. As with other NCBI Entrez databases (15,16), a simple free text keyword search is often sufﬁcient to locate relevant data. However, BioProject and BioSample data are extensively indexed under many ﬁelds, meaning that users can reﬁne their search by constructing ﬁelded queries. Some useful search ﬁelds are listed in Table 2. Users can write and execute their own search statements directly in the search boxes or, alternatively, use the Advanced search pages which assist users to construct complex multi-part ﬁelded search statements or activate Limits to restrict re- trievals to popular search categories. In addition, the BioProject database supports a browse By Project Attributes page that allows users to browse BioProjects in tabular format and to sort and ﬁlter by organism, project types and project data type. BioProject and BioSample records can be accessed by following Entrez links from another NCBI database. As depicted in Figure 1, BioProject and BioSample data are reciprocally linked to corresponding data in the archival databases. This allows users to link to, e.g. corresponding genome assembly records in Entrez Nucleotide or raw sequence reads in SRA where the data can be downloaded (see Figure 2 for location of links). Records are also linked to relevant PubMed, Gene, Genome and Taxonomy records, further facilitating navigation across diverse data domains. To download BioProject and BioSample descriptions, users can take advantage of the Send to: feature on the search results pages, which allows download of individual or batch BioProject and BioSample retrievals in text or XML formats. Also, BioProject data are available for bulk download in XML, or as a summary tab-delimited text ﬁle, from the FTP site at ftp://ftp.ncbi.nlm.nih.gov/ bioproject/. Furthermore, programmatic query, linking and download functions are available using a suite of NCBI Table 2. Selected search ﬁelds and example queries Database Find by . . . Example search ‘term[ﬁeld]’ BioProject and organism or insecta[Organism] BioSample taxonomic class BioProject project data type metagenome[Project Data Type] BioProject publication 10473380[Pubmed ID] BioProject submitter JGI[Submitter Organization] organization or consortium BioProject sample scope scope environment[Properties] BioProject material used material transcriptome[Properties] BioProject and database identiﬁer PRJNA33823 or PRJNA33823 BioSample [bioproject] or 33823[uid] or 33823[bioproject] BioSample attribute name age[Attribute Name] BioSample attribute and value cell line GM10847[Attribute] BioSample data source source coriell[Properties] Multi-part queries may be constructed by specifying the search terms, their ﬁelds and the Boolean operations AND, OR, NOT.