Searching for datasets
How to find datasets in iMicrobe
Quick Search
On every page there is a search box in the upper-right corner that is connected to the "quick search" of textual data in iMicrobe. For example, if you enter "prochlorococcus" as the term, you will find 65 items (including assemblies, projects, samples, and Centrifuge taxonomic assignments) containing that term (https://www.imicrobe.us/#/search/prochlorococcus).
Projects Search
The projects listing page (https://www.imicrobe.us/#/projects) allows users to filter by keyword (the "Search" box to the right of the "Projects" header) as well as by project type (Artificial metagenome, Isolate, Metagenome, Metatranscriptome, Transcriptome). Projects can also be sorted by column headers.
Sample Search
There are over 250 fields that describe the metadata associated with samples such as depth, temperature, dissolved oxygen, habitat, etc.. The sample search page (https://www.imicrobe.us/#/samples) allows you to layer in an unlimited number of fields and values which can be discrete (e.g., Longhurst province) or continuous (physiochemical properties).
Data Access
The ultimate goal of searching is to find datasets of interest. From the project details page (https://www.imicrobe.us/#/projects/1) or a samples details page (https://www.imicrobe.us/#/samples/1), it is possible to add samples to a cart which can be viewed (https://www.imicrobe.us/#/cart). Using the cart, the user can view all the files associated with the samples (https://www.imicrobe.us/#/files) and filter these by file type (reads, gene calls, contigs, etc.).
The data associated with sample is mirrored in the Cyverse Data Store and the iMicrobe FTP site (ftp://ftp.imicrobe.us). The Data Store can be accessed in two ways:
Following the above pattern, the same data can be retrieved via FTP (ftp://ftp.imicrobe.us/projects/1/samples/1/JGI_AMD_5WAY_IRNMTN_SMPL_20020301.fa.gz)
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