Downloading Data

Overview

There are many supported ways to download datasets from BIL. This section discusses how to locate datasets in BIL and download them using these methods.
  1. Locating Data First, find the location of the dataset of interest using the Brain Inventory or the metadata API.
  2. Using a web browser: How to download datasets using a web browser.
  3. Using wget How to download datasets using unix wget command.
  4. Globus: How to download datasets using Globus.
  5. Assistance and Help
  6. Distribution Licence
  7. Embargoed entries
  8. Citation of entries and use of non-embargoed pre-publication data

Download Steps

  1. Locating Data

    Find the location of the dataset of interest using the Brain Inventory web search tool or the metadata API

    If using the metadata API, look for the field "bildirectory" under the "Dataset" subsection.

    The path shown will be in the form:
    /bil/data/<c1c2>/<c3c4>/<16-digit-submission-identifier>/<subdirectoryName>

    where <c1c2> are replaced by the first and second characters of the submission identifier and <c3c4> are replaced by the third and fourth characters of the submission identifier. For example:

    /bil/data/ab/cd/abcdef0123456789/example_dataset_01/

  2. Using a web browser: HTTPS

    To access the files, enter the following URL in your web browser:

    https://download.brainimagelibrary.org/

    The URL to access the example dataset mentioned above would be:

    https://download.brainimagelibrary.org/ab/cd/abcdef0123456789/example_dataset_01/

  3. Using wget:

    To download the files, use wget with the -r option and the URL to the desired dataset without the /bil/data path.

    For example, to retreive the example dataset mentioned above with wget, enter:

    wget -r https://download.brainimagelibrary.org/ab/cd/abcdef0123456789/example_dataset_01/

  4. Using Globus:

    Login to the Globus transfer web service at www.globus.org. Select an Endpoint field and select 'Brain Image Library Download' (a shortcut is available as bil#download). Upon successful connection to the Brain Image Library Download server, you will land in the /bil/data directory, which lists the first layer of the 00..ff directory hierarchy. Navigate (or type the path in the Path field) to the directory containing the dataset(s) that you wish to download.

    In the other Endpoint field, select (and if needed, authenticate to) your destination server. This may be a remote GridFTP server or your Globus Connect Personal endpoint. In the Transfer Settings section at the bottom, select the settings that apply to your download needs, e.g., "preserve source file modification times", "verify file integrity after transfer", etc.

    Select the dataset(s) and/or files that you wish to download by highlighting their directory and/or file names.

    Click the arrow button in the direction of the transfer from the Brain Image Library Download side toward your target Endpoint. This will schedule your transfer to begin. At this point you may log out of the Globus user interface and let the transfer proceed.

    To check on the progress of your transfer, select the Activity tab in the globus.org interface, and then select the job corresponding to your transfer.

    Upon successful completion of your transfer, the status page for your transfer will show 'Condition SUCCEEDED' - you will also receive an e-mail to notify you if your Globus account settings are configured to do so.

  5. Assistance and Help

    If you need assistance with anything, please email: bil-support@psc.edu.

    If you are having networking issues related to data transfer (including slow transfer speeds), email us at at bil-support@psc.edu and one of our networking experts will get in contact with you.

  6. Distribution Licence

    BIL Data is distributed under the Creative Commons Attribution-ShareAlike 4.0 International License.

  7. Embargoed Entries

    Data submitted to the library, by default, will be released as soon as possible once data has been validated. Optionally, data submitters can select a limited embargo period for their submitted data. Entries deposited with NIH BRAIN Initiative funding may request an embargo period not exceeding the limits outlined in the Notice of Data Sharing Policy for the BRAIN Initiative. All other deposited entries may request an embargo period of up to one year. Data subjected to embargo can not be downloaded.

  8. Citation of entries and use of non-embargoed pre-publication data

    Please see this page for suggested acknowledgement text for entries from the Brain Image Library.

    Use of Non-embargoed Pre-publication Data.

    The library encourages researchers using datasets from the Brain Image Library for which there is no peer-reviewed publication identified, to contact the data producers to discuss possible coordinated publications and collaborations.