DATA MANAGEMENT Comprehensive Data Management Planning
One of the challenges of the South Dakota Biofilm Science and
Engineering Center is the integration of large-scale,
diverse datasets and analytic tools into a comprehensive
framework to help provide a basis for a system level
understanding of 2D materials – Biofilm interactions.
To facilitate sharing of data among participants and
with the broader scientific community, we will adopt
open-source data formats. Importantly, we will employ
the FAIR Data Principles
in order to ensure that the
data generated through this project is findable, accessible,
interoperable and reusable. We will follow the research community’s
minimum information about biofilm experiment
standards for storing, sharing and publishing our biofilm experimental data. Other Minimum Information
Standards will be used to standardize the description of other generated research data.
The 2D-BEST team has developed a workflow to facilitate data management,
sharing, and publishing. Once it is determined that experimental data should be shared
with the project team, researchers follow the requisite protocol to move the data, along with its
standard description, to shared storage (see Figure 1). This project is leveraging the
of South Dakota Data Store (SDDS) and
Globus in this data management plan. The SDDS
provides high-reliability, high-availability, network-accessible storage for South
Dakota researchers and collaborators. Globus is a not-profit service
for secure, reliable research data management.
Sharing Research Data
Determine the types and sources of data that will be shared (e.g.
samples, physical collections, code, software, curriculum materials and other materials).
For experimental data, determine if there is a minimum
information standard for your data type.
Minimum information standards are sets of guidelines and
formats for reporting data derived by specific high-throughput methods.
Their purpose is to ensure the data generated by these
methods can be easily verified, analysed and interpreted
by the wider scientific community. Ultimately,
they facilitate the transfer of data from journal articles
(unstructured data) into databases (structured data) in a
form that enables data to be mined across multiple data sets.
Minimal information standards are available for a vast
variety of experiment types including microarray (MIAME),
RNAseq (MINSEQE), metabolomics (MSI) and proteomics (MIAPE).
You can explore the data standards available for your field
For experimental, qualitative, raw, processed data:
Identify if there is minimum information standard for your data type.
Using the minimum standard and readme template, describe your data.
At this point, it will be likely that the readme file will be incomplete.
The readme file will be transfered and stored with the data.
The South Dakota Data Store will be leveraged to
enable 2D-BEST researchers to share their project data
with collaborators. This data storage will be made available to researchers
through Globus. Globus is a non-profit service for secure,
reliable research data management.
With Globus, researchers can move, share, & discover
data via a single interface through a web browser.
Click the Log In
option in the upper right corner.
Find your organization (e.g. USD, SDSU, MSU, UNO); optionally sign in
with ORCID ID. Note: USD, SDSU, MSU, and UNO with allow you to log in
using your institutional credentials. If you are not able to locate
your institution in the list, you can register for an ORCID ID.
Organizing the 2D-BEST data will be important in order to provide easy accessibility
to collaborators. Figure 2 offers an example of how that dataset collections could be categorized.
After you have determined what data you will share and have completed the readme file that describes
the data, the next step is to transfer the data to shared collection using the Globus platform.
To transfer data to shared storage:
Identify where in the data collection organization you will place your data.
The best way to approach this task is to contact one of the project data administrators.
Below is a list of the 2D-BEST Data Administrators
With help from a data administrator, create a data
collection folder if one does not already exist.
Upload your data into the identified collection
Globus allows you to create and manage groups of Globus
users that can then facilitate the sharing of collections, folders and files
with these groups. If your requisite use group does not exist, the following
steps describe how to create one.
Click on the Groups link in the left-hand panel in Globus.
Click on the Create new group link in upper right corner.
Enter the details describing your user group.
The "group members only" option indicates that all members of this group will be specifically
invited by you.
Once the group has been created, you have the option of inviting members.
To invite a user to become a member of your group, they must be registered in Globus.
Users are located using their email address. The system will send an email
to the person being invited and he/she has the option of accepting.
To access user's detail, simply click on the name of the member. This will
enable you to modify the member's role, status and notes.
The default role for members added to a group is "Member". This allows the user to access
group resources. You can decide to assign "Manger" or "Administrator" role to the
member which would allow them to access, add, remove resources. Additionally, the "Administrator"
role provides the ability to manage groups.
Once data has been moved to the data store and a group has been created,
you can share your data with the group. The following steps outline this process.
To share a file or folder with a user or group,
select the file or folder and then click the user group icon
in the right hand panel.
Then click the permissions option
in the upper right corner.
The "Add Permissions - Share With" interface (Figure 11) provides the functionality
to associate a file or folder with a user or group. For our example, we verify that
we are sharing the /Omics/Genomics/ folder and that we want to share it with the
Lushbough Lab group. Therefore we click the group radio button. We also want to specify if
the group member will have read, write, or read & write permissions. Click the select group button
and select your user group.
After the "Add Permissions - Share With" form is completed, click the "Add Permissions"
Publishing Research Data
We are still in the early days of publishing data.
Our plan will be to leverage USD's Research, Engage, Design (RED) services
to facilitate project data publishing. RED is a service of the University of
South Dakota University Libraries that promotes and shares the
scholarship, creative works, and data created by
South Dakota faculty, students, and institutional partners .