1. CCAMBIO and the mARS
project
Anton Van de Putte
CCAMBIO Annual Meeting
12 may 2014

2. Microbial Antarctic
Resources System
An information system dedicated to facilitate the
discovery, access and analysis of geo-
referenced,
molecular microbial diversity (meta)data generated
by Antarctic researchers, in an Open fashion.

3. What’s happened so far
• mARS Workshop hosted at the Belgian Science Policy
Office (BELSPO, Brussels) in May 2012
• mARS Workshop held during the SCAR Open
Science Conference (Portland, OR) in July 2012
• Technical mARS Workshop hosted at the Université
Libre de Bruxelles in December 2013
• Initiate the development of the database and
webplatform

4. Near future planning
• mARS Workshop held during the SCAR Open
Science Conference (Auckland, NZ) on 27 august
2014
• Present a proof of concept of the dataindrastructure to
be used for mARS

5. The Vision
4 incremental steps

6. Step 1
: Data description and
discovery
Integrated Publishing Toolkit
(IPT)

7. Step 2: Habitat and
Microbial Sequence
Metadata Entry
MiMARKS and mARS Sequence Set
Te m p l a t e

8. Step 3: Georeferenced-
molecular sequence database
integration

9. Step 4: Processing batch
sequence data
Circum-Antarctic microbial
diversity

10. Standard Operating
Procedure
How to get started

11. Getting Data into mARS
• Requires that
• Data is accessible in a public a public repository
(Genbank, IMG-M or other web accessible)
• 2 additional metadata files
• MiMARKS
• Microbial Sequence spreadsheet

12. 0. Before you start
• 1. Clearly Identify your needs
• You have a project that you would like to register
with mARS
• no sequence data or environmental data at this
point: skip Steps 1, 2, 4 and 7
• environmental data, but no publicly available
sequences yet, follow all Steps below, but do not
enter Sequence IDs in the forms.
• environmental data, and publicly available
sequences. Follow all Steps below.

13. 0. Before you start
• Send an email to request a username and password
from the IPT administrator

15. 0. Before you start
• Send an email to request a username and password
from the IPT administrator
• Make a copy of the MiMarks Googlesheet from the
RDP MiMarks Googlesheet (click on “Make copy” from
the “File” menu).

17. 0. Before you start
• Send an email to request a username and password
from the IPT administrator
• Make a copy of the MiMarks Googlesheet from the
RDP MiMarks Googlesheet (click on “Make copy” from
the “File” menu).
• Make a copy of the Microbial Sequence Set from the
mARS Googlesheet (click on “Make copy” from the
“File” menu).

19. 1. Prepare your MiMarks
spreadsheet• In the MiMarks Googlesheet you’ve created in step 0,
fill in your environmental metadata details using the
“Google Documents” interface, following the
instructions available from the MiMarks Googlesheet
documentation at RDP. Example files are available
from the mARS website.
• In the header for each column that will hold your
sequence set data, list the unique identifier of your
sequence set.
• Once you are finished, download your spreadsheet as
a CSV (Comma-separated Values) file on your
computer.

21. 2. Prepare your Microbial
Sequence Set spreadsheet
• In the Microbial Sequence Set Googlesheet you’ve
created in step 0, fill all the fields (replace the
examples available from the Googlesheet)
• Once you are finished, download your spreadsheet as
a CSV (Comma-separated Values) file on your
computer.

23. 3. Describe your data in the
IPT
• Login the IPT using your credentials:
• Use the form at the bottom of the “Manage Resource”
page to create a new resource. Provide a unique
"shortname" for your dataset.
• Click the “Create” button. You will arrive on the
Resource Management page.
• Click on the “Edit” button in the Metadata section on
the left and fill in the details for the different metadata
sections. A detailed instructions are available from IPT
quick reference guide. Hint: mention your grant
number in the “Project Data” section, to allow us to link
your resource to relevant projects in the GCMD/AMD.

24. 4. Upload your MiMarks and
Microbial Sequence Set
• 1. In your IPT session, from your Resource
Management page, click on the “Choose file” button in
the “Source data” section on the left of the page.
• 2. Point to your completed MiMarks CSV, and click on
“Choose”
• 3. Click on the “add” button in the “Source data”
section on the left of the page then click on the “Save”
button on the bottom. Your MiMarks CSV file is now
uploaded on the IPT.

25. 4. Upload your MiMarks and
Microbial Sequence Set
• 5. From your Resource Management page, click on
the “Choose file” button in the “Source data” section on
the left of the page.
• 6. Point to your completed Microbial Sequence Set
CSV, and click on “Choose”
• 7. Click on the “add” button in the Source data section
on the left of the page, then click on the “Save” button.
Your Microbial Sequence Set CSV file is now uploaded
on the IPT.

26. 5. Publish and register your
data
• From your Resource Management page, click on the
“Publish” button in the “Published release” section on
the left of the page. Do not worry when you see a
warning message “Source data or Darwin Core
mappings missing. No data archive generated
• By default, your resource’s visibility is set to “Private”.
To allow your resource to become visible on the IPT
for all users, click on the “Public” button in the
“Visibility” section.
• Request one of the administrators to “Register” your
dataset.