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- 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.
Notes de l'éditeur
- This step will capture information about molecular microbial diversity research efforts that are being or have been conducted by the Antarctic research community. The results of step 1 will facilitate communication and collaboration, augment comparative biodiversity studies, and provide a legacy- discoverable resource to advance science, conservation awareness and management. The scope of the information that can be entered in the IPT encompasses present, past, or future studies involving marker gene surveys (e.g.16S or 18S rRNA, functional genes), or meta “omic” projects from natural samples in Antarctic habitats, enrichment or pure culture efforts
- Secondly, users will be invited to upload habitat and molecular methods-specific (meta)data pertaining to the samples and the related sequencing data (including accession numbers) using standardized accessible on the mARS website. These templates can readily be shared with your collaborators and it works with GenBank submission tools (Sequin and WebIN). Used together, and uploaded with the corresponding IPT metadata entry (as described in Step 1), these templates will describe geo-referenced physiochemical information that relates to Antarctic microbial diversity studies as well as the matching sequencing information.
- In this step, sequence data files produced by different technologies (e.g. Sanger sequencing, 454, Illumina, Ion Torrent) will be linked back to the relevant entries as described in steps 1 and 2. mARSwill provide indexed searching capabilities and geo-server links to DNA sequence data from Antarctic studies that have been deposited in public repositories, providing rapid access to this information through the biodiversity.aqdata portal. There is currently no exhaustive resource that provides this level of information from a geo-referenced perspective. The Antarctic scientific community is actively engaged in molecular icrobial diversity and genomic surveys in both terrestrial and marine realms. mARSprovides a unique resource to harness this information.
- As the primary mandate of biodiversity.aqis to provide the scientific community access to Antarctic diversity information, biodiversity.aq staff will process the microbial diversity information referenced in mARS for selected, highly used regions of marker genes (for each domain of life) generated through both Sanger sequencing studies and NGS efforts in order to provide the users with a window into the microbial diversity present in Antarctica.
- This SOP details how you can upload (meta)data to mARS. To ensure this procedure only has to been carried out once, the mARS team has devoted special care to following widely-used standards for biodiversity data, as promoted by the Global Biodiversity Information Facility and the Genomics Standards Consortium. In this particular case, this SOP is built around two main types of standards, namely DarwinCore and MiMarks,ensuring maximal interoperability with internationally-recognized data and metadata repositories.