Getting your Data on mARS:
Standard Operating Procedure
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.
Frequently Asked Questions
- How do I cite this work?
The Microbial Antarctic Resource System by Murray A, Van de Putte A, Youdjou N, Danis B is licensed under a Creative Commons Attribution 4.0 International License. Please read and follow the Polar Information Commons Ethics and Norms of Behavior when contributing or using mARS data
- I’ve uploaded my data on mARS following your SOP, what happens next?
Give us a shout… If you’ve been through all the steps, your metadata will be harvested by biodiversity.aq, GBIF and OBIS. Your dataset will be discoverable through these information networks, as well as metadata repositories, such as the Global Change Master Directory or the Antarctic Master Directory. Periodically, your dataset will be ran through a Mothur pipeline to generate alignments, OTUs and non-redundant sequence data sets, OTU occurrence files, taxonomic assignments and diversity statistics etc..., which will be made available to all through the mARS website.
- Can I enter metadata in mARS without having any data yet?
Yes. If you would like to give some visibility to your project, you can tell the community about what you intend to do by entering basic metadata in the IPT, following the initial steps of the mARS SOP. You can complete the information as your projects makes progress.
- Should my sequence data be published in GenBank?
Yes, this allows us to link back to Genbank-hosted sequences, which is the only way for us to represent your data in the high-level analyses that will benefit the whole community. It also allows us to retrieve sequence data to run through the Mothur pipeline.
- Does mARS store sequences?
No. We require that your sequences are stored in a public repository, such as GenBank, IMG,... mARS offers you an access to sequences relevant to your microbial ecology-related questions.
- What is the difference between publishing, and registering data?
On the IPT, publishing data refers to the automatic generation of a database entry (DarwinCore Archive file) by our server. This file is later exchanged between the information networks. Registering refers to the exposition of your data on the internet, and triggers the harvesting process by the information networks.
- How do I proceed if I want to update my data or metadata?
The IPT system supports versioning. Each version receives a unique web identifier in the process. If you want to update your data or metadata, login to your IPT session, go to the ressource you wish to update and apply the modifications you want to make to the metadata. Don’t forget to save yoru changes. For the data, modify the relevant spreadsheet and upload the new versions to the IPT. Go through the publishing process for the new files.
- Can I share the metadata with a selected group of collaborators?
Yes. Use the “Resource managers” section on the resource managenemt page. The other managers need to obtain their own IPT credentials (simply send an email to the IPT administrator: firstname.lastname@example.org).
- What formats do you use for the metadata?
Our systems are compliant with EML (Ecological Markup Language), DIF (Data Interchange Format), ISO 19115, and FGDC (Federal Geographic Data Committee) metadata standards.