Genomic Standards Consortium

The Genomic Standards Consortium (GSC) is an open-membership working body formed in September 2005. The aim of the GSC is making genomic data discoverable. The GSC enables genomic data integration, discovery and comparison through international community-driven standards.

This project is maintained by GenomicsStandardsConsortium

Genomic Standards Consortium

MIxS Hydrocarbon Resources GSC Project

1. Project Title: Minimal Metadata for Environments pertaining to Hydrocarbon Resources: A MIxS extension

2. Project Lead: MIxS-HCR: Nicolas Tsesmetzis

3. Initial Team members: Nicolas Tsesmetzis, Pelin Yilmaz (GSC), Peter Marks, Nikos Kyrpides (GSC), Ian Head, Bart Lomans

4. Elevator pitch: A joined effort by academia and industry have led to the establishment of a MIxS extension to facilitate the recording and cataloguing of metadata from samples related to hydrocarbon resources (HCR). The proposed MIxS-HCR package incorporates the core features of the MIxS standard for marker gene (MIMARKS) and metagenomic (MIMS) sequences along with a HCR-customized environmental package. Adoption of the MIxS-HCR standard will enable the comparison and better contextualization of investigations related to hydrocarbon rich environments. The insights from such standardized way of reporting could be highly beneficial for the successful development and optimization of hydrocarbon recovery processes and management of microbiological issues in petroleum production systems.

5. Have you spoken about the project already within GSC? MIxS-HCR was presented to the GSC community at the GSC17 and GSC18. The project was also discussed and reviewed by the GSC Board during the GSC18 meeting

6. Which existing projects, if any, does this one replace/complement/subsume/expand? Explain briefly why an extra project is needed/justified (what gap does it fill?) This standard is tailored for HCR-related studies and aims at capturing key environmental parameters influencing microbial activity in these environments and standardizing their method of reporting. This is accomplished by the adoption of terms (such as temperature, pressure, porosity, etc.) from previously reported environmental packages (i.e. Water, Sediment, Wastewater/sludge, etc.) as well as the introduction of new checklist items specific to these environments. A checklist consisting of 93 fields from several disciplines including geology, geochemistry, petrophysics, reservoir engineering, and production chemistry has been compiled.

7. How does this project fit into GSC’s mission statement (might also expand it)? Providing contextualized metadata for sequence data from environments pertaining to hydrocarbon resources

8. Will you start a GSC working group (how far along are you?)? If not, why not (i.e. subgroup within developers group, existing external community, etc.) A GSC working group is currently under construction. It is expected to include Nikos Kyrpides, Pelin Yilmaz, Lynn Schriml, George Garrity, Nicolas Tsesmetzis, Ian Head, Bart Lomans, Lisa Gieg, Ken Wunch, Heike Hoffmann, Renato De Paula, Brett Geissler and any other interested parties.

9. How do you wish to further engage the GSC (recruit members to project, get consultation, link to other GSC projects, etc.)? Would be nice to engage with Pier Luigi Buttigieg and other experts on ontologies to help us develop an ontology on hydrocarbon resources.

10. Do you already have a website or do you wish to create a home page for the project in the GSC website (GSC maintains an open wiki at present, all working groups have a page)? We have set up a forum on Google Groups to promote the development, extensions and enhancements of the MIxS-HCR standard. (!forum/mixs-hcr)

11. What other resources might you like from what the GSC can offer (mailing lists, etc.)? Help the promotion of the MIxS-HCR standard by a) inviting the MIxS-HCR team members to the GSC meetings and b) sharing news and updates pertaining to this standard through the GSC’s website.

12. What kind of timeline are you working to for building consensus, releasing a first version etc.? The first MIxS-HCR release has already gained approval by the GSC board. We anticipate yearly reviews of the MIxS-HCR standard following review and approval by the GSC board.

13. What resources will be required for completion (funding, man power, etc.)? (This question is just to give an idea about the size of the project) The project is partly funded by Shell. The MIxS-HCR environmental package will be incorporated into MIxS standard in the near future. After that, it will be incorporated into INSDC.

14. What are your current plans for publishing/promoting the project? A manuscript describing the MIxS-HCR environmental package is ready for submission. A link to the publication will be posted here upon acceptance.

15. References or relevant websites (for further reading) See the MIxS-HCR forum:!forum/mixs-hcr