[Esip-soil-informatics] 10 March: Cyberinfrastructure for the CZIMEA

[Todd-Brown, Kathe]

Come join us for a presentation on March 10 at 1700 UTC by Emilio Mayorga (Applied Physics Lab, UW) titled “Cross-Site Soil and Microbial Ecology Cyberinfrastructure for the CZIMEA EarthCube Project”

Abstract: The CZIMEA (Critical Zone Integrative Microbial Ecology Activity, 2015-2020, https://github.com/BiG-CZ/CZIMEA/) EarthCube Integrative Activities project carried out a cross-site soil sampling and analysis research activity involving many universities affiliated with the 10 Critical Zone Observatories (CZO) across the US. The scientific goal was to gain insights into the differences between soil microbial communities as they vary across ecosystems and with depth along a profile, using a wide range of soil and environmental measurements and both metagenomic and amplicon high-throughput sequencing to analyze nearly 200 unique soil samples.

Cyberinfrastructure and interoperability were important components of this EarthCube project. To facilitate management, integration and dissemination of the cross-site metadata and data generated by CZIMEA, we set a goal to store information using the Observations Data Model 2 (ODM2, http://www.odm2.org) system with the CZ-Admin User Interface (http://odm2.github.io/CZ-Manager/), deployed on the cloud. ODM2 is enriched with cross-linkage to external data systems using universal identifiers that include DOI’s, ORCID’s and IGSN’s, in addition to ODM2-managed controlled vocabularies described online (http://vocabulary.odm2.org). The CZIMEA ODM2 relational database holds extensive, structured sampling and sample metadata, and initial steps were taken to store environmental measurement results as well, including soil moisture, field capacity, texture, carbon and nitrogen content and pH. The plan was to use universal identifiers to  link to genomic results stored externally in dedicated systems, particularly the MG-RAST metagenomics analysis server. We also developed the initial elements for storing landscape information derived from continental scale geospatial datasets, including site climatologies, land cover type, soil types, and terrain properties.

I will describe the architecture we developed, progress made and challenges encountered, hopefully illuminating common challenges and opportunities in soil informatics.

As a reminder the call-in information has changed! We are now using Zoom instead of GoToMeetings. Please check the meeting notes for the new link! https://docs.google.com/document/d/1_SIm_3e9xpni_64zdAU1DZrFEd8YcIerbsihDJq4qwY/edit?usp=sharing Also, if you are familiar with a specific data product, please go to the new GitHub issues page and add your description of sample location, organic carbon, bulk density, and hydrologic connectivity for our next working meeting.

Take care and see you next week!
-Kathe
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Katherine Todd-Brown, PhD

Assistant Professor
Environmental Engineering Sciences
Engineering School of Sustainable Infrastructure & Environment
Herbert Wertheim College of Engineering
University of Florida

Office: Rm B006, Phelps Lab, UF main campus
Twitter: @KatheMathBio

Mail: Dr Kathe Todd-Brown
Center for Wetlands
PO Box 116350
Gainesville, FL 32611


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