Nav: Home

Scientists seek to establish community-driven metadata standards for microbiomes research

March 25, 2020

"We are living through an explosion in the availability of microbiome data," according to JP Dundore-Arias, assistant professor of plant pathology at California State University, Monterey Bay. "In agricultural systems, the proliferation of research on plant and soil microbiomes has been coupled with excitement for the potential that microbiome data may have for the development of novel, sustainable, and effective crop management strategies."

While this is an exciting development, as the collective body of microbiome data for diverse crops grows, the lack of consistency in recording data makes it harder for the data to be utilized across research projects. In a recent article published in Phytobiomes Journal, Dundore-Arias and others in his field discuss the need for agriculture-specific metadata standards for microbiome research.

"Metadata is known as 'data about other data,' or in other words, the what, where, when, and how of the data or sample. This can include, for example, the crop, the sample location, the time of sampling, crop management factors, the method of DNA extraction, and many other factors," explains Dundore-Arias. "Developing a shared consensus of what needs to be reported about a microbiome sample is critical to advancing our field."

Consistent metadata allows researchers to determine whether data from other studies can be integrated for analysis into their own research. Standard recording and sharing practices will also provide a rigorous foundation for building understanding and increase the long-term value of microbiome data within the plant health community.

Through a workshop sponsored by the National Science Foundation-funded Agricultural Microbiomes Research Coordination Network, Dundore-Arias, Emiley Eloe-Fadrosh (LBNL, DOE-JGI), Lynn Schriml (University of Maryland School of Medicine) and Linda Kinkel (University of Minnesota) began the process of engaging the research community in an open process for developing consensus on Agricultural Microbiomes Metadata Standards.

They proposed a checklist of required and desirable metadata standards, which is meant to stimulate discussion and move the community toward standardized reporting of metadata, sampling, processing, and analytical pipelines in agricultural microbiome research. After gathering feedback, the next step, according to Dundore-Arias, "is to develop, along with members of the Genomic Standards Consortium (GSC), a MIxS-Ag metadata standard and ontology that will be incorporated into the GSC MIxS collection and released to other commonly used data management platforms and repositories."

During the process of developing this proposed list of metadata standards categories, and in the next step, developing the official metadata standards checklist for describing agricultural microbiome studies (MIxS-Ag), Dundore-Arias and colleagues have and will continue to seek feedback and endorsement from agricultural microbiome researchers representing diverse public and private sectors. Feedback can be given in the comments at the bottom of the article, found here.
For more information about this process, read "Community-Driven Metadata Standards for Agricultural Microbiome Research."

American Phytopathological Society

Related Data Articles:

Data centers use less energy than you think
Using the most detailed model to date of global data center energy use, researchers found that massive efficiency gains by data centers have kept energy use roughly flat over the past decade.
Storing data in music
Researchers at ETH Zurich have developed a technique for embedding data in music and transmitting it to a smartphone.
Life data economics: calling for new models to assess the value of human data
After the collapse of the blockchain bubble a number of research organisations are developing platforms to enable individual ownership of life data and establish the data valuation and pricing models.
Geoscience data group urges all scientific disciplines to make data open and accessible
Institutions, science funders, data repositories, publishers, researchers and scientific societies from all scientific disciplines must work together to ensure all scientific data are easy to find, access and use, according to a new commentary in Nature by members of the Enabling FAIR Data Steering Committee.
Democratizing data science
MIT researchers are hoping to advance the democratization of data science with a new tool for nonstatisticians that automatically generates models for analyzing raw data.
Getting the most out of atmospheric data analysis
An international team including researchers from Kanazawa University used a new approach to analyze an atmospheric data set spanning 18 years for the investigation of new-particle formation.
Ecologists ask: Should we be more transparent with data?
In a new Ecological Applications article, authors Stephen M. Powers and Stephanie E.
Should you share data of threatened species?
Scientists and conservationists have continually called for location data to be turned off in wildlife photos and publications to help preserve species but new research suggests there could be more to be gained by sharing a rare find, rather than obscuring it, in certain circumstances.
Futuristic data storage
The development of high-density data storage devices requires the highest possible density of elements in an array made up of individual nanomagnets.
Making data matter
The advent of 3-D printing has made it possible to take imaging data and print it into physical representations, but the process of doing so has been prohibitively time-intensive and costly.
More Data News and Data Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

There's so much we've yet to explore–from outer space to the deep ocean to our own brains. This hour, Manoush goes on a journey through those uncharted places, led by TED Science Curator David Biello.
Now Playing: Science for the People

#555 Coronavirus
It's everywhere, and it felt disingenuous for us here at Science for the People to avoid it, so here is our episode on Coronavirus. It's ok to give this one a skip if this isn't what you want to listen to right now. Check out the links below for other great podcasts mentioned in the intro. Host Rachelle Saunders gets us up to date on what the Coronavirus is, how it spreads, and what we know and don't know with Dr Jason Kindrachuk, Assistant Professor in the Department of Medical Microbiology and infectious diseases at the University of Manitoba. And...
Now Playing: Radiolab

Dispatch 1: Numbers
In a recent Radiolab group huddle, with coronavirus unraveling around us, the team found themselves grappling with all the numbers connected to COVID-19. Our new found 6 foot bubbles of personal space. Three percent mortality rate (or 1, or 2, or 4). 7,000 cases (now, much much more). So in the wake of that meeting, we reflect on the onslaught of numbers - what they reveal, and what they hide.  Support Radiolab today at