ESIP Partner Assembly Endorses New Guide for Publishing Physical Samples

The Partner Assembly of Earth Science Information Partners (ESIP) endorsed a new guide for authors publishing research using physical samples, authored by the ESIP Physical Sample Curation cluster. This guide will allow authors working with physical samples to unlock the full value of associated data and research.

We are thrilled to announce ESIP’s formal endorsement of the newly updated “Publishing Open Research Using Physical Samples: Guidance for Authors.“

Physical samples – whether they are geologic cores, water samples, or biological specimens – are the bedrock of Earth and environmental science. They are often collected with significant financial cost and effort. Yet, they often lack the digital visibility needed for easy reuse by other interested researchers.

This new guide aims to change that. Developed by the ESIP Physical Sample Curation Cluster, these guidelines provide a clear, standardized workflow to help authors make their sample-based research Open, FAIR (Findable, Accessible, Interoperable, and Reusable), and reproducible.

“Thanks to the sustained collaboration by the Physical Samples Curation Cluster,” says Yuhan (Douglas) Rao, ESIP Board President, “this guide will help us foster a resilient global ecosystem of samples and related data, which is more critical than ever.”

Why This Matters Now

In times when the risk of data loss is a persistent threat, the preservation and citation of physical samples and their associated data is more critical than ever. As we have seen, older data, including important contextual data about physical samples themselves, can become lost when projects conclude or when personnel transition, stymying the potential for future research and discoveries. Samples need to be just as accessible and FAIR as the data and studies derived from them. 

By following this guide, researchers can ensure their work contributes to a connected global ecosystem of samples and related data, rather than remaining isolated or undocumented altogether. Consistent sample citation also can allow academic institutions, repositories, and museums track the impact of their collections, demonstrating their value to funders and the community.

“The guidelines were motivated by questions from researchers across disciplines who use samples as a core unit of study, questions about how to better manage samples and data in a linked digital realm,” says Natalie Raia, a current co-chair of the Cluster. “From Earth sciences to archaeology to biomedicine and beyond, researchers are facing a shared set of core challenges in documenting and digitally archiving information about their samples and ensuring easy and efficient discovery and reuse. The technology needed to address these challenges exists, and an increasing variety of tools are available to support researchers in leveraging this technology. These guidelines for publishing physical samples aim to bridge the education gap and support greater adoption.”  

This guide is the product of years of collaboration between more than thirty people. Current Cluster co-chair Andrea Thomer says, “We strove to make these guidelines applicable to researchers in a broad range of fields in the Earth and environmental sciences. We are particularly indebted to past co-chairs Joan Damerow, Val Stanley, and Sarah Ramdeen for their work in bringing together such a broad group.”

Four Steps to Publishing Open Samples

The guide simplifies the process of publishing sample-based research into four actionable steps:

Step 1: Describe Samples with Rich Metadata

Metadata is “data about data” – the critical context needed to find and reuse samples. Researchers should catalog their samples using domain-specific metadata standards like SESAR’s schema for earth science, Darwin Core for biodiversity specimens, or MIxS for genomics samples.

Action: Create a metadata file (e.g., CSV) detailing key characteristics like collection location, date, and method.

Step 2: Assign and Use Consistent Identifiers

Identifiers are alphanumeric codes that are used to refer to a sample. Samples should be assigned a unique identifier – ideally a persistent identifier (PID) such as an IGSN or DOI, which can act as a globally unique link to your sample's metadata. PIDs allow machines to link your sample to the data derived from it, tracking research outputs across different labs, data repositories, and scholarly publications.

Action for users of curated collections: If you are using samples from a museum or sample repository, ask the collection manager about using existing identifiers/PIDs or creating new ones.

Action for new samples: If you collected new samples that will be used in multiple analyses, consider registering them for PIDs through an appropriate PID minting agent (e.g., through SESAR or your institution’s research data management system).

Step 3: Publish and Cite Samples in Datasets

In order to automate linking of sample-related research outputs, sample identifiers need to travel with the data. Include sample identifiers as part of your datasets, so that individual data points can be “connected” back to their originating sample. Consider including your rich metadata file (from Step 1) as part of the dataset upload to ensure all context is preserved. 

Action: When you publish your dataset in a repository (e.g., EarthChem, Zenodo, ESS-DIVE), include a specific column for “Sample PIDs” in your data files.

Step 4: Cite Sample Identifiers in the Paper

Finally, bring the PIDs into the text of your publication by citing them in the text of the paper or tables, as appropriate. Consistent formatting is critical for machine readability and for supporting more accurate and consistent linking of sample PIDs in scholarly publications. 

Action: Use consistent formatting when referring to samples in text,tables, or Data Availability statements. Ideally, use the standard compact format (e.g., igsn:10.58052/IEGRW002B) or the full URL.

A Note on Metadata: Consult Your Community

Different fields and repositories have different metadata requirements and best practices. Your use and selection of metadata standards and identifiers should be guided by your community of practice. The guide emphasizes that you should not wait until the end of the project to create metadata; instead, create metadata starting at the beginning of your project and update it as you work. Information that feels obvious to you (e.g., that a material is “soil”) might be the critical keyword a future researcher uses to find your work. By following the steps above and using your community’s preferred metadata standards, you make your samples discoverable and reusable, enabling powerful search tools to discover your work years in the future. 

Get Started Today

Ultimately, meticulous sample and data management is not just a best practice; it is an essential safeguard to maximize the return on scientific investments, prevent the loss of irreplaceable environmental baselines, and provide a durable, cost-effective foundation for future researchers to build upon. 

We encourage all authors, editors, and data managers to review and adopt these newly ESIP-endorsed guidelines. Small changes in how we reference physical samples can lead to massive leaps in scientific transparency and reuse, which are key to advancement of FAIR principles in the Earth Science Data community.

ESIP (Earth Science Information Partners) is a community of partner organizations and volunteers. We work together to meet environmental data challenges and find opportunities to expand, improve, and innovate across Earth science disciplines. Learn more and sign up for the weekly ESIP Update for #EarthScienceData events, funding, webinars and ESIP announcements.