JD Figueroa

January 2018

A recent EOS Meeting Report describes last year’s International Symposium on Linking Environmental Data and Samples, which gathered more than 70 participants from a variety of Earth and environmental disciplines such as the solid Earth sciences, marine science, oceanography, soil science, ecosystems science, biodiversity, and remote sensing. Researchers, including SESAR²’s Dr. Kerstin Lehnert, considered whether a uniform approach to data representation could be applied to disciplines and projects with widely varying approaches to sampling. Various sessions allowed attendees to discuss their motivations for linking samples and data, explore technical approaches to Web linking and identifiers, and evaluate the challenges in the adoption of common standards across different disciplines and sectors where incentives may vary widely. Participants agreed that relationships between samples, parts of samples, and sampling artifacts must be recorded to allow resulting observations to be related back to the world. Ultimately, the meeting achieved its theme of “linking” by bringing together multiple disciplines to improve our understanding of how linked data can work in practice for environmental samples and data.

November 2017

Undergraduate students in the Computer Sciences Department at the College of Charleston are developing open-source software applications that make it easier to document and register scientific samples in the System for Earth Sample Registration (SESAR) to improve discovery and access to these valuable research resources for future use. The students are working under the direction of Dr. Jim Bowring in the Cyber Infrastructure Research & Development Lab for the Earth Sciences (CIRDLES). Four of the students recently presented their work at the 2017 Geological Society of America Annual Meeting. MARS, Middleware for Assisting with the Registration of Samples, is highlighted below.

MARS: Middleware for Assisting with the Registration of Samples
Tia Curry is the latest student from the CIRDLES lab to work on developing MARS, an open-source, cross-platform desktop and web application that streamlines the bulk registration of samples in the SESAR² sample registry. The application, which is still in development, allows investigators to register samples using their own preferred sample metadata file, rather than having to rearrange sample metadata to fit into the SESAR² batch registration template. Users should also supply a mapping file that maps SESAR² metadata fields to fields in their sample metadata files. MARS takes advantage of existing SESAR² sample registration web services to validate and register samples. Once IGSNs are assigned, they are automatically inserted back into the user’s original sample metadata file, eliminating the need to copy and paste or wait for an email. Check out Curry’s recent presentation about MARS here.

MARS was originally developed to assist with the registration of thousands of legacy cores archived at the Scripps Institution of Oceanography. For Geological Collections Manager Alex Hangsterfer, the time required to rearrange countless spreadsheets worth of metadata in order to upload those spreadsheets to SESAR² was simply not feasible. Although MARS was initially prototyped to facilitate the registration of the Scripps core collection, its highly extensible architecture will allow broad adoption.

The idea for MARS originally came about when Hangsterfer shared her challenges with Bowring and others at the Kickoff Meeting of the EarthCube iSamples Research Coordination Network (RCN) in 2015 and from there, a working group was formed to investigate tools to lower the barriers to use of the International Geo Sample Number (IGSN), the globally-unique identifier for physical samples. The IGSN, itself, has been recognized as an important tool for uniquely identifying samples in the lab and in the literature, as well as for linking samples to data, publications, and funding awards. Because resources can vary widely from one organization to another, open-source and extensible development of tools like MARS is immensely important for facilitating widespread adoption and use of the IGSN. Efforts like the iSamples RCN are also pivotal for providing a forum for diverse stakeholders, like computer scientist Bowring and geological collections manager Hangsterfer, to engage with one another. The RCN also provided modest student support to carry out development.

March 2017

In a recent EOS Project Update, the Marine Annually Resolved Proxy Archives (MARPA) project became the most recent group to recommend the use of the International Geo Sample Number (IGSN) for uniquely identifying and properly documenting physical samples. MARPA specifically recommended the use of IEDA’s sample registry, SESAR². The article highlighted the ease of registering and documenting samples in SESAR² and showcased some of the SESAR²’s sample management tools (label printing, etc.). The MARPA project is an NSF EarthCube initiative that aims to build consensus around best practices for sample and data sharing, particularly within the the paleoceanography and paleoclimatology communities, where sample and data management has largely been left up to individual researchers, with samples stored in individual labs and documented only on personal computers or in field notebooks. Read the full article here.

As pictured above, the use of SESAR² and the IGSN allowed the Lamont-Doherty Core Repository to better document, label, and organize their sample (in this case, coral) collections.