Latest News

February 2019

This newsletter summarizes new improvements and features in the System for Earth Sample Registration (SESAR) as well as recent outreach and user highlights. Click on the links below for more detailed information.

 

Samples Added

Since November 5,011 samples were registered in SESAR. Browse the complete SESAR catalog with more than 4.3 million samples.

 

Recent SESAR Improvements

SESAR v.7.2.2 was released in November 2018. This new version introduced improved validation and new functionality for the Sub-Object Type and Classification fields and implemented a new version (4.0) of web service schema. See more release notes here.

 

SESAR Community

  • The SESAR team attended the AGU Fall Meeting held in Washington D.C from December 10-14, 2018. See more information below about our presentations at AGU, which included presentations about the IGSN and SESAR and participation in a town hall regarding geochemical data standards. If you were not able to catch up with us at AGU, contact us at info@geosamples.org with questions or comments about our resources.
    • IGSN: Toward a Mature and Generic Persistent Identifier for Samples: This presentation discussed the evolution of the IGSN and our efforts to redesign and improve its existing organization and technical architecture. Slides from this talk can be found here.
    • Increasing the Impact of Your Research by Enabling Persistently FAIR Physical Samples: The System for Earth Sample Registration (SESAR): This poster discussed the benefits of using IGSNs and SESAR, and how SESAR has grown beyond individual investigators to include repositories, museums, and many large-scale scientific initiatives. The poster can be viewed here.
    • Building a Global Network of Geochemical Data: This townhall discussed developing geochemical data standards in the Earth Sciences (and the IGSN as an existing standard that has improved discoverability) and opportunities for a global geochemical data network. To learn more, please refer to the presentation here.
  • Dr. Kerstin Lehnert and SESAR participated in PIDapalooza 2019, a conference dedicated to persistent identifiers (PIDs). Dr. Lehnert gave a presentation titled “Transitioning an Identifier System to Persistence” where she discussed the recent Sloan-funded effort to develop a mature organizational and technical structure for the IGSN that is scalable and extensible to other domains, ensuring persistence.
  • SESAR participated in the annual assembly of members of the International Implementation Organization for the IGSN (IGSN e.V.). The objective of the IGSN e.V. is to implement and promote standard methods for locating, identifying, and citing physical samples with confidence by operating an international IGSN registration service with a distributed infrastructure for use by and benefit to its members. Membership in the IGSN Implementation Organization is open to organizations who wish to run their own IGSN allocating service.
  • Join us on twitter @igsn_info!

 

User Spotlight

In this edition we spotlight Nichole Anest and the team at the Lamont-Doherty Core Repository. The Lamont-Doherty Core Repository (LDCR) contains one of the world’s most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository, which contains approximately 72,000 meters of core and associated metadata. Besides their mission to provide long-term curation and archiving of samples and cores, the Core Repository also fulfills sample requests, assists investigators in sample collection activities, and works tirelessly to educate teachers, students, and the public about the important role science and the Core Repository play in building a better understanding of Earth processes.

 

We caught up with Nichole to learn more about how the Core Repository uses the IGSN and SESAR to manage their samples, and to explore some of their exciting sample collections. Read more below:

 

Why do you use SESAR? We use SESAR because it makes it possible to track samples through time and publications. I get many students requesting samples that someone used in a paper years to decades ago but the information in the paper about the samples is usually limited or non-existent. So, we have to go back through our paper sampling histories to locate the PI, what core(s) and at what intervals they sampled, and try to piece together what samples' data were used for the published work. The use of IGSNs makes these sort of sample requests much easier as well as giving "automatic" acknowledgement to the repository where the samples came from.

 

Sample group highlight: There are about two hundred cores that were taken by the Bureau of Ocean Energy Management (BOEM), part of the US Dept of the Interior, to look for near-shore sand deposits. They wanted to identify where beach sand was transported after major coastal storms (such as Irene and Sandy) and see if it is feasible to use it to replenish the beaches after such storms. Check out the BOEM cores in SESAR which include core photos as well as grain size data.

 

The BOEM cores in the Lamont-Doherty Core Repository

 

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May 2018

May 2018. Nearly 7,000 holes drilled across the globe in collaboration with the Continental Scientific Drilling Coordination Office have been registered in SESAR. These holes now have persistent and globally unique identifiers (IGSNs) and can be linked to core samples extracted from the holes. Check them out in the SESAR Catalog by searching Set Name/IGSN -> IGSN begins with "CDR". These holes were registered as part of Open Core Data, an NSF-funded project that is radically improving discoverability, accessibility, citeability, preservation, and integration of data from past, current, and future drilling and coring projects.

 

 

CSDCO Hole Locations plotted in GeoMapApp



April 2018

Apr 2018. SESAR version 7.1.1 is released, which includes new features, enhancements, and improvements.
  

  • New Feature: An option to preview sample locations on a map is now provided when you upload a SESAR batch registration or batch upload template in MySESAR. You can access the map by clicking "View Locations on Map." Locations are only shown if you have entered values for Latitude and Longitude (not UTM). You can see if samples plot in expected locations and, if not, you can adjust coordinates in your batch template and re-upload it, eliminating the need to edit sample metadata at a later time or involve the SESAR curator. We recommend that you double-check your sample locations by viewing your samples on a map each time you upload a batch registration template.

 
Read all of the improvements at the SESAR Release Notes page.
 
 



January 2018

Jan 2018. SESAR version 7.1.0 is released, which includes many new features and improvements. Some highlights:
  

  • Users may now set release dates when registering samples. Release dates determine when sample metadata is publicly accessible and searchable. If no release dates are specified, sample metadata will be publicly accessible immediately (recommended).
  • Users may now update release dates for sample metadata by editing individual sample profiles in MySESAR, using the MySESAR batch update functionality, or using the update web service.
  • A new batch registration template can now be downloaded from MySESAR. This new template allows users to specify different release dates for each sample in the template, rather than setting a single release date for all samples in the template. If no release dates are specified, sample metadata will be publicly accessible immediately (recommended).
  • An email notification will now be sent to sample owners one month before their sample metadata release dates. This email will notify users of the upcoming release dates and recommend steps for editing release dates if desired.
  • Formatting for dates (e.g., collection date) in batch registration templates has been relaxed. Acceptable date formats now include YYYY-MM-DD and MM/DD/YYYY. Date cells no longer have to be formatted as text.

 

Read all of the improvements at the SESAR Release Notes page.
 

If you have any questions or comments about the new features, please contact info@geosamples.org.



Jan 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 SESAR'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 widelyParticipants 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

Nov 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 SESAR 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 SESAR batch registration template. Users should also supply a mapping file that maps SESAR metadata fields to fields in their sample metadata files. MARS takes advantage of existing SESAR 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 SESAR 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.



July 2017

Jul 2017. SESAR version 7.0.0 is released, which includes many new features and improvements. Some highlights:
 

  • Users may now update sample metadata for existing samples in bulk by uploading a batch template, a method that is very similar to the initial batch registration mechanism. Check out this tutorial about the new functionality.
  • Users can now assign IGSNs of up to 32 characters in length (A-Z, 0-9, '-', '.'). The new syntax follows recommendations of the IGSN e.V. at http://igsn.github.io/syntax/. The extended syntax is primarily intended for use by large repositories, where it may be necessary to use hierarchical syntax conventions. However, in consideration of human readability as well as the fact that the IGSN will appear on-line and in print, the IGSN e.V. recommends that the IGSN should be as concise as possible. If you are considering assigning IGSNs to your samples that are longer than 9 characters, please contact info@geosamples.org to discuss.
  • Users can now specify Elevation Unit when registering samples (must be either feet, meters, miles, or kilometers).

 

Read all of the improvements at the SESAR Release Notes page.
 

If you have any questions or comments about the new features, please contact info@geosamples.org.



May 2017

May 2017. Copernicus Publications, publisher of nearly 40 peer-reviewed open-access scientific journals, now encourages the use of the International Geo Sample Number (IGSN) in articles to promote reproducibility of scientific research. Copernicus allows authors to connect their publications with related "assets", such as other research data, model code, videos, and now physical samples via the IGSN. Authors are encouraged to include IGSNs for any physical samples in manuscript text, as well as cite the IGSN in the reference list and include a statement about sample availability. To learn more, see the Copernicus news release or the Copernicus Manuscript Preparation Guidelines for Authors (sample availability section).

 

 



March 2017

Mar 2017. SESAR has released 4 video tutorials listed below on sample registration on the IEDA YouTube Channel. The videos are aimed at simplifying the registration process and addressing frequently-asked questions. We plan to continue to grow our video tutorial collection, so please keep an eye on the SESAR YouTube Playlist for more. Tutorials will also be posted at http://www.geosamples.org/help. If you have questions or suggestions for new tutorials, please contact us at info@geosamples.org.

 



Mar 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, SESAR. The article highlighted the ease of registering and documenting samples in SESAR and showcased some of the SESAR'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 SESAR and the IGSN allowed the Lamont-Doherty Core Repository to better document, label, and organize their sample (in this case, coral) collections.

 

 

Dassié, Emilie, et al. (2017), Saving our marine archives, Eos, 98, https://doi.org/10.1029/2017EO068159.