Latest News

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.



March 2016

Mar 2016. SESAR version 6.4 beta is released, which includes many new features and improvements. Some highlights:

 

  • You can now assign permissions to others to view, edit, and/or register sample metadata on your behalf. This substantial new functionality is described in more detail here.
  • You can now contact the owner of a sample by selecting the option at the bottom of each public sample profile.
  • SESAR samples can now be discovered through the IEDA Data Browser. Once a user selects samples of interest, he/she can click "Explore", which will take the user to the SESAR catalog to further define search criteria.
  • A new sample metadata update web service now exists for updating sample metadata in bulk programmatically.

 

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.



Mar 2016. SESAR Release 6.4 introduced substantial new functionality to support sample metadata access, editing, and registration permissions. The new features enable a SESAR account owner to give varying levels of permission to others to view, edit, and/or register sample metadata on behalf of the account owner.
 
These new features were developed in response to user requests to share private metadata with select individuals and to share edit or registration permissions with, for example, a student that may help a SESAR user manage their samples for a period of time. You can give these privileges to others for an indefinite or set period of time. You can change the level of permissions or remove permission entirely at any point.
 
There are four levels of permissions that you can give to others for your user codes:

  1. Read: Give permissions to others to view the metadata for all of your samples under a specific user code, regardless of whether the sample metadata are public or private.
  2. Read, Edit: In addition to privileges listed in #1, give permissions to others to edit the sample metadata profiles for your samples.
  3. Read, Edit, Create: In addition to privileges listed in #1 and #2, give permissions to others to register samples under your user code (namespace) through both individual and batch sample registration.
  4. Read, Edit, Create, Delete: In addition to privileges listed in #1, #2, and #3, give permissions to others to request de-activation of sample metadata profiles. Sample de-activation should be rare, except in the case of an error or a test or duplicate profile.
     

To share permissions for your user code(s), please be sure that the person you would like to give permissions to has registered for a GeoPass account. Then, please log into MySESAR and click "Set Permission for my User code" under My Account. You will need to know the GeoPass ID (email address) of the person you would like to share permissions with.
 
If you have questions or comments about the new capabilities or SESAR in general, please contact info@geosamples.org.
 



January 2016

Jan 2016. In an EOS article published on Jan 7, 2016, Brooks Hanson, Director of AGU Publications, strongly encourages the use of the International GeoSample Number (IGSN) in journal papers. Hanson recognizes that including IGSNs in publications provides provenance information to readers, and more importantly links analyses of the same sample across the literature, ultimately fostering greater discovery.

The recommendations to use the IGSN to uniquely identify samples is part of a broader effort to incorporate open community identifiers, including ORCIDs (Open Researcher and Contributor ID) for authors and Fundref IDs for funders into publications. AGU Publications acknowledges that the use of these identifiers will simplify the manuscript submission and review process in the future. To read the full article, click here.
 
AGU Publications is just one of 36 signatories of the Statement of Commitment from Earth and Space Science Publishers and Data Facilities, which includes a commitment to, "promote the use of relevant community permanent identifiers for samples (IGSN), researchers (ORCID), and funders and grants (FundRef)."
 
Hanson, B. (2016), AGU opens its journals to author identifiers, Eos, 97, doi:10.1029/2016EO043183. Published on 7 January 2016.



November 2015

Nov 2015. If you are working with Earth and environmental samples as a researcher, educator, curator, data manager, software developer or architect, or as a publisher, please join us for an information and discussion forum on Sunday, December 13th, 4:00pm PST, at the San Francisco Marriott Marquis, Walnut Room; 780 Mission St., San Francisco, CA.
 
This forum is organized jointly by the EarthCube iSamples Research Coordination Network, the IGSN e.V. (International Geo Sample Number), and the System for Earth Sample Registration (SESAR) with the intent to provide an opportunity for you to:
  • learn about these organizations and how they support digital and physical sample management, sample citation in publications, developing a global sample catalog, and more
  • tell us about the challenges you encounter with your sample collections, their curation, documentation, and preservation.
  • engage in the iSamples RCN,
  • find out how to become a user of the IGSN or member of the IGSN e.V.,
  • check out tools that SESAR offers to help you manage your samples.

Please let us know if you are planning to attend (RSVP by email to mcarter@ldeo.columbia.edu) or simply stop by. Refreshments will be available.

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Learn more about the organizers:

  • iSamples (Internet of Samples in the Earth Sciences) is an EarthCube NSF-funded Research Coordination Network (RCN) that seeks to advance the use of innovative cyberinfrastructure to connect physical samples and sample collections across the Earth Sciences with digital data infrastructures to revolutionize their utility for science. The ultimate goal of the RCN is to dramatically improve the discovery, access, sharing, analysis, and curation of physical samples and the data generated by their study.
  • The IGSN e.V.the International Geo Sample Number (IGSN) Implementation Organization, provides the organizational and technical backbone for scientific communities to apply the IGSN, a globally unique and resolvable, actionable, and persistent identifier for physical sample materials that allows investigators to locate, identify, and cite physical samples with confidence.
  • SESAR (System for Earth Sample Registration) is a web-based registry that distributes the IGSN for samples and related sampling features from the Ocean, Earth, and Polar Sciences. SESAR’s objective is to promote sharing, linking, and integration of sample-based data through the use of the IGSN.

 



August 2015

Aug 2015. The Smithsonian National Museum of Natural History recently registered nearly 350,000 samples with IGSNs in SESAR, including specimens from the National Gem, National Mineral, and National Rock Collections. The inclusion of these samples in SESAR greatly enhances the discoverability of these valuable collections*. Furthermore, since data exists for many of these samples in PetDB, the IGSNs can now be added and used to link samples to analyses in different publications regardless of sample naming conventions of individual authors. Click here to view an example sample profile in SESAR, including a link to the Smithsonian Collections web pages. To view all samples, search the catalog for samples beginning with the namespace 'NHB'.

 

These registrations took advantage of the SESAR Web Services, which are documented here.

 

 

*Please note that the use of IGSNs in publications, alone, does not fulfill the Smithsonian loan policy stating that samples must be referenced by museum catalog numbers. Authors should include both museum catalog numbers and IGSNs.