Copernicus Publications Recommends IGSN
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).
New SESAR Video Tutorials
March 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. Also see our tutorials section of the website. If you have questions or suggestions for new tutorials, please contact us at info@geosamples.org.
- How to get a SESAR Account
- How to Download a SESAR Batch Registration Template
- How to Complete a SESAR Batch Registration Template
- How to Upload a SESAR Batch Registration Template
Saving Marine Archives Using the IGSN
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, 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.
New Role-Based Permissions in SESAR
March 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:
- 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.
- Read, Edit: In addition to privileges listed in #1, give permissions to others to edit the sample metadata profiles for your samples.
- 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.
- 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.
AGU Publications Recommends Use of IGSN
January 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.
Smithsonian Registers National Gem, Mineral, and Rock Collections with IGSNs in SESAR
April 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.
SESAR Registrations Triple in a Year
February 2015
The number of new samples registered in SESAR over the last four months was more than triple that registered over the same period of time last year. In addition to an increase in registrations and batches submitted, there has also been an increase in the number of different namespaces (owned by individuals or institutions) being used to register samples.
From Oct. 2013 to Feb. 2014, 8,817 samples from 21 namespaces were registered. Over that period of time, 33 batch registration templates were uploaded.
From Oct. 2014 to Feb. 2015, 29,084 samples (+230%) from 36 namespaces (+70%) were registered. Over that period of time, 96 batch registration templates (+190%) were uploaded.
The increases seen in SESAR registrations show that more researchers and organizations are finding SESAR and the IGSN to be useful tools for managing their physical samples and the metadata pertaining to them, as well as for making their physical samples discoverable in the global SESAR sample catalog. To learn more about the benefits of SESAR and the IGSN and how to start registering your physical samples, please visit our Resources or Registration pages, or see our tutorials.
Link your paper with IGSN and make your data more accessible and discoverable
April 2014
Online papers in Science Direct link directly to sample metadata profiles in SESAR, making all of the metadata about the sample quickly available. When submitting a paper to Elsevier, tables with column headers “IGSN” or text with the prefix “IGSN:” will be identified and linked directly to geosamples.org. For more information please see the International Geo Sample Number section in Elsevier’s Guide for Authors.
See examples:
- Beier et al., 2018, Lithos (Table 1)
- Dere et al., 2013, Geochimica et Cosmochimica Acta (Table 2)
From the Elsevier news item:
We are delighted to highlight the ongoing cooperation with IEDA by announcing the first published papers with linked International Geo Sample Numbers (IGSN). Take a look at Table 2 of this Geochimica et Cosmochimica Acta paper where you can click on specific IGSN numbers and be taken directly to the sample profile held in the SESAR sample metadata catalog at geosamples.org. By setting up links between databases and published papers, data is more accessible and discoverable, which benefits all researchers in the field.
DESC webinar video, presentations, and Q&A
June 2013
Thanks to everyone who participated in the DESC (Digital Environment for Sample Curation) Webinar. The materials are posted on this page.
Presentations
- Introduction to DESC, Digital Environment for Sample Curation (Kerstin Lehnert)
- Cyberinfrastructure Needs of the U.S. Core and Sample Repositories (Anthony Koppers)
- State Geological Surveys: Capabilities and Needs (Lee Allison)
- Development Considerations for DESC (Jeff Heard and Mary Whitton, RENCI)
Video
Discussion
- From Sarah Timm (Virginia Museum of Natural History)
- Q: I developed a program called EGEMS specifically for cataloging geological materials including but not limited to rocks, minerals, research products, etc and I am wondering if there is any room for collaboration. I agree with everything you have said about the importance of preserving our collections and increasing their accessibility and I spent my master’s thesis at Virginia Tech researching and developing a potential solution to this growing need. This was shortly before EarthCube was developed and the only programs for recording data for geological materials were very expensive and designed for large museums. I have given talks at GSA these past few years and have touched on almost all of the topics you have in this talk. I would very much like to be a larger part of this initiative, can you tell me if and how this might be possible? Thank you.
Information about EGEMS and screenshots of the program can be viewed at www.egemsinfo.com - A: Yes, please contact us at info@geosamples.org if you would like to take on a collaborative role. Another great way to participate is to fill out the DESC survey about data management and sample curation challenges.
- Q: I developed a program called EGEMS specifically for cataloging geological materials including but not limited to rocks, minerals, research products, etc and I am wondering if there is any room for collaboration. I agree with everything you have said about the importance of preserving our collections and increasing their accessibility and I spent my master’s thesis at Virginia Tech researching and developing a potential solution to this growing need. This was shortly before EarthCube was developed and the only programs for recording data for geological materials were very expensive and designed for large museums. I have given talks at GSA these past few years and have touched on almost all of the topics you have in this talk. I would very much like to be a larger part of this initiative, can you tell me if and how this might be possible? Thank you.
- From Ramona Walls (University of Arizona)
- Q: I am involved in an effort to develop an ontology for biological collections (http://code.google.com/p/bco/). One goal is to allow linking of data that is annotated with existing standards such as Darwin Core or MIxS. This is going hand in hand with other efforts, for example, to develop standard identifiers for biological specimens. The motivations were almost identical to what you have described for earth science collections during the first two talks. Many of the ontology design patterns we are developing for describing biological samples could be translated directly into earth science samples. It would be great to coordinate the efforts across our communities. Anyone who would like to contact us can use the mailing list at https://groups.google.com/forum/?fromgroups#!forum/bco-discuss.
Survey
- DESC Repository Survey: We need your help in gathering requirements for DESC. Please, tell us about your data management and sample curation challenges.
Mailing list
- Sign up for the community mailing list for DESC, SESAR, and IGSN
Please send any questions or comments to info@geosamples.org.
New linking to the Index to Marine & Lacustrine Geological Samples (IMLGS)
May 2013
SESAR is working with sample repositories to improve linking between existing sample information. The IMLGS (Index to Marine & Lacustrine Geological Samples) has provided links to their records for over 35,000 SESAR sample profiles for several sample repositories. The links appear at the bottom of the sample profiles.
Sample repositories with this improved linking include:
- The Antarctic Marine Geology Research Facility (example)
- The Lamont Doherty Core Repository (example)
- The Ocean Drilling Program (example)
- The University of Rhode Island Marine Geological Samples Laboratory (example)
- The Woods Hole Oceanographic Institution (example)
Any user can add relevant URL links to their own profiles by choosing the “edit” link in MySESAR. For bulk updates please contact info@geosamples.org.