Goldschmidt2019 Samples Workshop

Sample Registration
Made Easy
KERSTIN LEHNERT
System for Earth Sample Registration SESAR
http://www.geosamples.org
8.18/2019 GOLDSCHMIDT 2019 WORKSHOP "VIVE LES SAMPLES" 1

The Value of Samples
 Specimens/samples are the source of observational
data and measurements across disciplines.
◦ Study the inaccessible in time and space.
◦ Study properties that cannot be measured in-situ.
 Samples provide irreplaceable evidence of long-term
historical trends.
◦ Record the state of nature at a given place & time.
 Samples record unique events in history.
 Samples are essential to calibrate proxy data.
 Samples serve as standards or references.
“Research projects
involve the study of
physical objects
collected from places
ranging from the
earth’s interior to the
depths of the ocean to
the reaches of outer
space.”
“Scientific Collections: Mission-Critical
Resources for Federal Science Agencies”
IWGSC, 2009

Sharing Samples
Providing access to actual physical samples is important. .85 (.16)
Providing access to actual physical samples is easy. .38 (.23)
iSamples RCN Survey
Joel Cutcher-Gershenfeld, 2015

Sharing Samples: Community Concerns
 “Global Access to Global Collections: establish repositories for
all physical samples and the biological, geochemical and
physical measurements made from those samples.”
(Paleogeoscience)
 “Poor and uneven access and management of sample
collections, incomplete sample tracking and linking of samples
to analyses in the literature and databases, discoverability of
existing samples” (Petrology & Geochem)
 “Need central archive of experimental samples with integrated
workflows, database templates, and community-wide DOI
system for samples” (Mineral Physics & Rock Deformation)
4
From Executive Summaries of EarthCube Domain End-user Workshops 2013
8.18/2019 GOLDSCHMIDT 2019 WORKSHOP "VIVE LES SAMPLES"

GOLDSCHMIDT 2019 WORKSHOP "VIVE LES SAMPLES" 5
M. McNutt, K. Lehnert, B. Hanson, B. A. Nosek, A. M. Ellison, J. L.
King; SCIENCE Policy Forum, 04 MAR 2016
“Access to data, samples, methods, and reagents used to conduct
research and analysis, as well as to the code used to analyze and
process data and samples, is a fundamental requirement for
transparency and reproducibility.”
8.18/2019

AGU 2019 Union Session on Samples
(Inter)National Treasures: Advancing Earth, Environmental, & Planetary
Sciences Through Access, Accreditation, and Use of Natural History
Samples and Collections
Panelists:
 Marcia McNutt, National Academies of Sciences, Engineering & Medicine
 Carol Roetzel Butler, National Museum of Natural History
 David E Schindel, Smithsonian Institution
 Mark Wimer, USGS
 Dimitri Koureas, DISSCo/Naturalis, Netherlands
 Jennifer Mabuka-Maroa, African Academy of Sciences, Kenia
 Lesley Wyborn, Australian National University

Tracking Samples & Sample Data
Have you ever been able to find all data for a specific sample in the
literature?
Have you been able to figure out if samples in different publications
that have the same name or number are actually from the same
specimen?
Are you able to identify every samples in your lab or desk or archive
and find out within seconds where, when, and how you collected
the sample?
No?

Example 1
Problems:
Ambiguous sample naming
Lack of relevant metadata
 Data are not reproducible
 Sample cannot be located
“The key measurement was the one backarc basalt
called "PPTUW”...
Subsequent efforts to confirm the observation ran
into problems. The apparently-same sample was
variously called PPTU, PPTUW/5, PPTUW-1, and
TVZ19 in four other papers. None of those papers
gave its latitude and longitude…!”
(J. Gill and E. Todd, personal communication 2013, related to
IEDA data rescue effort)

Example 2
Problem:
Dear Dr. Goldstein,
I was re-reading your wonderful paper “A Sm-Nd isotope
study of atmospheric dusts and particulates from major river
systems” that was published in EPSL in 1984, and had a quick
question about the Mississippi River sample included in Table
1. I have a student who is working on the REE geochemistry of
the Mississippi River and its associated estuary for his PhD
dissertation and we are trying to compile all of the Nd isotope
data from the literature. Anyway, the sample you list in Table
1 of your paper is identified as a “bulk sample”, which I
assume is a bulk river sediment sample. Is this correct? Also,
do you remember approximately where it was collected along
the river?
Best wishes,
Karen
Incomplete and ambiguous metadata

Example 2
… Anyway, to answer your question, that sample was
provided by Bob Meade of the USGS. … But I don’t know if it
was suspended material, bedload, or deposited on the banks.
Best I can do with the location at this point is to refer to the
figure in the paper, which shows it was collected close on the
delta.
I noticed that it says in the paper that info on the samples is
available from the authors. That was true at the time, and
even probably a decade or so later, but at this point I don’t
know where the notes are for those samples, once again
showing the importance of IGSNs. When I’m back at LDEO I’ll
check to see if I can find that old notebook.
Loss of metadata
 Data cannot be re-used

ANDS Webinar IGSN | Linking Data and Samples
Why do we need a unique identifier for samples (Part 1) ?
In the EarthChem global geochemical database all
these samples are labeled ‘M1’
11

What Are the Problems?
 Lack of central or federated catalogs of sample metadata to find samples,
preserve, and provide persistent access to sample metadata
 Lack of common Best Practices for sample identification, documentation, and
registration that are essential to build such catalogs.
 Software tools that support personal or institutional sample management &
curation.
 Facilities for sample curation and archiving.

Addressing the Problems
 The International Geo Sample Number IGSN
 The System for Earth Sample Registration SESAR

IGSN International GeoSample Number
 A globally unique and persistent identifier for physical objects in the Earth
Sciences
◦ guaranteed to be unique via a centralized control mechanism (unique name spaces)
◦ resolves to virtual sample representations (sample metadata profiles) managed at federated
IGSN Allocating Agents.
8.18/2019 14GOLDSCHMIDT 2019 WORKSHOP "VIVE LES SAMPLES"
• Name: Kerstin Lehnert
• SSN: 768-90-6482
• Name: HLY0102 D3-1
• IGSN: KAL7J8F55
People Samples

Persistent Identifiers (PID)
Build a FAIR Data Ecosystem
 Locate (Find)
 Access
 Link (Interoperate)
 Cite
ESIP SUMMER MEETING 2019 15
Programs
Cruise DOI
Dataset publication
Dataset DOI
Funding
FundRef#
Article publication
Publication DOIORCID
Researchers
Samples
IGSN

IGSN Overview: what does it do?
 Provides identifiers that are guaranteed to be unique via an international
governance system (like assigning IP addresses)
 Allows discovery and access to physical samples online:
◦ Web applications and programmatic access to sample metadata catalogues
◦ Networks with sample repositories and data centres
 Ensures preservation of, and access to sample data
 Aids in the unambiguous identification of samples in the literature and of data
derived from them
 Try it out: http://igsn.org/ICDP5054ESYI201 or http://igsn.org/AU1101

What IGSN can be used for
 Geological samples and other materials
(rocks, water, biological materials, …)
 Collections (groupings of samples)
 Sampling features (boreholes, outcrops, …)
 Samples can be linked to each other through
the “related identifier” metadata element
(e.g., minerals separated from a parent rock,
legs from a fossil beetle

Tracking the sample life cycle
IGSN supports tracking of samples and
sample logistics.
◦ In the field: unambiguous identification,
metadata capture with mobile app.
◦ In the lab: identification and tying data to
samples.
◦ In the sample repository: identify collections
and samples in storage, catalogue, manage
sample logistics.
◦ In the data repository: link samples to data and
publications; link data to a for a given sample in
different publications and databases.

IGSN: Supports Shared Collections
“Samples collected during collaborative Field
Institutes will be assigned International
GeoSample Numbers (IGSNs) and registered
with the System for Earth Sample
Registration (SESAR).
In contrast to a traditional “field trip”, wherein
an expert leads a group of participants
through the field area pointing out features of
interest along the way the quickly moving on
to the next stop, the mission of ExTerra Field
Institutes is to spend a longer amount of time
at a smaller number of stops, making field
observations and collecting samples for group
research.”
http://geoprisms.org/exterra/sample-data-management/

IGSN: Enables Linking of Samples with
Data and Publications
 Specimen (IGSN) Spectral Results (DOI) Publication (DOI)

IGSN in the Literature
 Earth science publishers recommend the use of
IGSN to reference samples in community
commitment statements*
◦ Example: Dere, A. L., T. S. White, R. H. April, B.
Reynolds, T. E. Miller, E. P. Knapp, L. D. McKay, and S. L.
Brantley (2013), Climate dependence of feldspar
weathering in shale soils along a latitudinal gradient,
Geochimica et Cosmochimica Acta, 122, 101–126,
http://dx.doi.org/10.1016/j.gca.2013.08.001.
*see: https://copdess.org/community-commitment-statements/

Adoption
Repositories will strive to: “... Ensure that unique, persistent identifiers are used for
authors (e.g., ORCID), research objects (e.g., Digital Object Identifier), and physical
samples (e.g., IGSN).”
Publishers will strive to: “... Implement standard identifiers for all authors (e.g., ORCID),
author contributions (e.g., CRediT), samples (e.g., IGSN), institutions, funders and grants,
and other identifiers as they are developed and adopted.

IGSN Adoption: Publishers
GOLDSCHMIDT 2019 WORKSHOP "VIVE LES SAMPLES" 238.18/2019

IGSN Adoption: Publishers
24
“… AGU Publications also strongly encourages use of
other identifiers in our journal papers. International Geo
Sample Numbers (IGSNs) uniquely identify items, such
as a rock sample, a piece of coral, or a vial of water
taken from the natural environment, and provide
important, consistent information about these samples.
Registering samples and including the IGSN in papers
helps secure provenance information but most
importantly connects common samples across multiple
studies in the literature. IGSNs also will help you keep
track of your samples. These identifiers can be reserved
before a field season or assigned afterward.”
Hanson, B. (2016), AGU opens its journals to author identifiers,
Eos, 97, doi:10.1029/2016EO043183.
Published on 7 January 2016.
GOLDSCHMIDT 2019 WORKSHOP "VIVE LES SAMPLES"8.18/2019

IGSN in Publications
2504/03/2017

IGSN in Data Systems: EarthChem Library

The IGSN Organization
 24 members in the IGSN e.V.
 In 5 countries (4 continents)
 8 functional Allocating Agents (AA)
 Multiple AAs under development
◦ British Geological Survey
◦ USGS
◦ CNRS
◦ SAEON (South Africa)
27
4,344,036
2,364,916
136,476
32,633
7,948
4,258
246
2
SESAR GeoSciAus MARUM CSIRO GFZ IFREMER KIGAM ARDC
Number of Registered Samples by Allocating Agent
Logscale

... And Growing
 iSamples project (in development): adoption of IGSN in biology and archeology
 DiSSCo (Distributed System of Scientific Collections in Europe): committed to
using IGSN, 2 billion specimens to be registered!
 Ocean Discovery Program (ODP): Repository at MARUM already using IGSN,
JAMSTEC and TAMU are planning implementation
 Smithsonian Institution (beyond National Mineral Collection)
 NASA: Astromaterial collections registration in process
 National Labs: LLNL, LBNL, BNL starting
28

Recent Developments
 Organization has grown substantially over the last 2-3 years with major
organizations joining IGSN e.V.
 Expansion beyond Earth sciences is happening.
 IGSN2040 project funded by Sloan Foundation in 2018.
“develop a strategic plan and roadmap that will guide the IGSN system in its next
chapter so it will be able to fulfill its mission of providing persistent, sustainable, and
reliable PID services to the international science community.”

SESAR System for Earth Sample Registration
 Web-based database that catalogs and preserves metadata of samples
submitted by users (incl. researchers, repositories, labs)
 Allocating Agent in the IGSN e.V. (International Geo Sample Number)
 Authenticated workspace for users to submit and manage sample metadata
 Online search of the metadata catalog
www.iedadata.org
www.geosamples.org

How to Register Your Samples

SESAR
Sample Registration Options
SESAR
Web services
Batch form (upload)
Web form

SESAR: Login

Create Your
Customized
Metadata Template

To see a list of SESAR controlled and
suggested vocabularies, including Object
Type, see
www.geosamples.org/help/vocabularies.

• Check off metadata fields you
wish to complete
• Click “Submit to create template”
• Open zip file with the batch
template and the SESAR Quick
Guide
• the Guide provides examples,
definitions and additional
instructions for entering metadata
for each field in the template.

Complete the Template!
40
NOTE:
• Currently a template is for a single sample type only
• Private/public setting applies to all samples in a single
template
• Check the instructions for date format.
Improvements coming soon!

Upload Your
Completed
Template

You will receive an email usually within a
day confirming the samples have been
registered and providing the assigned IGSNs.

View & Edit Metadata

Editing Sample Metadata 46
Add Images
Add Links to External
Data & Metadata
(URLs, DOIs)

Update Sample Metadata in Bulk
GOLDSCHMIDT 2019 WORKSHOP "VIVE LES SAMPLES"
478.18/2019

Pre-registering Samples
Before Fieldwork or
Subsampling
48
Example:
Upload metadata for pre-registered
samples after field work is completed.
Other use cases:
- change release data for private
samples
- add more specific metadata after
samples have been studied in the lab
- add parent IGSNs if they were
unknown at time of registration8.18/2019

Batch Update: Before and After
498.18/2019

Sample Registration: Important Advice
 Samples should be registered by the sample owner (who has the physical object)
◦ Metadata management can be collaborative (sample owner can share SESAR account privileges)
◦ Sample metadata can be transferred if the sample ownership changes
 Register samples as soon as possible after collection (in the field, in the repository)
◦ Possibility to ‘pre-register’ IGSNs so you can label samples with IGSNs in the field
 Register any subsamples and splits and link to the ‘parent sample’
 Ensure that your sample metadata are as comprehensive as possible from the start
◦ You can add metadata later, but will you?
◦ How discoverable and re-usable are your samples without critical metadata?

SESAR Help Resources
https://www.youtube.com/user/iedadata
http://www.geosamples.org/help

iSamples RCN Resources
 Training modules for Sample Management
◦ Created by Early Career Scientists (A.Dere, B. Hallett)
◦ Sample type specific (soil cores, rock outcrop samples)
◦ Published in EarthChem Library
 MARS (Middleware for Assisting with the Registration of Samples, J. Bowring)
◦ software prototype that allows users to seamlessly push metadata from a preferred sample
metadata format to SESAR
https://www.earthcube.org/group/isamples

Thanks! Questions?
Contact us: info@geosamples.org
Join us at AGU Fall Meeting 2017
- IEDA booth in exhibit hall (#1519)
- IGSN Information Session (for date
and location, check our web site)
Spread the word!

Goldschmidt2019 Samples Workshop

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