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Identifying and Linking Physical Samples with Data: Using IGSN

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7 June 2017
This webinar is the second in a series examining persistent identifiers and their use in research. This webinar:

It introduced the IGSN, outlining its structure, use, application and availability for Australian researchers and research institutions
discussed the international symposium Linking Environmental Data and Samples.

Watch full webinar: https://www.youtube.com/watch?v=mOJRaLwOaCs

Published in: Education
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Identifying and Linking Physical Samples with Data: Using IGSN

  1. 1. Identifying and Linking Physical Samples with Data: Using IGSN ANDS PID Short Bites #2 | 07 June 2017
  2. 2. ANDS Webinar IGSN | Linking Data and Samples Outline This webinar is the second in a series examining persistent identifiers and their use in research. This webinar will: introduce the IGSN identifier for physical samples, outlining its structure, use, application and availability for Australian researchers and research institutions discuss the international symposium Linking Environmental Data and Samples. Speakers: Lesley Wyborn (Adjunct Fellow, National Computational Infrastructure Facility and Research School of Earth Sciences at ANU) Jens Klump (OCE Science Leader Earth Science Informatics, CSIRO)
  3. 3. ANDS Webinar IGSN | Linking Data and Samples Rationale What is it and how do you use it? Science use case: Researcher collecting samples, doing a publication with data How do I get an IGSN
  4. 4. 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’
  5. 5. ANDS Webinar IGSN | Linking Data and Samples Why do we need a unique identifier for samples (Part 2) ? Different names for dredge sample 3 from the Amphitrite cruise As national/international data aggregations emerge, we need to be able to uniquely identify samples and analytical data and publications derived from these samples
  6. 6. ANDS Webinar IGSN | Linking Data and Samples IGSN Overview: what does it do? Provides identifiers that are guaranteed to be unique via a hierarchical governance system (like assigning IP addresses) Facilitates internet-based discovery and access to physical samples: 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 identification of samples in the literature and of data derived from them Try it out: http://igsn.org/ICDP5054ESYI201 or http://igsn.org/AU1101
  7. 7. ANDS Webinar IGSN | Linking Data and Samples 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
  8. 8. ANDS Webinar IGSN | Linking Data and Samples Tracking the sample life cycle IGSN is used in CSIRO for tracking samples and to support sample logistics. In the field: unambiguous identification, metadata capture with mobile app. In the lab: identification and tying data to samples. In the Repository: identify collections and samples in storage, catalogue, manage sample logistics.
  9. 9. ANDS Webinar IGSN | Linking Data and Samples IGSN enables inking of samples with data and publications Specimen (IGSN) Spectral Results (DOI) Publication (DOI)
  10. 10. ANDS Webinar IGSN | Linking Data and Samples Using IGSN in the Literature Elsevier and Copernicus earth science journals use IGSN. The use of IGSN is also endorsed by the Coalition for Publishing Data in the Earth and Space Sciences (COPDESS). 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.
  11. 11. ANDS Webinar IGSN | Linking Data and Samples IGSN System Overview A. Sample registration: a. Clients register samples with an allocating agent b. the allocating agent registers the samples with IGSN e.V. (IGSN Implementation Organization). B. IGSN allocating agents in Australia a. CSIRO b. Geoscience Australia c. Curtin University
  12. 12. ANDS Webinar IGSN | Linking Data and Samples IGSN @ CSIRO CSIRO became a member of IGSN in 2013. IGSN are currently used for: Repository of the ARRC (Rock, Mineral, Soil) National Collection of Mineral Reference Spectra (Mineral, Rock, Synthetic Material) Capricorn Distal Footprints Project (Water, Vegetation, Soil, Rock, Regolith) Future use cases: Soils collection Insect collection
  13. 13. ANDS Webinar IGSN | Linking Data and Samples IGSN @ Geoscience Australia GA became a member of IGSN in 2014. IGSN are currently used in the GA collection. 1.6 Million samples registered Rocks Mineral Separates Thin sections Fossils GA is the IGSN Registration Agent for the Geological Surveys of the Australian states and territories.
  14. 14. ANDS Webinar IGSN | Linking Data and Samples IGSN @ Curtin University Curtin University became a member of IGSN in 2015. IGSN is currently used in the John de Laeter Centre for Geochemistry. IGSN and data management are supported by the Curtin University Library. JdLC, CSIRO, Univ. Western Australia and Geol. Survey of Western Australia work together in the Natural Resources Research Precinct. This project was supported by ANDS Major Open Data Collections Project
  15. 15. ANDS Webinar IGSN | Linking Data and Samples Australian IGSN Portal A grant from the NCRIS Research Data Services programme made it possible to develop a demonstrator for a common Australia Geo Sample Portal. Metadata are harvested into a common metadata portal to facilitate the discovery of samples curated by Australian IGSN members. Samples are described in a common metadata schema. http://igsn2.csiro.au
  16. 16. ANDS Webinar IGSN | Linking Data and Samples Linking to a Global Perspective IGSN Implementation Organization e.V. is a charitable organisation incorporated under German law in Potsdam, Germany. IGSN e.V. currently has 19 members on 4 continents.
  17. 17. ANDS Webinar IGSN | Linking Data and Samples Governance Model The governance model of IGSN is based on hierarchical delegation. IGSN identifiers are registered through IGSN agents. Each IGSN agent is given namespaces for the registration of IGSN. Examples: AU… Geoscience Australia CS… CSIRO CSCAP… CDF Project (CSIRO)
  18. 18. ANDS Webinar IGSN | Linking Data and Samples Technical Base IGSN builds upon an existing technical base and community. IGSN are based on the Handle System. The IGSN technical architecture is developed in close alignment with DataCite. http://igsn.github.io (documentation) https://github.com/igsn (repository)
  19. 19. ANDS Webinar IGSN | Linking Data and Samples Status Still work in progress. Active registration agents: ● CSIRO ● Curtin University ● Geoscience Australia ● GFZ Potsdam ● IEDA (Columbia University) ● MARUM (Univ. Bremen) ● BGR (by proxy) ● USGS (by proxy)
  20. 20. ANDS Webinar IGSN | Linking Data and Samples Samples moving between institutions What happens when samples move from one institution to another? Case 1: Laboratory IGSN available: The laboratory uses the already assigned IGSN. IGSN not available: The laboratory assigns a new IGSN. Case 2: Subsampling A subsample should be identified by its own IGSN. This case depends on the details of the setting.
  21. 21. ANDS Webinar IGSN | Linking Data and Samples Future Outlook Build a developer community around IGSN, document best practices, build reference implementations of services. Expand identifying and linking to objects in other domains. Other domains start reusing IGSN technology.
  22. 22. ANDS Webinar IGSN | Linking Data and Samples Report from “Linking Environmental Data and Samples” A “Cutting edge science symposium” Seed funding from CSIRO Research Plus office Goals: Bring international research leaders to Australia Provide forum for Early Career Researchers to engage
  23. 23. ANDS Webinar IGSN | Linking Data and Samples Web Page and Sponsors https://confluence.csiro.au/display/LEDS/Linking+Environmental+Data+and+Samples or https://goo.gl/FaexqL
  24. 24. ANDS Webinar IGSN | Linking Data and Samples Science Drivers We have a rich resource of samples supporting scientific investigation. How can we link these to the data sets that were derived from these samples? How can we link samples and data to the literature where they are interpreted and put into context? How can we include machines as users?
  25. 25. ANDS Webinar IGSN | Linking Data and Samples Solutions What is the role of infrastructure for building the linked data federation? How can we support the evolution of linked data? Heterogeneity is inherent, we need to have mediation mechanisms. How precise do terms need to be? We can suffer some degree of imprecision. Vocabularies will be adopted if they are useful. The fabric of science: which elements produce output? The process of science: which outputs are produced? The language of science: how do we describe the elements?
  26. 26. ANDS Webinar IGSN | Linking Data and Samples Social and Community Factors in LOD Greatest organisational effectiveness: when technology systems fit social systems. (Paul Box, CSIRO) Who bears the costs in current systems? What would be the incentive to contribute? Fail patterns: The 'anti-Life-of-Brian' pattern (but I'm different!) The "Too Big to Fail" pattern (should have ended long ago, but too much invested)

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