Physical Samples as Part of Cyberinfrastructure

1. Town Hall @ AGU Fall Meeting 2012 Physical Samples as Part of Cyberinfrastructure Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

2. Topics Credit: Lesley Wyborn, Geoscience Australia • Why we need to talk about Samples in CI/EC • Info about relevant activities: IGSN, DESC • Discussion: Next steps, community engagement Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

3. EarthCube Special Interest Group • brings together a community that is concerned with physical samples collected in the Earth Sciences, and their integration with the evolving digital data and information infrastructure. Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

4. WHY we need to talk about physical samples as part of cyberinfrastructure Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

5. Samples Matter in CI • Samples are a basic unit for Geoscience observations. • basic unit for data discovery, access, & analysis. • Physical specimens serve to provide real world data observations. • help calibrate remotely sensed and/or proxy data sets • complement sensor-based data acquired in oceanic, terrestrial or atmospheric observatories • Physical samples are increasingly expensive to collect. • collection in remote areas • collection via expensive sampling techniques such as drill holes, submersibles, or ocean dredging Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

6. Samples Matter in the CI • Access to information about the samples is required for proper evaluation & interpretation of sample-based data. • Access to the physical samples is required to verify & reproduce observations. • Access to both is required to advance utility and re-use of samples & data. Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

7. Samples Benefit From CI • Software tools can support and streamline collection management. • Online sample catalogs can dramatically improve discovery and access of collections for broad audiences. • Interoperability can provide unprecedented capabilities to • Link data, samples, and publications • Link all data acquired on a single sample & subsamples • Integrate sample-based data with other data types Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

8. Requirements • We need to connect the physical objects with the digital data • virtual representations of samples • unique identification • We need to curate & provide access to the physical objects: • storage facilities to curate actual physical objects; • software & resources for digital collection management • maintenance of sample catalog • online access to collection catalog Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

9. Current Status • Samples have ambiguous and non-persistent names. They cannot be identified without doubt and properly cited. • Samples cannot be located, there is no central or federated catalog. • Sample metadata are often inaccessible, incomplete, inconsistent, and disconnected from the data. This prevents proper re-use of samples and sample-based data. Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

10. Building the Internet of Samples • Technical infrastructure • Standards (metadata, data exchange protocols, etc.) • Catalogs, registries, services • Software tools • Standards & best practices • Organizational structure / governance Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

11. Relevant Initiatives • International Geo Sample Number IGSN • Unique identification of samples • Persistent access to sample metadata • Digital Environment for Sample Curation DESC • shared cyberinfrastructure for collection management • Energistics (Lee Allison) Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

12. The International Geo Sample Number (IGSN) IGSN International Geo Sample Number SESAR System for Earth Sample Registration: www.geosamples.org Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

13. IGSN • Unique identifier for physical samples collected from our natural environment and related sampling features. igsn:HRV003M16 http://www.igsn.org http://www.geosamples.org Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

14. IGSN: Concept • provide identifiers that are guaranteed to be unique via a centralized control mechanism • catalog sample metadata through user-based registration • establish best practices for describing, identifying, and citing samples Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

15. IGSN Syntax IGSN:ODP000234 • Alphanumeric string of characters (9 digits). • Mostly unintelligent (no encoded information). • User-specific pre-fix (centrally controlled name space) to allow delegation of identifier assignment. • Does not replace personal or institutional sample identifiers. • Short enough to fit labels and data tables in publications. Unique user code [name space] String of random characters [name specific string] Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

16. Metadata • Identification • Sample name(s), registrant • Description • Material, classification, age, size, comments • Geospatial information • Geographical names, coordinates • Collection • Expedition/cruise, platform, date, collector, technique • Archiving/access • Physical location of sample (repository), contact Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

17. Sample Types • ‘Sampling features’ • Locations such as drill-holes, wells, soil pits, sections • ‘Parent objects’ such as cores, dredges, CTDs • Individual specimens • Categorized by material (rock, mineral, fluid, etc.) • Sub-divided by physical appearance: hand specimen, rock powder, thin section Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

18. IGSN Sample Geneology Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

19. IGSN Applications • find and access samples in the IGSN Metadata Catalog • find, link, & integrate distributed data for a sample • link samples, data, and publications • preserve sample metadata for long-term access Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

20. IGSN Status • ca. 4 million IGSNs issued • International governance established: IGSN e.V. • New, more scalable architecture under development • Tools for sample registration, metadata management, and catalog search available at SESAR (www.geosamples.org) • MySESAR as personal workspace • Web services for client-based registration • Integration into publication process in progress Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

21. Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

22. Entity linking with SESAR through ScienceDirect slides courtesy of BethanKeall, Elsevier Elsevier creates a text link to http://www.geosamples.org/profile?igsn:HRV0035F0 Author highlights/mentions IGSN of their sample in text of paper … igsn:HRV0035F0…. Researchers can link through to the sample at SESAR in one click – more efficient Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

23. How to Participate • As an individual • register your samples (currently at SESAR) • use the IGSN • sample labels, data tables on your computer and in publications • As an organization (non-profit) • become a member of the IGSN e.V. • as a regular member at act as an Allocating Agent • as an affiliate member to promote & support the IGSN Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

24. DESC: Digital Environment for Sample Collections Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

25. DESC: What? • “Shared Cyberinfrastructure for Sample Repositories and Collections” • Provide a web hosted software solution to facilitate management and access of sample collections • Advance best practices, standards, policies for sample curation, distribution, attribution, and citation Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

26. DESC: Why? • Addresses the urgent need for many sample repositories to efficiently manage their collections • many collections still operate with non-digital procedures (spreadsheets, analog records) of samples and loans • lack the resources (staff, funding) and infrastructure (hardware, software, IT support) to develop and operate web-enabled, searchable databases • professional collection management software is expensive, requires IT support, or does not fulfill requirements Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

27. History • Past years: Preliminary requirements defined by a group of sample curators and SESAR • 2011: Informal meeting at AGU FM • Aug 2012: Funding secured from NSF OCI for a 1 year planning effort • Workshop to define requirements • Develop implementation plan • IEDA/SESAR, AGS, U MN (LacCore), OSU, RENCI Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

28. Partners • American Association of State Geological Surveys • Antarctic Research Facility, FSU • LDEO Deep-sea Core Repository • LacCore, University of Minnesota • NGDC/NOAA (Index of Marine & Lacustrine Geological Samples) • Oregon State University, Core Repository • Strouds Water Research Center • University of HawaiiSample repository • University of Rhode Island, Core & Dredge Repository • US Polar Rock Repository • WHOI Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

29. DESC: Objectives • create and maintain software tools needed to support collection management and online presence, • encourage and further the development of common data and collection management standards and procedures, • establish joint practices for the recognition of and respect for intellectual property, • create sustainable business models for continuing maintenance and evolution of managing sample resources, • integrate the sample management life-cycle into professional and cultural practice of science. Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

30. Online Sample Curation: Services • Facilitate development & maintenance of a digital collection catalog • Support administration of the physical collection • Provide tools & workflow to process & track requests for samples and/or loans • Provide a customizable UI for public online access to the collection Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

31. DESC: Next Steps • Webinar in late December or early Januaryto review existing specifications & system requirements and gather more input • Develop an initial specifications document & implementation plan • Workshop in spring 2013 (March/April) to refine specs & implementation plan • Fall 2013: Proposal for DESC development Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

32. How You Can Get Engaged • EarthCube Special Interest Group on “Physical Samples as Part of Cyberinfrastructure • Upcoming EarthCube Domain Workshops • Upcoming DESC webinars & workshops • Membership in IGSN e.V. Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

33. EarthCube Domain Workshops • Experimental Stratigraphy • Dec 11-12, 2012 (University of Texas, Austin) • Engaging the Critical Zone Community to Bridge Long Tail Science with Big Data • Jan 21-23, 2013 (University of Delaware) • Cyberinfrastructure for Paleogeoscience • Feb 4-6, 2013 (University of Minnesota) • Developing a CI Vision for Petrology & Geochemistry • March 6-7, 2013 (Smithsonian Institution, NMNH) Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure

34. Discussion • Community-based sample archives: What do we need? How can we get there? Who should be involved? Workshop? • How can we make best use of the EarthCube SIG? Do we need more? • How can we advance best practices & standards for samples? Town Hall AGU 2012: Physical Samples as Part of Cyberinfrastructure