Publishing Physical Sample Records on the Web
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The document discusses the importance of unique identification for physical samples in mineral resources, emphasizing the use of the International Geo Sample Number (IGSN) for establishing a standardized metadata schema. It outlines the implementation and system architecture for IGSN registration at CSIRO, facilitating better curation and sharing of sample metadata. Ongoing efforts include expanding the application of these solutions and improving accessibility through web portals and metadata harvesting.
Publishing Physical Sample Records on the Web
- 1. Publishing Physical Sample Records on the Web MINERAL RESOURCES Anusuriya Devaraju, Jens Klump, Victor Tey and Ryan Fraser Computational and Simulation Sciences and eResearch Annual Conference and Workshops 2016. Session: Earth Observation Informatics, 3rd March 2016. images: metlab.com.au, agronomy.k-state.edu
- 2. Introduction • Physical samples are usually lie isolated, i.e., curated by individual researchers, laboratories, state agencies or museums. • Known issues – different ways of naming and documenting samples. • When sharing metadata of samples to other users, the unique identification of samples becomes essential. 2 | Publishing Physical Sample Records on the Web | Anusuriya Devaraju
- 3. Examples: Naming Ambiguity of Samples Publishing Physical Sample Records on the Web | Anusuriya Devaraju3 | Different names representing the same sample on PetDB, the Petrological Database. The EarthChem data portal returns 71 samples called ‘A-1’
- 4. International Geo Sample Number (IGSN) • Persistent and unique alphanumeric code for identifying physical samples. Publishing Physical Sample Records on the Web | Anusuriya Devaraju4 | GRO000076 Fraser River water sample Image by @igsn_info http://hdl.handle.net/10273/GRO000076 globally resolvable identifier
- 5. IGSN @ CSIRO 5 | • CSIRO became a member of IGSN in 2013. • Use of IGSN was initiated in mineral resources research in CSIRO. • IGSN is used to identify existing samples collections: • Capricorn Distal Footprints Project • Rock Repository of the Australian Resources Research Centre • Australian National Collection of Mineral Reflectance Spectra* • CSIRO collaborates with Geoscience Australia and Curtin University to implement IGSN for the Australian geoscience community.Simplified system architecture of the IGSN registration. Publishing Physical Sample Records on the Web | Anusuriya Devaraju
- 6. IGSN Registration Implementation Publishing Physical Sample Records on the Web | Anusuriya Devaraju6 | System architecture. IGSN e.V. Registry Metadata Store (PostgreSQL) HTTPS HTTPS (basic access authentication) Allocating Service (RESTful web service) REST Endpoint : http://{server-name}/2.0/ POST /2.0/subnamespace (Register sub-namespace) GET /2.0/subnamespace/all (Get all sub-namespaces) POST /2.0/igsn/ (Register samples) GET /2.0/metadata/{igsn} (Get metadata of a sample) POST /2.0/metadata/ (Get metadata of samples) DELETE/2.0/metadata/{igsn} (Mark a sample’s registration as ‘deprecated’) Samples Curation Systems (Clients) • Capricorn Distal Foortprints Project • Rock Store • Clients, e.g., individual researchers, data centres and projects, obtain IGSNs for their samples through the registration service deployed by an allocating agent. • Clients send registration requests based on the descriptive metadata schema developed by the respective agent.
- 7. Publishing Physical Sample Records on the Web | Anusuriya Devaraju7 | IGSN-CSIRO Descriptive Metadata Schema (Partial view of the CSIRO-IGSN Descriptive Metadata Schema)
- 8. Publishing Physical Sample Records on the Web | Anusuriya Devaraju8 | IGSN-CSIRO Descriptive Metadata Schema • The descriptive schema defines the essential characteristics of physical samples: a. Sample identification b. Sampling activity c. Sample curation d. Other related information • Mandatory elements: o sampleNumber, sampleName, isPublic, landingPage, sampleType, sampleCuration…. • Controlled vocabularies based on CUAHSI Master Controlled Vocabulary o sampleTypes, e.g., grab sample, core section .. o featureTypes, e.g., borehole, soilPitSection.. o materialTypes, e.g., rock, soil, surface water, tissue..
- 9. IGSN Registration Example 9 | IGSN e.V. Registry Allocating Service (implemented by CSIRO) http://hdl.handle.net/10273/CSRWASC00630 Publishing Physical Sample Records on the Web | Anusuriya Devaraju Rock Store # IGSN (22.02.2016) Collection : 674 Sub-collection : 931 Sample: 24720
- 10. Publishing Physical Sample Records on the Web | Anusuriya Devaraju10 | IGSN in Practice • Physical world connected to the virtual. • Physical samples can contain a hyperlink! (e.g., smart labels)
- 11. Publishing Physical Sample Records on the Web | Anusuriya Devaraju11 | IGSN in Practice Embed IGSNs in publications, e.g., articles, grant proposals, reports. Visibility - Discovery of physical samples beyond data curators! Publication URL : http://dx.doi.org/10.1016/j.gca.2013.08.001
- 12. • Registration and management of physical samples based on IGSN in CSIRO. o The descriptive metadata schema may be adapted to different types of physical samples. o The solutions developed are useful to identify samples unambiguously and to facilitate sharing of samples metadata on the Web in a systematic manner. • Ongoing work o Apply the solutions developed to other sample stores in CSIRO o Support different ways of registering samples, e.g., LIMS, field apps, csv importer o Develop a web portal and a metadata harvester to gather samples from different allocating agents in Australia via the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH). o Interested? o Primary contact in CSIRO: Dr Jens Klump (Mineral Resources) o IGSN Implementing Organization : http://www.igsn.org/ o Technical documentation of the CSIRO-IGSN system: https://confluence.csiro.au/display/AusIGSN/CSIRO+IGSN+IMPLEMENTATION Conclusions 12 | Publishing Physical Sample Records on the Web | Anusuriya Devaraju
- 13. Anusuriya Devaraju Postdoctoral Research Fellow t +61 8 6436 8703 e anusuriya.devaraju@csiro.au w http://www.anusuriya.com MINERAL RESOURCES Thank You