Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO
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The document discusses CSIRO's implementation of the International Geo-Sample Number (IGSN) system to provide unique identifiers and metadata for physical samples. It describes how CSIRO established IGSN allocation rules and implemented registration services and schemas. Assigning IGSNs to samples in various CSIRO collections helps make them discoverable online and allows cross-referencing between related resources like sub-samples, datasets, and publications. The use of IGSNs is expected to expand across CSIRO facilities and collections.
Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO
- 1. Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO MINERAL RESOURCES, LAND & WATER Anusuriya Devaraju, Jens Klump, Victor Tey, Ryan Fraser, Pavel Golodoniuc, Peter Warren, Simon Cox eResearch Australasia 2016, 13th October 2016
- 2. Challenges: Sample Curation & Publication • Physical samples may not be easily discoverable: • The lack of metadata catalogues for accessing their descriptions. • Different ways of naming and documenting samples. 2 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. The EarthChem data portal returns 71 samples called ‘A-1’ Different names representing the same rock sample on PetDB (Petrological Database)
- 3. Example 3 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al.
- 4. International Geo-Sample Number (IGSN) • Globally unique, persistent identifiers for physical samples (rocks, water, bio specimens), sample collections, and sampling features (boreholes). 4 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. IGSN:GRO000076 http://hdl.handle.net/10273/GRO000076 Fraser River water sample (image source: @igsn_info) Facilitate online discovery and access to physical samples
- 5. IGSN System Overview • Clients register samples with an allocating agent; the allocating agent registers the samples with IGSN e.V. (IGSN Implementation Organization). • IGSN allocating agents in Australia are CSIRO, Geoscience Australia, Curtin University. 6 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. Allocating Agent registration schema description schema Handle.net Registry Community Portal Harvest catalogue (OAI-PMH) IGSN e.V. Clients (Simplified system architecture of the IGSN registration)
- 6. IGSN @ CSIRO • CSIRO became a member of IGSN in 2013. • Use of IGSN was initiated by Mineral Resources in CSIRO. • 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 are soil and insect collections. 7 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al.
- 7. Identifier Governance in CSIRO • Following the IGSN Technical Specification, we established rules for allocating IGSNs in different parts of the organisation. • Different namespace strategies may be used by other allocating agents. 8 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. Allocating Agent Namespace 3 2 IGSN : CSRWASC00630 21 3 1 Sub namespace of a client Sample code specified by the client
- 8. System Implementation 9 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. IGSN e.V. Registry Metadata Store (PostgreSQL) CSIRO-IGSN Registration Service CSIRO OAI-PMH Data Provider Service OAI-PMH Harvester OAI-PMH data provider service of other allocating agents Australian IGSN Portal CSIRO-IGSN Clients: • Capricorn Distal Footprints • ARRC Collections • Mineral Reference Spectra harvest harvest register register CSIRO-IGSN Registration Service : https://igsn.csiro.au/csiro POST /subnamespace (Register sub-namespace) GET /subnamespace/all (Get all sub-namespaces) POST /igsm/ (Register samples) GET /metadata/{igsn} (Get metadata of a sample) POST /metadata/ (Get metadata of samples) DELETE /metadata/{igsn} (Mark a sample metadata as ‘deprecated’) CSIRO-IGSN Description Schema: https://igsn.csiro.au/schemas 2 1
- 9. Metadata Schema (Description, Registration) 10 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. IGSN-CSIRO Description Schema IGSN Registration Schema 1 2
- 10. IGSN Applications 11 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. Smart labels for sample inventory management. Discover samples and collections from other repositories through a common Australia Geo Sample Portal.
- 11. IGSN Applications • Reference samples by using IGSNs in publications, e.g., reports, articles, grant proposals. 12 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. Publication URL : http://dx.doi.org/10.1016/j.gca.2013.08.001
- 12. IGSN Applications • Cross-reference between registered samples and other related resources (sub-samples, datasets, publications). 13 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al. Specimen (IGSN) Spectrum (DOI) cross-reference Publication (DOI) cross-reference
- 13. Conclusions • We described the implementation of IGSN to identify and publish physical samples and sample collections in CSIRO. • This serves as a working example for implementing IGSN in a large organization. • Related Links: • CSIRO-IGSN Metadata Schema : https://igsn.csiro.au/schemas • CSIRO-IGSN Registration Service : https://igsn.csiro.au/csiro/ • CSIRO-IGSN OAI-PMH Data Provider Service : http://igsn.csiro.au/oai • Australian IGSN Portal (demo) : https://igsn2.csiro.au/ • The use of IGSN in CSIRO may be expanded to other collections and operated as a central service by Information Management and Technology (IM&T) as part of CSIRO’s National Facilities and Collections. 14 | Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al.
- 14. Mineral Resources Anusuriya Devaraju Postdoctoral Fellow e anusuriya.devaraju@csiro.au Mineral Resources Jens Klump Science Leader Earth Science Informatics e jens.klump@csiro.au Mineral Resources Victor Tey Senior Software Engineer e victor.tey@csiro.au Mineral Resources Ryan Fraser Research Manager e ryan.fraser@csiro.au Mineral Resources Pavel Golodoniuc Team Leader, Research Projects Officer e pavel.golodoniuc@csiro.au Mineral Resources Peter Warren Software Engineer e Peter.Warren@csiro.au Land & Water Simon Cox Chief Research Scientist e simon.cox@csiro.au MINERAL RESOURCES