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Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO
Anusuriya Devaraju
Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO
MINERAL RESOURCES
Anusuriya Devaraju, Jens Klump, Victor Tey, Ryan Fraser, Pavel Golodoniuc, Peter Warren, Simon CoxeResearch Australasia 2016, 13th October 2016
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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.
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The EarthChem data portal returns 71 samples called ‘A-1’
Different names representing the same rock sample on
PetDB (Petrological Database)
Example
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International Geo-Sample Number (IGSN)• Globally unique, persistent identifiers for physical samples (rocks, water,
bio specimens), sample collections, and sampling features (boreholes).
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IGSN:GRO000076http://hdl.handle.net/10273/GRO000076
Fraser River water sample (image source: @igsn_info)
Facilitate online discovery and access to
physical samples
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.
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Allocating Agent
registration schema
description schema
Handle.net Registry
Community PortalHarvest catalogue
(OAI-PMH)
IGSN e.V.
Clients
(Simplified system architecture of the IGSN registration)
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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.
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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.
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Allocating Agent Namespace
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IGSN : CSRWASC00630
21 3
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Sub namespace of a client
Sample code specified by the client
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System Implementation
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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
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Metadata Schema (Description, Registration)
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IGSN-CSIRO DescriptionSchema
IGSN Registration Schema
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IGSN Applications
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Smart labels for sample inventory management.
Discover samples and collections from other repositories through a common Australia Geo
Sample Portal.
IGSN Applications• Reference samples by using IGSNs in publications, e.g., reports, articles,
grant proposals.
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Publication URL :http://dx.doi.org/10.1016/j.gca.2013.08.001
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IGSN Applications• Cross-reference
between registered samples and other related resources (sub-samples, datasets, publications).
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Specimen (IGSN) Spectrum (DOI)
cross-reference
Publication (DOI)
cross-reference
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.
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International Geo Sample Number (IGSN) Symposium 2016• Convened by Geoscience Australia, CSIRO and ANDS.
• Wednesday, 2nd November 2016
• 10:00 AM – 4:00 PM AEDT
• Location : Geoscience Australia, Jerrabomberra Avenue, Symonston, ACT 2609
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Mineral ResourcesAnusuriya DevarajuPostdoctoral Fellowe [email protected]
Mineral ResourcesJens KlumpScience Leader Earth Science Informaticst +61 8 6436 8828e [email protected] www.csiro.au/en/Research/MRF
Mineral ResourcesVictor TeySenior Software Engineere [email protected]
Mineral ResourcesRyan FraserResearch Managere [email protected]
Mineral ResourcesPavel GolodoniucTeam Leader,Research Projects Officere [email protected]
MINERAL RESOURCES