Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO

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 CoxeResearch Australasia 2016, 13th October 2016

Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO | Anusuriya Devaraju et al.

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

http://hdl.handle.net/10273/GRO000076




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)


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

3

2

IGSN : CSRWASC0063021 3

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Sub namespace of a client

Sample code specified by the client

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/csiroPOST /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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1

https://igsn.csiro.au/schemas

https://igsn.csiro.au/schemas


Metadata Schema (Description, Registration)

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IGSN-CSIRO Description Schema

IGSN Registration Schema

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2


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

http://dx.doi.org/10.1016/j.gca.2013.08.001




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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Mineral ResourcesAnusuriya DevarajuPostdoctoral Fellowe [email protected]

Mineral ResourcesJens KlumpScience Leader Earth Science Informaticse [email protected]

Mineral ResourcesVictor TeySenior Software Engineere [email protected]

Mineral ResourcesRyan FraserResearch Managere [email protected]

Mineral ResourcesPavel GolodoniucTeam Leader,Research Projects Officere [email protected]

Mineral ResourcesPeter WarrenSoftware Engineere [email protected]

Land & WaterSimon CoxChief Research Scientiste [email protected]

MINERAL RESOURCES