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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

3

2

IGSN : CSRWASC00630

21 3

1

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

2

1

Metadata Schema (Description, Registration)

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IGSN-CSIRO DescriptionSchema

IGSN Registration Schema

1

2

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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 anusuriya.devaraju@csiro.au

Mineral ResourcesJens KlumpScience Leader Earth Science Informaticst +61 8 6436 8828e jens.klump@csiro.auw www.csiro.au/en/Research/MRF

Mineral ResourcesVictor TeySenior Software Engineere victor.tey@csiro.au

Mineral ResourcesRyan FraserResearch Managere pavel.golodoniuc@csiro.au

Mineral ResourcesPavel GolodoniucTeam Leader,Research Projects Officere pavel.golodoniuc@csiro.au

MINERAL RESOURCES