Publishing Physical Sample Records on the Web

Publishing Physical Sample Records on the Web

MINERAL RESOURCES

Anusuriya Devaraju, Jens Klump, Victor Tey and Ryan FraserComputational 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

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.

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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’

International Geo Sample Number (IGSN)

• Persistent and unique alphanumeric code for identifying physical samples.


GRO000076

Fraser River water sampleImage by @igsn_info

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

globally resolvable identifier

IGSN @ CSIRO

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• 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

IGSN Registration Implementation


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.


IGSN-CSIRO Descriptive Metadata Schema

(Partial view of the CSIRO-IGSN Descriptive Metadata Schema)


IGSN-CSIRO Descriptive Metadata Schema

• The descriptive schema defines the essential characteristics of physical samples:

a. Sample identificationb. Sampling activityc. Sample curationd. Other related information

• Mandatory elements:

o sampleNumber, sampleName, isPublic, landingPage, sampleType, sampleCuration….

• Controlled vocabularies based on CUAHSI Master Controlled Vocabularyo sampleTypes, e.g., grab sample, core section ..o featureTypes, e.g., borehole, soilPitSection..o materialTypes, e.g., rock, soil, surface water, tissue..

IGSN Registration Example

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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 : 674Sub-collection : 931Sample: 24720


IGSN in Practice

• Physical world connected to the virtual.

• Physical samples can contain a hyperlink! (e.g., smart labels)


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

• 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 worko 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

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http://www.igsn.org/

https://confluence.csiro.au/display/AusIGSN/CSIRO+IGSN+IMPLEMENTATION

Anusuriya DevarajuPostdoctoral Research Fellow

t +61 8 6436 8703e [email protected] http://www.anusuriya.com

MINERAL RESOURCES

Thank You

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Publishing Physical Sample Records on the Web