Towards A Web-Enabled Geo-Sample Web: An Open Source Resource Registration and Management System for Connecting Geo-Samples to the Web

TOWARDS A WEB-ENABLED GEO-SAMPLE WEB: AN OPEN SOURCE
RESOURCE REGISTRATION AND MANAGEMENT SYSTEM FOR CONNECTING
GEO-SAMPLES TO THE WEB
1MINERAL RESOURCES, 2LAND AND WATER
Anusuriya Devaraju1, Jens Klump1, Victor Tey1, Simon Cox2 and Ryan Fraser1
International Conference for Free and Open Source Software for Geospatial (FOSS4G 2017), August 14-19, 2017, Boston, MA.

Presentation Outline
• Challenges in sample identification and discovery
• International Geo Sample Number (IGSN)
• IGSN Implementation in CSIRO
• Applications
• Lessons Learned and Conclusions

Challenges
• Inconsistent sample
cataloguing practices.
• The lack of online
catalogues for
discovering physical
samples.
3 |
The EarthChem data portal returns 71
samples called ‘A-1’.
Different names representing
the same rock sample on the
PetDB (Petrological Database)
Towards a Web-enabled Geo-sample Web: An Open Source Resource Registration and Management System for Connecting Geo-Samples to the Web | Anusuriya Devaraju et al.

Examples
4 | Towards a Web-enabled Geo-sample Web: An Open Source Resource Registration and Management System for Connecting Geo-Samples to the Web | Anusuriya Devaraju et al.

International Geo Sample Number (IGSN)
• Globally unique, persistent identifiers for physical samples (e.g., rocks, water,
bio specimens), sample collections, and sampling features (e.g., boreholes).
6 |
IGSN:GRO000076
http://hdl.handle.net/10273/GRO000076
Fraser River water sample
(image source: @igsn_info)
IGSN ensures
preservation and access
of sample metadata

IGSN System Overview
• Clients send sample registrations to an allocating agent; the allocating agent
forwards the registrations to the IGSN e.V.
• Australian IGSN allocating agents are CSIRO, Geoscience Australia, Curtin Uni.
7 |
(Hierarchical architecture of the IGSN)
HTTP Request
(OAI Verb)
HTTP Response
(Valid XML)
IGSN Implementation Organization (IGSN e.V.)
(International IGSN Registration Service)
Handle.net Registry
Clients
(e.g., individual users and laboratories)
OAI
Data Provider
Allocating Agent
(e.g., CSIRO’s IGSN Registration Service)
National IGSN
Sample Catalogue
IGSN registration requests are specified based on
description schema developed by the agent
IGSN registration requests are specified based on
registration schema developed by the IGSN e.V.
OAI
Service Provider

Metadata Schemas
8 |
IGSN-CSIRO
Description
Schema
IGSN Registration Schema

IGSN Implementation in CSIRO
• CSIRO became a member of IGSN in 2013, and the use of IGSN was initiated by
CSIRO Mineral Resources.
• IGSN are currently used for:
• Future use cases are National Soil Archive and Australian National Insect
Collection.
Sample Data Repositories Material Types Registrations (as at 31.05.2017)
Repository of the Australian Resources
Research Centre(ARRC)
rock, mineral, soil 25652
Capricorn Distal Footprints rock, vegetation, water, regolith 4232
Reflectance Spectra Reference Libraries mineral, rock, synthetic material 94

Identifier Governance in CSIRO
• Different namespace strategies may be used by other allocating agents.
• Following the IGSN Technical Specification, we established rules for allocating
IGSNs in different parts of the organisation.
11 |
Allocating agent namespace (‘CS’ represents CSIRO)
3
2
IGSN : CSRWASC00630
21 3
1
Sub-namespace of a client
Sample code specified by the client

System Implementation

A Web Front-End for Sample Registrations
13 |
Prefix and user
registration can be
performed via the
user interface from
the Registrant menu
option.
Individual users
may register
their samples
through the
GUI.

CSIRO-IGSN Description Metadata Schema
• Built upon the DataCite Metadata Schema (v4.0).
• An XML Schema which represents the core concepts of physical samples:
• Sample identification, e.g., identifier, alternate identifiers, title, visibility, material, specimen type..
• Sampling activity, e.g., location, time, purpose, method…
• Sample curation, e.g., curator, curation location and time…
• Related resources, e.g. publications, datasets…
• Supports batch sample registrations and has minimal restrictions on mandatory
metadata elements.
• Captures the provenance of sample curation, and the relations between
samples and related resources.
• Flexible in terms of representing spatial and temporal information.

SKOS-based Controlled Vocabularies
Vocabularies Examples Service Provider
Material types soil, rock, vegetation Master Controlled Vocabulary Registry
for ODM2
CUAHSI
Specimen types thin section, grab,
dredge, cuttings
Master Controlled Vocabulary Registry
for ODM2
CUAHSI
Nil-reason types missing, unknown, withheld. OGC definitions of nil reasons CSIRO CSIRO
Contributor types originator, custodian, point of contact. Linked Data Registry CSIRO
*Registration types physical sample, sample collection,
sampling features.
ANDS Research Vocabularies Australia CSIRO & Geoscience Australia
*Identifier types DOI, IGSN, LSID, ORCID ANDS Research Vocabularies Australia CSIRO & Geoscience Australia
*Relation types isDerivedFrom, hasDocument,
hasDigitalRepresentation.
ANDS Research Vocabularies Australia CSIRO & Geoscience Australia
A list of existing and newly developed SKOS vocabularies. New vocabularies are indicated by asterisks*.

CSIRO-IGSN Allocating Agent Service
• Sample registrations must be specified based on the CSIRO-IGSN Description
Schema.
• A RESTful web service that enable clients to
• Register a sub-namespace
• Get all registered sub-namespaces
• Register samples
• Get metadata of a sample or a list of samples
• Mark a sample metadata as deprecated.

Applications
Tracking samples from the field to the sample repository.
IGSN pre-allocation in mobile field data acquisition systems.
Images courtesy of Reid, N. (2015), Golodoniuc, P. (2017)

IGSN Applications
19 |
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.
20 |
Publication URL :
http://dx.doi.org/10.1016/j.gca.2013.08.001

IGSN Applications
Cross-reference
between the
registered samples
and their related
resources (sub-
samples, datasets,
publications).
21 |
Specimen (IGSN) Spectrum (DOI)
cross-reference
Publication (DOI)
cross-reference

Lessons Learned
• We ensure the global uniqueness of registered identifiers within the
organization through the IGSN namespace governance.
• Integration of identifiers into new and existing systems
• New sampling campaigns – adopt IGSN at the early stage of the sampling activity.
• Existing sample curation systems – prepend the IGSN namespace to the local sample identifiers.
• What can be identified with IGSNs? We used IGSNs to identify not only physical
samples but also sample collections and sampling features..
• Outreach, e.g., talks, meetings, and workshops.
• Documentations & public repositories.
• National collaboration, i.e., a joint project with the other allocating agents in
Australia (e.g., Geoscience Australia and Curtin University).

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.
• Benefits of implementing IGSN in CSIRO
• Identify samples unambiguously and discover them easily.
• Avoid duplicate sampling activities.
• Promote re-use of the samples for new purposes.
• 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.

Related Links
Components Link
CSIRO Allocating Agent Service https://igsn.csiro.au/igsn30/api
Description Metadata Schema https://igsn.csiro.au/schemas/3.0/
Metadata Store (source) https://github.com/AuScope/igsn30/tree/master/sql
CSIRO-IGSN OAI-PMH Data
Provider
https://igsn.csiro.au/igsn30/api/service/30/oai
National IGSN Web Portal http://igsn.org.au
OAI-PMH Harvester and National IGSN Web
Portal (source repositories)
https://github.com/AuScope/NatPortalIGSN
Sample Registration and Management GUI https://igsn.csiro.au/igsn30
A list of the components developed and their links.

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
Land and Water
Simon Cox
Chief Research Scientist
e simon.cox@csiro.au
Mineral Resources
Ryan Fraser
Research Manager
e ryan.fraser@csiro.au
MINERAL RESOURCES

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