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
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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.
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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
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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.
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IGSN-CSIRO Descriptive Metadata Schema
(Partial view of the CSIRO-IGSN Descriptive Metadata Schema)
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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
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Rock Store # IGSN (22.02.2016)Collection : 674Sub-collection : 931Sample: 24720
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IGSN in Practice
• Physical world connected to the virtual.
• Physical samples can contain a hyperlink! (e.g., smart labels)
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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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Anusuriya DevarajuPostdoctoral Research Fellow
t +61 8 6436 8703e [email protected] http://www.anusuriya.com
MINERAL RESOURCES
Thank You