An Open Source Web Service for Registering and Managing Environmental Samples

MINERAL RESOURCES FLAGSHIP

Anusuriya Devaraju, Jens Klump and Pavel GolodoniucFree and Open Source Software for Geospatial 2015, 17th September 2015.

Motivation

• Environmental samples are usually lie isolated, i.e., kept by sample curators, laboratories, state agencies, or museums.

• Each curator may follow their own way of documenting the sampleso Naming of samples is ambiguouso Samples descriptions are incomplete and not standardized.

• When sharing metadata of samples in a globally distributed environment, the unique identification of samples becomes essential.

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Motivation

• The International Geo Sample Number (IGSN) is a persistent and unique alphanumeric code for identifying environmental samples and specimens.

Sample image: https://twitter.com/igsn_info3 |

Simplified system architecture of the IGSN registration.

IGSN : IECCR0001

2Agent

namespace

code

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Allocating Agent : IEDA

The sample code of a coral from the CoreRepository at Lamont-Doherty Earth Observatory (LDEO)

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OAI-PMH

(Registry Metadata)

(Descriptive Metadata)

IGSN Allocation at 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 has joint projects with Geoscience Australia and Curtin University (Perth) to implement IGSN for the Australian geoscience community.

Related Work

• The IGSN is based on precursor work at LDEO, which was developed as the System for Earth Sample Registration (SESAR).

• Our work is expansion of precursor work in SESAR to suit Australian geo-community needs.

MySESAR : http://www.geosamples.org/mysesar5 |

• Initially developed with the requirements of individual geochemical investigators.

• There are shortcomings in its technical implementation.

Goal & Scope

• Develop an allocating agent web service and a descriptive metadata schema to support namespace governance, registration of IGSNs and associated metadata within CSIRO.

6 | The web site of the IGSN e.V. : http://www.igsn.org/

IGSN Registry Metadata

Hierarchical architecture of the IGSN registration through CSIRO

CUAHSI Master Controlled Vocabulary Registry for ODM 2.0 : http://vocabulary.odm2.org/7 |

Descriptive Metadata Schema a. Sample Identification

b. Sampling Activity

c. Sample Curation

d. Related Information

• The descriptive schema defines the essential characteristics of multiple 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., snow, soil and tissueo featureTypes, e.g., borehole, soilPitSection

• Reuse elements & data types from the IGSN registry schema• relatedResourceIdentifier, relationType

Descriptive Metadata Schema

CSIRO Descriptive Schema : https://github.com/kitchenprinzessin3880/csiro-igsn-schema.git 8 |

Sample IdentificationSampling Activity

Allocating Agent Web Service

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• Implements a REST API

• All requests are authenticated by passing in HTTP Basic Authentication headers.

Allocating Agent Service API

Request URI Descriptions Method Response Headers Response Body /igsn-service/subnamespace/

Register a sub-namespace

POST - 201 or non-201

/igsn-service/subnamespace/all

Retrieve all registered sub-namespaces.

GET Content-Type: application/json

200 with JSON representing registered namespaces or non-200 status with explanation

/igsn-service/igsn/ Register IGSNs for samples. Update the sample description if the IGSN exists.

POST Content-Type: application/json

201 with a list of successful and unsuccessful samples or non-201

/igsn-service/metadata/{igsn}

Return the descriptive metadata associated with a given {igsn}.

GET Content-Type: application/xml

200 with XML representing a dataset or non-200 status code with explanation

IGSN Registration via CSIRO Web Service

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System Implementation

• The Capricorn Distal Footprints project

• A collaboration between industry, the Geological Survey of Western Australia (GSWA), academia and CSIRO to address the issue of exploration through cover by examining the geophysical and geological footprints of ore deposits at multiple scales across the Capricorn Orogen in WA.

Distal Footprints Project : http://www.sief.org.au/FundingActivities/RP/Distal.html11 |

System architecture.

Results

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http://hdl.handle.net/10273/TEST/CSCAP0001

Landing page hosted by the Capricorn Distal Footprints Sample Curation System.

The IGSN registry (Metadata Store) shows that the samples have been successfully registered.

• A descriptive metadata schema and a web service for namespace governance and samples registration at an organizational scale.o The metadata schema can be adapted to respond to the samples’ diversity and requirements.

o The solutions developed are useful to identify samples unambiguously and to facilitate sharing of samples metadata on the Web in a systematic manner.

• Future worko Test and apply the solutions developed to data from other sample stores, e.g., the Australian

Resources Research Centre (ARRC) and the National Collection for Mineral Reflectance Spectra.

o Document the mappings between the descriptive metadata elements and the concepts specified in existing data standards, e.g., ISO, OGC and GeoSciML.

o Develop a web portal which harvests metadata from repositories of different allocating agents in Australia via the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH).

Conclusions

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Mineral Resources FlagshipAnusuriya DevarajuPostdoctoral Research Fellow

t +61 8 6436 8703e anusuriya.devaraju@csiro.auw http://www.anusuriya.com

MINERAL RESOURCES FLAGSHIP

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