An Open Source Web Service for Registering and Managing Environmental Samples Anusuriya Devaraju , Jens Klump and Pavel Golodoniuc Free and Open Source Software for Geospatial 2015, 17 th September 2015. MINERAL RESOURCES FLAGSHIP
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 samples o Naming of samples is ambiguous o Samples descriptions are incomplete and not standardized. • When sharing metadata of samples in a globally distributed environment, the unique identification of samples becomes essential. 2 |
Motivation • The International Geo Sample Number (IGSN) is a persistent and unique alphanumeric code for identifying environmental samples. (Registry Metadata) OAI-PMH IGSN : IECCR0001 1 2 code Agent (Descriptive Metadata) namespace 1 Allocating Agent : Interdisciplinary Earth Data Alliance (IEDA) Simplified system architecture of the 2 The sample code of a coral from the CoreRepository at IGSN registration. Lamont-Doherty Earth Observatory (LDEO) 3 | Sample image: https://twitter.com/igsn_info
IGSN Allocation at CSIRO • 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. 4 |
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. • Initially developed with the requirements of individual geochemical investigators. • There are shortcomings in its technical implementation. 5 | MySESAR : http://www.geosamples.org/mysesar
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. IGSN Registry Metadata Hierarchical architecture of the IGSN registration through CSIRO 6 | The web site of the IGSN e.V. : http://www.igsn.org/
Descriptive Metadata Schema a. Sample Identification • The descriptive schema defines the essential characteristics of multiple samples: a. Sample identification b. Sampling activity c. Sample curation b. Sampling d. Other related information Activity • Mandatory elements: o sampleNumber, sampleName, isPublic, landingPage, sampleType,sampleCuration …. • Controlled vocabularies based on CUAHSI Master Controlled Vocabulary o sampleTypes , e.g., snow, soil and tissue o featureTypes , e.g., borehole, soilPitSection • Reuse elements & data types from the IGSN registry schema c. Sample Curation • relatedResourceIdentifier , relationType …. d. Related Information 7 | CUAHSI Master Controlled Vocabulary Registry for ODM 2.0 : http://vocabulary.odm2.org/
Descriptive Metadata Schema Sampling Activity Sample Identification 8 | CSIRO Descriptive Schema : https://github.com/kitchenprinzessin3880/csiro-igsn-schema.git
Allocating Agent Web Service • Implements a REST API • All requests are authenticated by passing in HTTP Basic Authentication headers. Request URI Descriptions Method Response Headers Response Body /igsn- Register a sub- POST - 201 or non-201 service/subnamespace/ namespace /igsn- Retrieve all registered GET Content-Type: 200 with JSON service/subnamespace/ application/json representing registered sub-namespaces. all namespaces or non-200 status with explanation /igsn-service/igsn/ Register IGSNs for POST Content-Type: 201 with a list of successful samples. Update the application/json and unsuccessful samples sample description if or non-201 the IGSN exists. /igsn- Return the descriptive GET Content-Type: 200 with XML representing service/metadata/{igsn} metadata associated application/xml a dataset or non-200 with a given {igsn}. status code with explanation Allocating Agent Service API 9 |
IGSN Registration via CSIRO Web Service 10 |
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. System architecture. 11 | Distal Footprints Project : http://www.sief.org.au/FundingActivities/RP/Distal.html
Results The IGSN registry (Metadata Store) shows that the samples have been successfully registered. http://hdl.handle.net/10273/TEST/CSCAP0001 Landing page hosted by the Capricorn Distal Footprints Sample Curation System. 12 |
Conclusions • 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 work o 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. 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). 13 |
Thank You 고맙습니다 Mineral Resources Flagship Anusuriya Devaraju Postdoctoral Research Fellow t +61 8 6436 8703 e anusuriya.devaraju@csiro.au w http://www.anusuriya.com MINERAL RESOURCES FLAGSHIP
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