Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO

Transcription

1 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju, Jens Klump, Victor Tey, Ryan Fraser, Pavel Golodoniuc, Peter Warren, Simon Cox eresearch Australasia 2016, 13 th October 2016 MINERAL RESOURCES 1

2 Challenges: Sample Curation & Publication Physical samples may not be easily discoverable: The lack of metadata catalogues for accessing their descriptions. Different ways of naming and documenting samples. The EarthChem data portal returns 71 samples called A-1 Different names representing the same rock sample on PetDB (Petrological Database) 3 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. Example 4 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. 2

3 International Geo-Sample Number (IGSN) Globally unique, persistent identifiers for physical samples (rocks, water, bio specimens), sample collections, and sampling features (boreholes). IGSN:GRO Fraser River water sample (image Facilitate online discovery and access to physical samples 5 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. IGSN System Overview Clients register samples with an allocating agent; the allocating agent registers the samples with IGSN e.v. (IGSN Implementation Organization). IGSN allocating agents in Australia are CSIRO, Geoscience Australia, Curtin University. IGSN e.v. registration schema Allocating Agent description schema Clients Harvest catalogue (OAI-PMH) Handle.net Registry Community Portal (Simplified system architecture of the IGSN registration) 7 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. 3

4 CSIRO CSIRO became a member of IGSN in Use of IGSN was initiated by in CSIRO. IGSN are currently used for: Repository of the ARRC (Rock, Mineral, Soil) National Collection of Mineral Reference Spectra (Mineral, Rock, Synthetic Material) Capricorn Distal Footprints Project (Water, Vegetation, Soil, Rock, Regolith) Future use cases are soil and insect collections. 8 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. Identifier Governance in CSIRO Following the IGSN Technical Specification, we established rules for allocating IGSNs in different parts of the organisation. Different namespace strategies may be used by other allocating agents Allocating Agent Namespace Sub namespace of a client Sample code specified by the client IGSN : CSRWASC Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. 4

5 System Implementation Australian IGSN Portal CSIRO-IGSN Registration Service : POST /subnamespace (Register sub-namespace) GET /subnamespace/all (Get all sub-namespaces) POST /igsm/ (Register samples) GET /metadata/{igsn} (Get metadata of a sample) POST /metadata/ (Get metadata of samples) DELETE /metadata/{igsn} (Mark a sample metadata as deprecated ) CSIRO-IGSN Description Schema: IGSN e.v. Registry 2 register OAI-PMH Harvester harvest CSIRO OAI-PMH Data Provider Service CSIRO-IGSN Registration Service 1 register CSIRO-IGSN Clients: Capricorn Distal Footprints ARRC Collections Mineral Reference Spectra harvest OAI-PMH data provider service of other allocating agents Metadata Store (PostgreSQL) 10 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. Metadata Schema (Description, Registration) 1 IGSN-CSIRO Description Schema 2 IGSN Registration Schema 11 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. 5

6 IGSN Applications Smart labels for sample inventory management. Discover samples and collections from other repositories through a common Australia Geo Sample Portal. 12 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. IGSN Applications Reference samples by using IGSNs in publications, e.g., reports, articles, grant proposals. Publication URL : 13 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. 6

7 IGSN Applications Cross-reference between registered samples and other related resources (sub-samples, datasets, publications). Specimen (IGSN) Spectrum (DOI) Publication (DOI) cross-reference cross-reference 14 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. 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. Related Links: CSIRO-IGSN Metadata Schema : CSIRO-IGSN Registration Service : CSIRO-IGSN OAI-PMH Data Provider Service : Australian IGSN Portal (demo) : 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. 15 Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. 7

8 International Geo Sample Number (IGSN) Symposium 2016 Convened by Geoscience Australia, CSIRO and ANDS. Wednesday, 2 nd November :00 AM 4:00 PM AEDT Location : Geoscience Australia, Jerrabomberra Avenue, Symonston, ACT Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIRO Anusuriya Devaraju et al. Anusuriya Devaraju Postdoctoral Fellow e anusuriya.devaraju@csiro.au Jens Klump Science Leader Earth Science Informatics t e jens.klump@csiro.au w Ryan Fraser Research Manager e pavel.golodoniuc@csiro.au Pavel Golodoniuc Team Leader, Research Projects Officer e pavel.golodoniuc@csiro.au Victor Tey Senior Software Engineer e victor.tey@csiro.au MINERAL RESOURCES 8