This document discusses the challenges of inconsistent sample cataloguing practices and lack of online sample discovery. It introduces the International Geo Sample Number (IGSN) as a solution to provide globally unique identifiers for physical samples. It then describes the implementation of IGSN at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia, including developing an allocating agent service, description metadata schema, and sample registration system. Finally, it discusses applications of IGSN for sample tracking, discovery, and linking samples to related resources, and lessons learned from CSIRO's implementation.
Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIROAnusuriya Devaraju
The document discusses CSIRO's implementation of the International Geo-Sample Number (IGSN) system to provide unique identifiers and metadata for physical samples. It describes how CSIRO established IGSN allocation rules and implemented registration services and schemas. Assigning IGSNs to samples in various CSIRO collections helps make them discoverable online and allows cross-referencing between related resources like sub-samples, datasets, and publications. The use of IGSNs is expected to expand across CSIRO facilities and collections.
Integrated Earth Data Applications: Enhancing Reliable Data Services Through ...iedadata
The document discusses how Integrated Earth Data Applications (IEDA) uses persistent identifiers to enhance reliable data services. IEDA assigns Digital Object Identifiers (DOIs) and International Geo Sample Numbers (IGSNs) to datasets, samples, and other objects to improve accessibility, reliability, and citability of data. These identifiers help link related data within IEDA systems and to external publications, samples, and other resources. They also support long-term archiving and attribution of research data.
An Open Source Web Service for Registering and Managing Environmental SamplesAnusuriya Devaraju
This document describes the development of an open source web service for registering and managing environmental samples. The system was created to address issues with identifying and sharing metadata for samples that are isolated in different collections. It implements the International Geo Sample Number (IGSN) standard for uniquely identifying samples and includes a descriptive metadata schema and REST API web service to register samples and namespaces within CSIRO. The system was tested on the Capricorn Distal Footprints sample collection project and successfully registered samples and metadata. Future work includes applying the system to additional sample collections and mapping the metadata elements to existing data standards.
Cross-domain data discovery and integration Simon Cox
Simon Cox presented on cross-domain data discovery and integration. He discussed using cross-domain data catalogs and aligning metadata standards to facilitate finding data across different domains. Various metadata standards were shown including DCAT and EML that could be combined or "mashed up" to improve data discovery for multi-disciplinary applications.
The Implementation of the International Geo Sample Number in CSIRO: Experienc...Anusuriya Devaraju
In 2014 the Commonwealth Scientific and Industrial Research Organisation (CSIRO) began to implement the International Geo Sample Number (IGSN) to allow unambiguous identification of physical samples and data derived from these samples. In this paper we describe the requirements for the implementation of persistent identifiers for physical samples in the organisation and technical solutions we developed to meet these requirements.
Web-enabled Physical Samples: Curating and Publishing Physical Samples in CSIROAnusuriya Devaraju
The document discusses CSIRO's implementation of the International Geo-Sample Number (IGSN) system to provide unique identifiers and metadata for physical samples. It describes how CSIRO established IGSN allocation rules and implemented registration services and schemas. Assigning IGSNs to samples in various CSIRO collections helps make them discoverable online and allows cross-referencing between related resources like sub-samples, datasets, and publications. The use of IGSNs is expected to expand across CSIRO facilities and collections.
Integrated Earth Data Applications: Enhancing Reliable Data Services Through ...iedadata
The document discusses how Integrated Earth Data Applications (IEDA) uses persistent identifiers to enhance reliable data services. IEDA assigns Digital Object Identifiers (DOIs) and International Geo Sample Numbers (IGSNs) to datasets, samples, and other objects to improve accessibility, reliability, and citability of data. These identifiers help link related data within IEDA systems and to external publications, samples, and other resources. They also support long-term archiving and attribution of research data.
An Open Source Web Service for Registering and Managing Environmental SamplesAnusuriya Devaraju
This document describes the development of an open source web service for registering and managing environmental samples. The system was created to address issues with identifying and sharing metadata for samples that are isolated in different collections. It implements the International Geo Sample Number (IGSN) standard for uniquely identifying samples and includes a descriptive metadata schema and REST API web service to register samples and namespaces within CSIRO. The system was tested on the Capricorn Distal Footprints sample collection project and successfully registered samples and metadata. Future work includes applying the system to additional sample collections and mapping the metadata elements to existing data standards.
Cross-domain data discovery and integration Simon Cox
Simon Cox presented on cross-domain data discovery and integration. He discussed using cross-domain data catalogs and aligning metadata standards to facilitate finding data across different domains. Various metadata standards were shown including DCAT and EML that could be combined or "mashed up" to improve data discovery for multi-disciplinary applications.
The Implementation of the International Geo Sample Number in CSIRO: Experienc...Anusuriya Devaraju
In 2014 the Commonwealth Scientific and Industrial Research Organisation (CSIRO) began to implement the International Geo Sample Number (IGSN) to allow unambiguous identification of physical samples and data derived from these samples. In this paper we describe the requirements for the implementation of persistent identifiers for physical samples in the organisation and technical solutions we developed to meet these requirements.
Identifying and Linking Physical Samples with Data: Using IGSNARDC
7 June 2017
This webinar is the second in a series examining persistent identifiers and their use in research. This webinar:
It introduced the IGSN, outlining its structure, use, application and availability for Australian researchers and research institutions
discussed the international symposium Linking Environmental Data and Samples.
Watch full webinar: https://www.youtube.com/watch?v=mOJRaLwOaCs
Validation of services, data and metadataLuis Bermudez
Now days organizations are making available data (e.g. vector data, rasters) via web services, that follow open standards and are easier to integrate with other data. Validation of these services is important to guarantee that clients (e.g. web portals, mobile applications) can properly discover and download the data that a user needs. Validation can also serve as curation process to improve discovery on registries [1][2] or for certification purposes [3]. This session will provide an overview and a demo of the Open Geospatial Consortium (OGC) Validation tools. The participants will understand how to invoke a test and install the tools in their own environment. The validation tools are used to test servers, data and clients. The tests can be customized to not only test implementations against OGC standards but also community profiles. The validation engine and the tests are available as open source in GitHub.
[1] ESIP Discovery Cluster Testbed: Validate and Relate Data & Services - Draft - http://commons.esipfed.org/node/406
[2] Community Inventory of EarthCube Resources for Geosciences Interoperability - http://earthcube.org/group/cinergi
[3] OCG Validation Website - http://cite.opengeospatial.org/teamengine/
Presentation about the IGSN and ongoing initiatives for the Internet of Samples at the EGU 2015 short course "Open Science Goes Geo: Beyond Data and Software".
EarthCube Monthly Community Webinar- Nov. 22, 2013EarthCube
This webinar features project overviews of all EarthCube Awards (Building Blocks, Research Coordination Networks, Conceptual Designs, and Test Governance), followed by a call for involvement, and a Q&A session.
Agenda:
EarthCube Awards – Project Overviews
1.. EarthCube Web Services (Building Block)
2. EC3: Earth-Centered Community for Cyberinfrastructure (RCN)
3. GeoSoft (Building Block)
4. Specifying and Implementing ODSIP (Building Block)
5. A Broker Framework for Next Generation Geoscience (BCube) (Building Block)
6. Integrating Discrete and Continuous Data (Building Block)
7. EAGER: Collaborative Research (Building Block)
8. A Cognitive Computer Infrastructure for Geoscience (Building Block)
9. Earth System Bridge (Building Block)
10. CINERGI – Community Inventory of EC Resources for Geoscience Interoperability (BB)
11. Building a Sediment Experimentalist Network (RCN)
12. C4P: Collaboration and Cyberinfrastructure for Paleogeosciences (RCN)
13. Developing a Data-Oriented Human-centric Enterprise for Architecture (CD)
14. Enterprise Architecture for Transformative Research and Collaboration (CD)
15. EC Test Enterprise Governance: An Agile Approach (Test Governance)
A Call for Involvement!
sers, Applications and the Community of Practice for the Air Quality ScenarioRudolf Husar
The document discusses the GEOSS (Global Earth Observation System of Systems) architecture for the air quality community. It proposes an architecture where air quality services could register with the GEOSS registry and be discovered and invoked by users. This would allow data analysts to compose and visualize air quality data workflows to inform decision makers. It also discusses establishing an air quality community of practice to facilitate collaboration.
2008-05-05 GEOSS UIC-ADC AQ Scen W shop TorontoRudolf Husar
The document discusses the GEOSS (Global Earth Observation System of Systems) architecture for the air quality community. It proposes an architecture where air quality services register with the GEOSS registry and are discoverable through the GEOSS clearinghouse. This would allow users to find, select, and link to relevant air quality services. The architecture envisions community air quality catalogs that aggregate catalog listings and allow users to access data and models through composed workflows.
Virtual Research Environments supporting tailor-made data management service...Blue BRIDGE
Presented by Pasquale Pagano of CNR at the BlueBRIDGE Workshop at SeaTech Week 2016 in Brest, France. http://www.bluebridge-vres.eu/events/join-bluebridge-10th-biennial-sea-tech-week-brest-france
The BlueBRIDGE approach to collaborative researchBlue BRIDGE
Gianpaolo Coro, ISTI-CNR, at BlueBRIDGE workshop on "Data Management services to support stock assessement", held during the Annual ICES Science conference 2016
Citizen Observatory Framework with Access Management Federation in GEOSS - Ba...COBWEB Project
Presentation given by Bart De Lathouwer (Interoperability Program, OGC and COBWEB Project) on Thursday 10th October, at the ENVIP'2013 Workshop, part of ISESS (International Symposium on Environmental Software Systems) 2013 in Neusiedl am See, Austria.
Find out more about the COBWEB Project at:
http://cobwebproject.eu/dissemination/
GeoChronos: An On-line Collaborative Platform for Earth Observation ScientistsGeoChronos
Presentation given by John Gamon at the AGU Fall Meeting in San Francisco on Dec. 14, 2009. The presentation highlights features and supporting technologies of the GeoChronos Platform
This document summarizes an update from the Entomological Collections Network meeting in 2012. It discusses the iDigBio initiative to facilitate the digitization of biodiversity collections data through developing standards, providing portal access to data, and planning for long-term sustainability. It describes the seven Thematic Collection Networks and over 130 participating institutions. It provides details on the development of the iDigBio HUB portal and API to enable access to digitized specimen records along with upcoming workshops and activities.
VREs and Research Tools - supporting collaborative researchChristopher Brown
A summary of the Jisc funded VRE and Research Tools programmes and projects. Presented at the Jisc Regional Support Centre London webinar on 20 November, 2013 (http://jiscevents.force.com/E/EventsDetailPage?id=a06U000000Efx52IAB&srvc=JISC%20RSC%20London)
Semantic Web technologies, both those envisaged and those already realised, have the potential to benefit domains where issues such as volume, complexity and heterogeneity can overcome traditional techniques. Sensor networks are one such area where the application of semantics is indicated by scale, complexity, and the need to integrate over heterogeneous standards, sensors and systems for multiple purposes and multiple disciplines.
The Semantic Sensor Networks W3C Incubator is an international initiative to develop standards for sharing information collected by sensors and sensor networks over the Web, including an ontology for different types of sensing devices and their observations, and new approaches for the semantic markup of sensor descriptions and services that support sensor data exchange and sensor network management.
Kerry will describe the ongoing effort to increase the quality and reduce the cost of capturing environmental data, to address the growing demand for information about the environmental systems that support Australia’s agricultural, resource and process-based industries.
A presentation given by Manjula Patel (UKOLN) at the Repository Curation Environments (RECURSE) Workshop held at the 4th International Digital Curation Conference, Edinburgh, 1st December 2008,
http://www.dcc.ac.uk/events/dcc-2008/programme/
EarthCube EISWG Spring Meeting Presentation - 4.28.2014EarthCube
The document provides an overview of EarthCube, which aims to transform geoscience research through community-driven cyberinfrastructure. It discusses EarthCube's purpose of facilitating unprecedented data sharing to better understand interactions within the Earth system. The presentation outlines EarthCube's history and current efforts, which include funded building blocks, research coordination networks, and conceptual design awards. It also summarizes key challenges identified by end-users, such as the need for improved data discovery, interoperability, and long-term sustainability of geoscience data and tools.
The International Geo Sample Number (IGSN) is designed to provide an unambiguous globally unique persistent identifier (PID) for physical samples. It facilitates the location, identification, and citation of physical samples used in research.
Released on July 1, the ANDS IGSN minting service was developed in collaboration with AuScope to enable the Australian earth science community to assign IGSNs to geologic and environmental samples such as rocks, drill cores and soils, as well as related sampling features such as sections, dredges, wells and drill holes.
Join us for this webinar to:
--learn more about IGSN and their place in the PID ecosystem
--understand the many benefits of assigning IGSN to research samples
--gain insights into the current status and future directions for IGSN implementation in Australia and internationally
--find out about the ANDS IGSN service including service scope and access, as well as plans to expand the service beyond the earth sciences domain
--hear from IGSN experts and ask questions of them
Our speaker line up includes:
--Prof Brent McInnes, Curtin University
--Dr Jens Klump, CSIRO
--Dr Lesley Wyborn, NCI
--Joel Benn, ANDS
Workflows, provenance and reporting: a lifecycle perspective at BIH 2013, RomeCarole Goble
Workflow systems support the design, configuration and execution of repetitive, multi-step pipelines and analytics, well established in many disciplines, notably biology and chemistry, but less so in biodiversity and ecology. From an experimental perspective workflows are a means to handle the work of accessing an ecosystem of software and platforms, manage data and security, and handle errors. From a reporting perspective they are a means to accurately document methodology for reproducibility, comparison, exchange and reuse, and to trace the provenance of results for review, credit, workflow interoperability and impact analysis. Workflows operate in an evolving ecosystem and are assemblages of components in that ecosystem; their provenance trails are snapshots of intermediate and final results. Taking a lifecycle perspective, what are the challenges in workflow design and use with different stakeholders? What needs to be tackled in evolution, resilience, and preservation? And what are the “mitigate or adapt” strategies adopted by workflow systems in the face of changes in the ecosystem/environment, for example when tools are depreciated or datasets become inaccessible in the face of funding shortfalls?
This document discusses FAIR (Findable, Accessible, Interoperable, Reusable) principles for data management and describes an approach for assessing how well research data complies with the FAIR principles. The approach involves developing metrics based on the FAIR principles, an automated tool called F-UJI that assesses data using the metrics, and providing consultation to help data repositories improve their FAIRness over time based on the assessment results. The tool has been used to assess over 10,000 datasets across several data repositories. Challenges and lessons learned are also discussed, such as balancing machine-readable metrics with human aspects of the principles and ensuring assessments account for different types and contexts of data. The overall aim is to
The document provides a 7-step guide to effective research data sharing: 1) Publish your dataset with a persistent identifier; 2) Be generous when describing your data with metadata; 3) Use machine-readable controlled vocabularies; 4) Link related resources with persistent identifiers; 5) Choose an appropriate license; 6) De-identify sensitive data if applicable; 7) Make data available in a format for long-term accessibility and choose a trustworthy research data repository. The guide emphasizes making data findable, accessible, interoperable and reusable (FAIR).
More Related Content
Similar to Towards A Web-Enabled Geo-Sample Web: An Open Source Resource Registration and Management System for Connecting Geo-Samples to the Web
Identifying and Linking Physical Samples with Data: Using IGSNARDC
7 June 2017
This webinar is the second in a series examining persistent identifiers and their use in research. This webinar:
It introduced the IGSN, outlining its structure, use, application and availability for Australian researchers and research institutions
discussed the international symposium Linking Environmental Data and Samples.
Watch full webinar: https://www.youtube.com/watch?v=mOJRaLwOaCs
Validation of services, data and metadataLuis Bermudez
Now days organizations are making available data (e.g. vector data, rasters) via web services, that follow open standards and are easier to integrate with other data. Validation of these services is important to guarantee that clients (e.g. web portals, mobile applications) can properly discover and download the data that a user needs. Validation can also serve as curation process to improve discovery on registries [1][2] or for certification purposes [3]. This session will provide an overview and a demo of the Open Geospatial Consortium (OGC) Validation tools. The participants will understand how to invoke a test and install the tools in their own environment. The validation tools are used to test servers, data and clients. The tests can be customized to not only test implementations against OGC standards but also community profiles. The validation engine and the tests are available as open source in GitHub.
[1] ESIP Discovery Cluster Testbed: Validate and Relate Data & Services - Draft - http://commons.esipfed.org/node/406
[2] Community Inventory of EarthCube Resources for Geosciences Interoperability - http://earthcube.org/group/cinergi
[3] OCG Validation Website - http://cite.opengeospatial.org/teamengine/
Presentation about the IGSN and ongoing initiatives for the Internet of Samples at the EGU 2015 short course "Open Science Goes Geo: Beyond Data and Software".
EarthCube Monthly Community Webinar- Nov. 22, 2013EarthCube
This webinar features project overviews of all EarthCube Awards (Building Blocks, Research Coordination Networks, Conceptual Designs, and Test Governance), followed by a call for involvement, and a Q&A session.
Agenda:
EarthCube Awards – Project Overviews
1.. EarthCube Web Services (Building Block)
2. EC3: Earth-Centered Community for Cyberinfrastructure (RCN)
3. GeoSoft (Building Block)
4. Specifying and Implementing ODSIP (Building Block)
5. A Broker Framework for Next Generation Geoscience (BCube) (Building Block)
6. Integrating Discrete and Continuous Data (Building Block)
7. EAGER: Collaborative Research (Building Block)
8. A Cognitive Computer Infrastructure for Geoscience (Building Block)
9. Earth System Bridge (Building Block)
10. CINERGI – Community Inventory of EC Resources for Geoscience Interoperability (BB)
11. Building a Sediment Experimentalist Network (RCN)
12. C4P: Collaboration and Cyberinfrastructure for Paleogeosciences (RCN)
13. Developing a Data-Oriented Human-centric Enterprise for Architecture (CD)
14. Enterprise Architecture for Transformative Research and Collaboration (CD)
15. EC Test Enterprise Governance: An Agile Approach (Test Governance)
A Call for Involvement!
sers, Applications and the Community of Practice for the Air Quality ScenarioRudolf Husar
The document discusses the GEOSS (Global Earth Observation System of Systems) architecture for the air quality community. It proposes an architecture where air quality services could register with the GEOSS registry and be discovered and invoked by users. This would allow data analysts to compose and visualize air quality data workflows to inform decision makers. It also discusses establishing an air quality community of practice to facilitate collaboration.
2008-05-05 GEOSS UIC-ADC AQ Scen W shop TorontoRudolf Husar
The document discusses the GEOSS (Global Earth Observation System of Systems) architecture for the air quality community. It proposes an architecture where air quality services register with the GEOSS registry and are discoverable through the GEOSS clearinghouse. This would allow users to find, select, and link to relevant air quality services. The architecture envisions community air quality catalogs that aggregate catalog listings and allow users to access data and models through composed workflows.
Virtual Research Environments supporting tailor-made data management service...Blue BRIDGE
Presented by Pasquale Pagano of CNR at the BlueBRIDGE Workshop at SeaTech Week 2016 in Brest, France. http://www.bluebridge-vres.eu/events/join-bluebridge-10th-biennial-sea-tech-week-brest-france
The BlueBRIDGE approach to collaborative researchBlue BRIDGE
Gianpaolo Coro, ISTI-CNR, at BlueBRIDGE workshop on "Data Management services to support stock assessement", held during the Annual ICES Science conference 2016
Citizen Observatory Framework with Access Management Federation in GEOSS - Ba...COBWEB Project
Presentation given by Bart De Lathouwer (Interoperability Program, OGC and COBWEB Project) on Thursday 10th October, at the ENVIP'2013 Workshop, part of ISESS (International Symposium on Environmental Software Systems) 2013 in Neusiedl am See, Austria.
Find out more about the COBWEB Project at:
http://cobwebproject.eu/dissemination/
GeoChronos: An On-line Collaborative Platform for Earth Observation ScientistsGeoChronos
Presentation given by John Gamon at the AGU Fall Meeting in San Francisco on Dec. 14, 2009. The presentation highlights features and supporting technologies of the GeoChronos Platform
This document summarizes an update from the Entomological Collections Network meeting in 2012. It discusses the iDigBio initiative to facilitate the digitization of biodiversity collections data through developing standards, providing portal access to data, and planning for long-term sustainability. It describes the seven Thematic Collection Networks and over 130 participating institutions. It provides details on the development of the iDigBio HUB portal and API to enable access to digitized specimen records along with upcoming workshops and activities.
VREs and Research Tools - supporting collaborative researchChristopher Brown
A summary of the Jisc funded VRE and Research Tools programmes and projects. Presented at the Jisc Regional Support Centre London webinar on 20 November, 2013 (http://jiscevents.force.com/E/EventsDetailPage?id=a06U000000Efx52IAB&srvc=JISC%20RSC%20London)
Semantic Web technologies, both those envisaged and those already realised, have the potential to benefit domains where issues such as volume, complexity and heterogeneity can overcome traditional techniques. Sensor networks are one such area where the application of semantics is indicated by scale, complexity, and the need to integrate over heterogeneous standards, sensors and systems for multiple purposes and multiple disciplines.
The Semantic Sensor Networks W3C Incubator is an international initiative to develop standards for sharing information collected by sensors and sensor networks over the Web, including an ontology for different types of sensing devices and their observations, and new approaches for the semantic markup of sensor descriptions and services that support sensor data exchange and sensor network management.
Kerry will describe the ongoing effort to increase the quality and reduce the cost of capturing environmental data, to address the growing demand for information about the environmental systems that support Australia’s agricultural, resource and process-based industries.
A presentation given by Manjula Patel (UKOLN) at the Repository Curation Environments (RECURSE) Workshop held at the 4th International Digital Curation Conference, Edinburgh, 1st December 2008,
http://www.dcc.ac.uk/events/dcc-2008/programme/
EarthCube EISWG Spring Meeting Presentation - 4.28.2014EarthCube
The document provides an overview of EarthCube, which aims to transform geoscience research through community-driven cyberinfrastructure. It discusses EarthCube's purpose of facilitating unprecedented data sharing to better understand interactions within the Earth system. The presentation outlines EarthCube's history and current efforts, which include funded building blocks, research coordination networks, and conceptual design awards. It also summarizes key challenges identified by end-users, such as the need for improved data discovery, interoperability, and long-term sustainability of geoscience data and tools.
The International Geo Sample Number (IGSN) is designed to provide an unambiguous globally unique persistent identifier (PID) for physical samples. It facilitates the location, identification, and citation of physical samples used in research.
Released on July 1, the ANDS IGSN minting service was developed in collaboration with AuScope to enable the Australian earth science community to assign IGSNs to geologic and environmental samples such as rocks, drill cores and soils, as well as related sampling features such as sections, dredges, wells and drill holes.
Join us for this webinar to:
--learn more about IGSN and their place in the PID ecosystem
--understand the many benefits of assigning IGSN to research samples
--gain insights into the current status and future directions for IGSN implementation in Australia and internationally
--find out about the ANDS IGSN service including service scope and access, as well as plans to expand the service beyond the earth sciences domain
--hear from IGSN experts and ask questions of them
Our speaker line up includes:
--Prof Brent McInnes, Curtin University
--Dr Jens Klump, CSIRO
--Dr Lesley Wyborn, NCI
--Joel Benn, ANDS
Workflows, provenance and reporting: a lifecycle perspective at BIH 2013, RomeCarole Goble
Workflow systems support the design, configuration and execution of repetitive, multi-step pipelines and analytics, well established in many disciplines, notably biology and chemistry, but less so in biodiversity and ecology. From an experimental perspective workflows are a means to handle the work of accessing an ecosystem of software and platforms, manage data and security, and handle errors. From a reporting perspective they are a means to accurately document methodology for reproducibility, comparison, exchange and reuse, and to trace the provenance of results for review, credit, workflow interoperability and impact analysis. Workflows operate in an evolving ecosystem and are assemblages of components in that ecosystem; their provenance trails are snapshots of intermediate and final results. Taking a lifecycle perspective, what are the challenges in workflow design and use with different stakeholders? What needs to be tackled in evolution, resilience, and preservation? And what are the “mitigate or adapt” strategies adopted by workflow systems in the face of changes in the ecosystem/environment, for example when tools are depreciated or datasets become inaccessible in the face of funding shortfalls?
Similar to Towards A Web-Enabled Geo-Sample Web: An Open Source Resource Registration and Management System for Connecting Geo-Samples to the Web (20)
This document discusses FAIR (Findable, Accessible, Interoperable, Reusable) principles for data management and describes an approach for assessing how well research data complies with the FAIR principles. The approach involves developing metrics based on the FAIR principles, an automated tool called F-UJI that assesses data using the metrics, and providing consultation to help data repositories improve their FAIRness over time based on the assessment results. The tool has been used to assess over 10,000 datasets across several data repositories. Challenges and lessons learned are also discussed, such as balancing machine-readable metrics with human aspects of the principles and ensuring assessments account for different types and contexts of data. The overall aim is to
The document provides a 7-step guide to effective research data sharing: 1) Publish your dataset with a persistent identifier; 2) Be generous when describing your data with metadata; 3) Use machine-readable controlled vocabularies; 4) Link related resources with persistent identifiers; 5) Choose an appropriate license; 6) De-identify sensitive data if applicable; 7) Make data available in a format for long-term accessibility and choose a trustworthy research data repository. The guide emphasizes making data findable, accessible, interoperable and reusable (FAIR).
F-UJI : An Automated Assessment Tool for Improving the FAIRness of Research DataAnusuriya Devaraju
The document describes F-UJI, an automated tool for assessing the FAIRness of research data. It was developed as part of the FAIRsFAIR project to test metrics and a badging scheme for evaluating how well individual datasets adhere to the FAIR data principles. The tool extracts metadata about datasets from repositories, applies 15 core metrics corresponding to the FAIR principles, and returns an assessment report. It was piloted on over 500 datasets each from 5 repositories, to provide recommendations to improve data FAIRness. Feedback from the repositories was incorporated into further developing the metrics and tool.
An Automated Assessment of the FAIRness of Research DataAnusuriya Devaraju
This document discusses developing metrics and an automated tool to assess how FAIR (findable, accessible, interoperable, reusable) research data is. It describes the FAIR principles, the FAIRsFAIR project aims, developing object assessment metrics in collaboration with repositories, and the F-UJI tool which automatically assesses data based on the metrics. Pilots with several repositories provided recommendations to improve data FAIRness and status updates. The approach aims to iteratively improve FAIR assessment considering repository contexts.
Data You May Like: A Recommender System for Research Data DiscoveryAnusuriya Devaraju
This document describes a recommender system developed for the CSIRO Data Access Portal to help users discover research data. It examines two types of recommender systems: content-based, which uses item properties, and collaborative filtering, which uses user similarities. The system was built using both explicit metadata and implicit user behavior data. It calculates similarity between datasets across various features using techniques like TF-IDF and develops recommendations. An evaluation found the top recommendations were relevant 98% of the time. Future work includes enhancing the model and further evaluation.
Using Feedback from Data Consumers to Capture Quality Information on Environm...Anusuriya Devaraju
Data quality information is essential to facilitate reuse of Earth science data. Recorded quality information must be sufficient for other researchers to select suitable data sets for their analysis and confirm the results and conclusions. In the research data ecosystem, several entities are responsible for data quality. Data producers (researchers and agencies) play a major role in this aspect as they often include validation checks or data cleaning as part of their work. It is possible that the quality information is not supplied with published data sets; if it is available, the descriptions might be incomplete, ambiguous or address specific quality aspects. Data repositories have built infrastructures to share data, but not all of them assess data quality. They normally provide guidelines of documenting quality information. Some suggests that scholarly and data journals should take a role in ensuring data quality by involving reviewers to assess data sets used in articles, and incorporating data quality criteria in the author guidelines. However, this mechanism primarily addresses data sets submitted to journals. We believe that data consumers will complement existing entities to assess and document the quality of published data sets. This has been adopted in crowd-source platforms such as Zooniverse, OpenStreetMap, Wikipedia, Mechanical Turk and Tomnod. This paper presents a framework designed based on open source tools to capture and share data users’ feedback on the application and assessment of research data. The framework comprises a browser plug-in, a web service and a data model such that feedback can be easily reported, retrieved and searched. The feedback records are also made available as Linked Data to promote integration with other sources on the Web. Vocabularies from Dublin Core and PROV-O are used to clarify the source and attribution of feedback. The application of the framework is illustrated with the CSIRO’s Data Access Portal.
CAPTURING DATA PROVENANCE WITH A USER-DRIVEN FEEDBACK APPROACHAnusuriya Devaraju
Various portals have been developed to provide an easy way to discover and access public research data sets from various organizations. Data sets are made available with descriptive metadata based on common (e.g., OGC, CUAHSI, FGDC, INSPIRE, ISO, Dublin Core) or proprietary standards to facilitate better understanding and use of the data sets. Provenance descriptions may be included as part of the metadata and are
specified from a data provider’s perspective. These can include, for example, different entities and activities involved in a data creation flow, such as sensing platforms, personnel, and data calculation and transformation processes. Moving beyond the provider-centric descriptions, data provenance may be complemented with
forward provenance records supplied by data consumers. The records may be gathered via a user-driven feedback approach. The feedback information from data consumers gives valuable insights into application and assessment of published data sets. This might include descriptions about a scientific analysis in which the data
sets were used, the corrected version of an actual data set or any discovered issues and suggestions concerning the quality of the published data sets. Data providers might then use this information to handle erroneous data and improve existing metadata, their data collection and processing methods. Contributors can use the feedback channel to share their scientific analyses. Data consumers can learn more about data sets based on
other people’s experiences, and potentially save time by avoiding the need for interpreting or cleaning data sets. The goals of the study are to capture feedback from data users on published research data sets, link this to actual data sets, and finally support search and discovery of research data using feedback information. This
paper reports preliminary results addressing the goals. We provide a summary of current practices on gathering feedback from end-users on research data portals, and discuss their relevance and limitations. Examples from the Earth Science domain on how commentaries from data users might be useful in practice are also included.
Then, we present a data model representing key aspects of user feedback. We propose a system architecture to gather and manage feedback from end-users. We describe how the core PROV model may be used to represent the provenance of user feedback information. Technical solutions for linking feedback to existing data portals are also specified.
The rapid development of sensing technologies had led to the creation of large volumes of environmental observation data. Data quality control information informs users how it was gathered, processed, examined. Sensor Web is a web-centric framework that involves observations from various providers. It is essential to capture quality control information within the framework to ensure that observation data are of known and documented quality. In this paper, we present a quality control framework covering different environmental observation data, and show how it is implemented in the TERENO data infrastructure. The infrastructure is modeled after the OGC’s Sensor Web Enablement (SWE) standards.
Representing and Reasoning about Geographic Occurrences in the Sensor WebAnusuriya Devaraju
Observations are fed into the Sensor Web through a growing number of environmental sensors, including technical and human observers. While a wealth of observations is now accessible, there is still a gap between low-level observations and the high-level descriptive information they reflect. For example, we may ask what the measurements mean when a weather buoy provides a temperature time series. The challenge is not to gather a vast number of observations, but rather to make sense of them in environmental monitoring and decision making.
In order to infer meaningful information about occurrences from observations, a description of how one gets from the former to information about the latter must be expressed. This thesis develops an ontology to formally capture the relationships between geographic occurrences and the properties observed by in situ sensors. Building upon the existing positions on experiential and historical perspectives, stimulus-centric sensing, event-process algebra and thematic roles, the ontology elucidates the key concepts associated with geographic occurrences that are particularly significant from a sensing point of view. A use case for reasoning about blizzards and their temporal parts from real time series supplied by the Environment Canada illustrates the ontological approach. This thesis evaluates its findings on the basis of a comparison with an alternative approach in the Sensor Web, a verification of the use case results using an official event report published by the weather agency and an analytical assessment approached from the system development perspective.
The theoretical contribution of the thesis lies in the development of a formal model, which constitutes common building blocks for constructing application ontologies that account for inferences of geographic events from observations. With regards to its practical contribution, the thesis has demonstrated how ontological vocabularies are exploited with reasoning mechanisms to infer information about events, and to formulate symbolic spatio-temporal queries.
This document provides an overview of geospatial semantics and interoperability. It defines key concepts like semantics, interoperability, integration, and heterogeneities. It discusses types of heterogeneities that can occur like structural, domain, data, and language conflicts between data sources. Standards and specifications aim to provide syntactic interoperability but semantic interoperability requires identifying and resolving heterogeneities. The document also introduces geospatial semantic web and observations data standards that can help achieve greater interoperability.
The document discusses the Sensor Web and Semantic Sensor Web. It provides definitions and examples of the Sensor Web from NASA and OGC. The key components of Sensor Web Enablement (SWE) are described including sensor models, encodings, and web services. The role of semantics and ontologies in the Semantic Sensor Web is explained to provide contextual meaning to sensor observations. Rules can be used to derive additional knowledge from semantically annotated sensor data.
The document introduces the principles of Linked Data, which aims to share data rather than documents on the web. It describes the four rules of Linked Data and provides examples of existing Linked Data datasets as well as tools for publishing and using Linked Data. The document also discusses extending Linked Data to include geospatial and sensor data by linking web resources, structured geospatial databases, and unstructured geographic information.
Combining Process and Sensor Ontologies to Support Geo-Sensor Data RetrievalAnusuriya Devaraju
This document discusses combining a Sensor Network Ontology (SNO) with a Process-centric Hydrology Domain Ontology (HDO) to provide an integrated view of the Semantic Sensor Web. SNO describes sensors and observations at different levels of abstraction. HDO specifies relations between geo-processes, participants, and properties and handles naming issues in the hydrology domain. Together they allow complex observation requests involving sensors, features, and properties. The ontologies are being improved ongoing, with SNO aligned with W3C standards and HDO refining descriptions.
This document proposes a process-centric ontological approach to integrate geo-sensor data by relating observed properties to underlying geo-processes. It aligns the DOLCE foundational ontology with concepts from surface hydrology to develop an ontology of hydrological processes and their participants. This allows semantic integration of sensor data by resolving naming ambiguities and enabling process-based retrieval of observations through participation and property relations. Further work is needed to clarify the bearers of qualities and specify participant roles.
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Towards A Web-Enabled Geo-Sample Web: An Open Source Resource Registration and Management System for Connecting Geo-Samples to the Web
1. 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.
2. Presentation Outline
• Challenges in sample identification and discovery
• International Geo Sample Number (IGSN)
• IGSN Implementation in CSIRO
• Applications
• Lessons Learned and Conclusions
3. 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.
4. 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.
5. Presentation Outline
• Challenges in sample identification and discovery
• International Geo Sample Number (IGSN)
• IGSN Implementation in CSIRO
• Applications
• Lessons Learned and Conclusions
6. 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
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.
7. 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
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.
8. Metadata Schemas
8 |
IGSN-CSIRO
Description
Schema
IGSN Registration Schema
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.
9. Presentation Outline
• Challenges in sample identification and discovery
• International Geo Sample Number (IGSN)
• IGSN Implementation in CSIRO
• Applications
• Lessons Learned and Conclusions
10. 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.
10 | 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.
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
11. 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
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.
12. System Implementation
12 | 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.
13. A Web Front-End for Sample Registrations
13 |
Prefix and user
registration can be
performed via the
user interface from
the Registrant menu
option.
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.
Individual users
may register
their samples
through the
GUI.
14. 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.
14 | 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.
15. SKOS-based Controlled Vocabularies
15 | 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.
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*.
16. 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.
16 | 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.
17. Presentation Outline
• Challenges in sample identification and discovery
• International Geo Sample Number (IGSN)
• IGSN Implementation in CSIRO
• Applications
• Lessons Learned and Conclusions
18. Applications
Tracking samples from the field to the sample repository.
18 | 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.
IGSN pre-allocation in mobile field data acquisition systems.
Images courtesy of Reid, N. (2015), Golodoniuc, P. (2017)
19. IGSN Applications
19 |
Smart labels for sample inventory
management.
Discover samples and collections from
other repositories through a common
Australia Geo Sample Portal.
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.
20. 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
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.
21. 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
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.
22. Presentation Outline
• Challenges in sample identification and discovery
• International Geo Sample Number (IGSN)
• IGSN Implementation in CSIRO
• Applications
• Lessons Learned and Conclusions
23. 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).
23 | 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.
24. 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.
24 | 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.
25. Related Links
25 | 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.
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.
26. 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