Towards Globally Unique Identification of Physical Samples: Governance and Technical Implementation of the IGSN Global Sample Number

Klump, Jens; Lehnert, Kerstin; Ulbricht, Damian; Devaraju, Anusuriya; Elger, Kirsten; Fleischer, Dirk; Ramdeen, Sarah; Wyborn, Lesley

doi:10.5334/dsj-2021-033

Cited by 13 publications

(15 citation statements)

References 30 publications

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“… 2017 , DOI Foundation 2019 , Klump et al. 2021 ). This has had the effect of making large volumes of biodiversity and geosciences specimen data openly accessible and available on the Internet but these have largely remained disconnected from other data, including that derived from the same specimens.…”

Section: Digitizing and Mobilizing Collections Datamentioning

confidence: 99%

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

et al. 2022

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The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.

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Section: Digitizing and Mobilizing Collections Datamentioning

confidence: 99%

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

et al. 2022

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“…For its lithology and mineral lists, the platform utilises the comprehensive Mindat.org database (Mindat 2021) and associated hierarchical data structures, enabling more efficient and intelligent querying of the AusGeochem database. In addition to the five required sample metadata, users should also upload the IGSN (International Geo Sample Number, Lehnert et al 2011, Klump et al 2021) of a sample, if previously minted. The use of globally unique and persistent IGSN identifiers for physical samples prevents unintentional sample ID duplication and enables samples to be discoverable on the internet (Klump et al 2021).…”

Section: Geosample Registrymentioning

confidence: 99%

“…In addition to the five required sample metadata, users should also upload the IGSN (International Geo Sample Number, Lehnert et al 2011, Klump et al 2021) of a sample, if previously minted. The use of globally unique and persistent IGSN identifiers for physical samples prevents unintentional sample ID duplication and enables samples to be discoverable on the internet (Klump et al 2021).…”

Section: Geosample Registrymentioning

confidence: 99%

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AusGeochem: An Open Platform for Geochemical Data Preservation, Dissemination and Synthesis

Boone

Dalton

Prent

et al. 2022

Geostandard Geoanalytic Res

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To promote a more efficient and transparent geochemistry data ecosystem, a consortium of Australian university research laboratories called the AuScope Geochemistry Network assembled to build a collaborative platform for the express purpose of preserving, disseminating and collating geochronology and isotopic data. In partnership with geoscience‐data‐solutions company Lithodat Pty Ltd, the open, cloud‐based AusGeochem platform (https://ausgeochem.auscope.org.au) was developed to simultaneously serve as a geosample registry, a geochemical data repository and a data analysis tool. Informed by method‐specific groups of geochemistry experts and established international data reporting practices, community‐agreed database schemas were developed for rock and mineral geosample metadata and secondary ion mass spectrometry U‐Pb analysis, with additional models for laser ablation‐inductively coupled‐mass spectrometry U‐Pb and Lu‐Hf, Ar‐Ar, fission‐track and (U‐Th‐Sm)/He under development. Collectively, the AusGeochem platform provides the geochemistry community with a new, dynamic resource to help facilitate FAIR (Findable, Accessible, Interoperable, Reusable) data management, streamline data dissemination and advanced quantitative investigations of Earth system processes. By systematically archiving detailed geochemical (meta‐)data in structured schemas, intractably large datasets comprising thousands of analyses produced by numerous laboratories can be readily interrogated in novel and powerful ways. These include rapid derivation of inter‐data relationships, facilitating on‐the‐fly data compilation, analysis and visualisation.

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“…We propose to explore the practical implementation of FAIR Digital Objects (FDO) for biological life science physical samples and practically how to create an FDO framework centralized around biospecimen samples, linked datasets, sample information and PIDs (Persistent Identifiers) Klump et al 2021. This effort is highly relevant to enhancing the portability of sample information between multiple repositories and other kinds of resources (e.g.…”

mentioning

confidence: 99%

Biospecimens in FDO world

El-Gebali¹,

Macneil²,

Edmunds³

et al. 2022

RIO

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With the advent of technological advances in research settings, scientific collections including sample material became on par with big data. Consequently there is a widespread need to highlight and recognise the inherent value of samples coupled with efforts in unlocking sample potential as resources for new scientific discovery. Samples with informative metadata can be more easily discoverable, more readily shared and reused, allowing reanalysis of associated datasets, avoiding duplicate efforts, and providing metaanalysis yielding considerably enhanced insight. Metadata provides the framework for a consistent, systematic and standardized collection of sample information, enabling users to identify the availability of research output from the samples, relevancy to their intended use, and a way to conveniently identify sample material as well as access provenance information related to the physical samples. Researchers need this essential information aiding their decision making process on the quality, usability and accessibility of the samples and associated datasets. We propose to explore the practical implementation of FAIR Digital Objects (FDO) for biological life science physical samples and practically how to create an FDO framework centralized around biospecimen samples, linked datasets, sample information and PIDs (Persistent Identifiers)Klump et al. 2021. This effort is highly relevant to enhancing the portability of sample information between multiple repositories and other kinds of resources (e.g. e-infrastructures). In this session we would like to present our current work in order to mobilize the community to define the FAIR Digital Object Architecture for biospecimen in life science including all infrastructure components e.g. metadata, PIDs and their integration with technical solutions. To that end, in our community of practice we aim to: What: Identify the minimum set of attributes required for describing biospecimen in biological life science (Minimal Information About a Biological Sample, MIABS) with ontological mapping for semantic unambiguity and machine actionability.Identify the required attributes for registering PIDs for biospecimens and how that will operate in an FDO ecosystem. This will pave the way for a framework of coupling the descriptive metadata to the digital object in a FAIR and comprehensive manner. How:Define a semantic FDO model for biospecimens.Define the role of biospecimen PIDs registration information and kernel attributes and how that translates to machine actionability and programmatic decisions.Define the implementation specifics for integration of biospecimen FDOs with operational infrastructure e.g. e-infrastructures, repositories and machines. What: Identify the minimum set of attributes required for describing biospecimen in biological life science (Minimal Information About a Biological Sample, MIABS) with ontological mapping for semantic unambiguity and machine actionability.Identify the required attributes for registering PIDs for biospecimens and how that will operate in an FDO ecosystem. This will pave the way for a framework of coupling the descriptive metadata to the digital object in a FAIR and comprehensive manner. Identify the minimum set of attributes required for describing biospecimen in biological life science (Minimal Information About a Biological Sample, MIABS) with ontological mapping for semantic unambiguity and machine actionability. Identify the required attributes for registering PIDs for biospecimens and how that will operate in an FDO ecosystem. This will pave the way for a framework of coupling the descriptive metadata to the digital object in a FAIR and comprehensive manner. How:Define a semantic FDO model for biospecimens.Define the role of biospecimen PIDs registration information and kernel attributes and how that translates to machine actionability and programmatic decisions.Define the implementation specifics for integration of biospecimen FDOs with operational infrastructure e.g. e-infrastructures, repositories and machines. Define a semantic FDO model for biospecimens. Define the role of biospecimen PIDs registration information and kernel attributes and how that translates to machine actionability and programmatic decisions. Define the implementation specifics for integration of biospecimen FDOs with operational infrastructure e.g. e-infrastructures, repositories and machines. Relevant technologies include: RO-Crate, Persistent identifiers, and metadata schemas Relevant technologies include: RO-Crate, Persistent identifiers, and metadata schemas The recent partnership between IGSN and DataCite described below is a catalyst in this call of action to the FDO community to build a Community of Practice (CoP) specifically focused on biospecimen samples. Community of practice: IGSN e.V. announced a partnership with DataCite, in which DataCite’s registration services and supporting technology for Digital Object Identifiers (another type of PID) are now being leveraged to register IGSN IDs, and thus ensure the ongoing sustainability of the IGSN ID infrastructure. Importantly, the two organizations are also focusing the community’s efforts on advocacy of PIDs for physical samples and expanding the global sample ecosystem. Assisted by the DataCite Samples Community Manager, the IGSN e.V. is establishing working groups (Communities of Practice) within different research domains to support development and promotion of standardized methods for identifying, citing, and locating physical samples. In particular, the partnership wishes to work with the Biosamples community to elaborate the necessary information (metadata) such that those within the community have a full understanding of a physical sample when its descriptive webpage is accessed via its PID, see this example.

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Towards Globally Unique Identification of Physical Samples: Governance and Technical Implementation of the IGSN Global Sample Number

Cited by 13 publications

References 30 publications

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

AusGeochem: An Open Platform for Geochemical Data Preservation, Dissemination and Synthesis

Biospecimens in FDO world

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