Report on FAIR Signposting and its Uptake by the Community

Cite as

Mark D Wilkinson, Susanna-Assunta Sansone, Marjan Grootveld, Richard Dennis, David Hecker, Robert Huber, Stian Soiland-Reyes, Herbert Van de Sompel, Andreas Czerniak, Milo Thurston, Allyson L. Lister, Alban Gaignard (2024):
Report on FAIR Signposting and its Uptake by the Community.
EOSC FAIR Metrics and Data Quality Task Force
https://doi.org/10.5281/zenodo.10490289

Report on “FAIR Signposting” and its uptake by the community

Mark D Wilkinson1,3, Susanna-Assunta Sansone2,4, Marjan Grootveld2,5, Richard Dennis2,6, David Hecker2,7, Robert Huber8, Stian Soiland-Reyes9, Herbert Van de Sompel5, Andreas Czerniak10, Milo Thurston4, Allyson L. Lister4, Alban Gaignard11

1 Co-Chair, EOSC Task Force on FAIR Metrics and Data Quality
2 Member, EOSC Task Force on FAIR Metrics and Data Quality
3 Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)
Consejo Superior de Investigaciones Científicas (CSIC), Madrid, ES, Spain
4 Oxford e-Research Centre, Department of Engineering Science, University of Oxford, UK
5 Data Archiving and Networked Services (KNAW-DANS), The Netherlands
6 Novo Nordisk Foundation Center for Stem Cell Medicine - reNEW, the University of Copenhagen, Copenhagen, Denmark
7German Aerospace Centre, Research Data Management, Germany
8 MARUM - Cen­ter for Ma­ri­ne En­vi­ron­men­tal Sci­en­ces, Uni­ver­si­ty of Bre­men, Germany
9Department of Computer Science, The University of Manchester, UK
Informatics Institute, University of Amsterdam, NL
10 Bielefeld University Library, Germany
11Nantes Université, CNRS, INSERM, L’Institut du Thorax, Nantes, France

All TF members have had the opportunity to review and edit this document, invitations to be on the authorship list were open to all hackathon participants

Executive Summary

The FAIR Metrics subgroup of the EOSC Task Force on FAIR Metrics and Data Quality is dedicated to scrutinizing the adoption and impact of FAIRness metrics and the practicality of FAIRness evaluations. Previous reports have highlighted the inconsistency in results when the same digital object is evaluated by different tools, attributing these disparities to varied interpretations of the Metrics, metadata publishing practices, and the fundamental objectives of FAIR principles. The authors of this report, representing the FAIR Metrics subgroup, have facilitated six workshops and hackathon-style gatherings, convening diverse FAIR assessment stakeholders—including tool developers, standards and repository experts, and interoperability specialists.

The initial workshops, as outlined in an earlier report endorsed by EOSC, pinpointed a metadata publishing design pattern known as “FAIR Signposting.” This approach offers a transparent, compliant, and straightforward mechanism for guiding automated agents through metadata spaces to locate three essential FAIR elements: the globally unique identifier (GUID), the data records, and the corresponding metadata records. Furthermore, these sessions led to the development of a paradigm for creating reference environments. These environments serve as benchmarks for evaluating the compliance of metadata harvesters with FAIR Signposting criteria and for standardizing the metadata harvesting process of FAIR assessment tools.

This report provides an updated overview of the recent progress achieved by the FAIR Metrics subgroup, encapsulating the advances from the latest two hackathon events. We outline the progress towards developing an integrated suite of FAIR assessment tests, which are now becoming standardized across various FAIR assessment instruments. Additionally, we present preliminary insights into the community’s adoption of these practices and report on the ongoing effort to establish a FAIR testing governance body, along with strategies to ensure its enduring viability.

We, the authors, advocate for the EOSC Association and the EOSC Task Force on Long-term Data Preservation to endorse FAIR Signposting, along with the outcomes of our endeavours, as formal recommendations for EOSC-linked resources and EOSC-funded initiatives. We aim to promote an EOSC infrastructure where FAIR-enabling services can be assessed with clarity and uniformity. This will also ensure that tools designed for the EOSC will function with a standardized set of expectations applicable to all stakeholders - providers and users.

Background

In our earlier reports [Wilkinson 2022a, Wilkinson 2022b], we made several observations about the landscape of FAIR assessment, including that:

The problem of inconsistency between FAIR assessment tools is a wicked problem, as it requires that they behave identically when faced with an unpredictable world of conflicting and often improperly implemented attempts to “be FAIR.” For this reason, the FAIR Metrics subgroup of the EOSC Task Force (TF) concluded that it would be better for EOSC and of benefit to the broader community if there were a recommended approach to provisioning FAIR (meta)data for resources that wish to be recognized as participating in the Open Science Cloud. While the FAIR Principles neither suggest nor recommend any technology or paradigm, this does not prevent individual communities from establishing recommendations, expectations, norms, or even policies that harmonise their participants and improve interoperability between them, in fact, this is recognized as an expectation in FAIR Principle R1.3, where FAIR publishers are encouraged to follow community standards.

With this in mind, the final two hackathon events focused on exclusively utilizing the FAIR Signposting metadata publication design patterns for their metadata harvesting, using this metadata as the substrate upon which the participants jointly designed a set of generic FAIR tests. This included clearly defined expectations for what a data publisher should consider a success versus a failure. These expectations were then codified into a new set of benchmark Web pages, such reference environments can circumscribe and validate the behaviour of FAIR assessment tools authored by any stakeholder, both contemporary and future.

Hackathons 3 and 4

The final two hackathon events were held virtually, on Sept 27 and 29, 2023, using the virtual conferencing software “Remo”. Participants were invited using the mailing list from the prior events, with an invitation to all recipients to forward the invitation to any other potentially interested parties. As expected, given that it was a more technically focused meeting, the overall attendance was lower than at previous events, where more open discussions were the focus. In attendance were:

Name Affiliations FAIR assessment project or tool
Mark Wilkinson EOSC TF Co-chair, Universidad Politécnica de Madrid FAIR Evaluator & FAIR Champion
Susanna-Assunta Sansone EOSC TF Member, University of Oxford, ELIXIR Interoperability Platform FAIRsharing
Stian Soiland-Reyes The University of Manchester, University of Amsterdam, RO-Crate chair, ELIXIR Signposting Reference Environment Signposting Python library
Milo Thurston University of Oxford FAIRsharing
Herbert Van de Sompel DANS FAIR Signposting
Andreas Czerniak Bielefeld University Library, Germany OpenAIRE FAIR validator
Wilko Steinhoff DANS EOSC SYNERGY & FAIRCORE4EOSC
Robert Huber EOSC TF Member, Universität Bremen F-UJI, FAIR-IMPACT
Allyson Lister University of Oxford FAIRsharing
Alban Gaignard CNRS, Nantes University, ELIXIR-FR FAIR Checker
Richard Dennis EOSC TF Member Observer

Each event lasted from 9 AM to 5 PM, with an opening discussion to set the tasks for the day and a final hour of updates and conversation. Participants would occasionally return to the virtual meeting space to discuss issues that required coordination. The remaining time the participants spent coding and running tests or reference environments. At this event, we focused on the “Findability” tests. We began exploring tests for “Reusability.”

In each case, we examined the corresponding Maturity Indicators from the Research Data Alliance (RDA) FAIR Maturity Model[^5], as well as the implementations of the automated assessment platform authors. This included selecting standards for what should be considered a “pass” versus a “fail” for a given test. It also became clear that it was necessary to have a category of test result that was “undetermined” - this would be applicable in cases where, for example, a community claimed the existence of a community standard that they were following, but that standard could not be found in a standards registry such as the RDA-endorsed FAIRsharing. An “undetermined” result would warn the community that they should register this standard but that this result does not imply failure.

The “F” Metrics

Considerable time was spent exploring the “Findability” Metrics. Issues included, for example, the selection of which GUID schema would be acceptable to the testing platform, agreement on the regular expression that would be used to match those schemas, discussion of the use of FAIRsharing as a way to validate such schema, to avoid hard-coding GUID schemas into the assessment tools, and discussion of whether there should be secondary confirmation that a GUID was valid (e.g., via lookup).

Perhaps the most critical conversation regarding the “F” metrics was related to the meaning of “Globally Unique Identifier” in the context of the Web in general and FAIR Signposting in particular. Specifically, the FAIR Principles call for a globally unique and (usually) resolvable identifier for all data and metadata elements.

In Signposting, identifiers resolve to pages containing typed links, pointing to metadata and data. The uniqueness of an identifier in the context of a Signposting-enabled network, therefore, is the combination of the identifier itself (generally the HTTP URI rendition of a PID) and the “path” that is followed by the agent to arrive at the metadata or data element it desires to resolve, the selection of the desired path is further refined by the “type” attribute and “profile” attribute that is included in the Signposting Link.

This is a somewhat distinct interpretation of the meaning of an “identifier”, however, these Signposting paths are globally unique, transparent, unambiguous, and resolvable, thus consistent with the F Principles. Further work is, however, needed to record HTTP-level provenance for a client following content negotiation using Signposting, although we note that RFC9264 Linksets are interpretable as JSON-LD.

Here, we will provide just one example conclusion from these discussions, others will be published in the working document, associated reference environments in the benchmarks, and as records of FAIR metrics standards in FAIRsharing.

Example: FAIR Signposting-based tests for FAIR Principle F1: (Meta) data are assigned globally unique and persistent identifiers

Hackathon participants decided that the four RDA MI Metrics for Principle F1 could be merged into a single assessment, this is a consequence of the Signposting path-based definition of a GUID (described earlier), thus providing the same GUID for both the metadata and the data. In addition, persistence required by F1 means that GUIDs also have to be PIDs to comply with the EOSC PID policy [EC 2020]. The details of this decision were:

The other F Principles and the R1 principle went through similar processes of detailed exploration, resulting in identical sets of decisions and the publication of associated benchmark environments (now totaling 75) to ensure convergence of FAIR assessment tools into the future.

As a next step for the TF participants, in collaboration with other stakeholders such as FAIR-IMPACT, we wish to generate a detailed list of ‘Signposting FAIR Metrics’ that we can recommend to the EOSC-A based on the findings described above and the benchmark tests published at GitHub.

Comparison of Signposting with the FDO Initiative

The EOSC Interoperability Framework [EC 2021] has promoted the FAIR Digital Object (FDO) concept as a set of principles and requirements [Anders 2023] to improve the machine-actionability of research outputs, with a strong focus on persistent identifiers and definitions. While the FDO concept can be realised in several ways [EC 2018], including a “classic” Digital Object approach entirely based on the Handle system, Signposting has been highlighted [van de Sompel 2022] as a lightweight Web-based approach [Soiland-Reyes 2022] to implement FDO [Bach 2023].

In this approach, the FDO’s “PID Record” is mainly a navigable data structure where the actual details of the digital object are described in separate metadata resources. It is, therefore, essential to not just have syntactic type information on the possible metadata (e.g., RDF in JSON-LD format) but also profiles of their use (e.g., RO-Crate or Bioschemas [Castro 2023]). Profiles can also be nested, for instance, the WorkflowHub registry has implemented [Soiland-Reyes 2023] FDO using Signposting and JSON-LD, where the metadata is typed not just an RO-Crate but conforming to a particular Workflow RO-Crate profile.

By the FDO principles, structural elements such as type definitions and profiles should be FDOs. This reflects on the FAIR principle I2 (meta)data use vocabularies that follow FAIR principles. Still, the FDO community also considers how the existing FAIR vocabularies and persistent identifiers can co-exist with more stringent FDO representations. FAIR Signposting (a subset of the links proposed in the full Signposting specification) is here seen as a non-intrusive overlay that can bridge the gap and make the otherwise informal FAIR conventions become explicit and give predictable machine actionability.

The persistent identifier (DO PID) redirects to a landing page, from which signposting represents a lightweight FDO Record adding type (PID in controlled vocabulary to classify the object), describes (metadata), item (downloads of the object), author (e.g. PIDs to ORCID) and cite-as back to the PID. Inverse links (e.g., describes, collection) allow the FDO to be identified also from these constituent resources, e.g., if discovered from a search engine. Adapted from [van de Sompel 2022].

Signposting is considered as a FAIR Digital Object implementation

The persistent identifier (DO PID) redirects to a landing page, from which signposting represents a lightweight FDO Record adding type (PID in controlled vocabulary to classify the object), describes (metadata), item (downloads of the object), author (e.g. PIDs to ORCID) and cite-as back to the PID.
Inverse links (e.g., describes, collection) allow the FDO to be identified also from these constituent resources, e.g., if discovered from a search engine.
Adapted from [van de Sompel 2022].

Community Uptake of FAIR Signposting

The overarching mission of the FAIR principles and the EOSC is to streamline the accessibility and reusability of the vast and varied data pool. Given this diversity, providing detailed metadata by data sources enables effective data discovery and comprehension. Unlike specialized repositories, which define their data purpose, semantics, and structure, generalist repositories use depositors to characterize their data, making source-provided metadata even more pivotal. Yet, the motivation to furnish such metadata is minimal, as its utility is often only realized after downloading the data.

The FAIR Signposting framework offers a solution, presenting generalist repositories with a transparent methodology to explicitly reference source-provided metadata for the first time. This allows computational agents to facilitate data discovery and reuse more effectively. The widespread adoption of FAIR Signposting would thus serve the broader community and the EOSC substantially—not only enhancing the homogeneity of FAIR assessments but also empowering the discovery and interpretation of metadata before the data download.

Shortly after the hackathon, TF members reached out to the US National Institute of Health (NIH) Generalist Repository Ecosystem Initiative (GREI), which represents the major global generalist repositories such as Dataverse, Zenodo, Figshare, OSF, Vivli, Mendeley Data, and Dryad. We requested an opportunity to present the FAIR Signposting ideas to them, to explain the benefits, and to explore the costs. Concerning the expenses, there seem to be two critical Signposting behaviours that will have different costs for implementation by the GREI community:

  1. Explicit references to the repository-provided metadata and the metadata provided by, e.g., DataCite, and detailed references to the records in the deposit. In these cases, the links are already known by the repository. They can easily be added to the existing landing pages (in some cases, they are already provided by the repository as links, but using links for this purpose could be more consistent). This will likely be a low cost for implementation.
  2. Explicit references to user-provided metadata. In most cases, the generalist repositories must provide a detailed mechanism for distinguishing metadata records from data records in the deposit. Thus, while Signposting would allow that metadata to be discovered and used, it would likely require a more significant re-design of the repository infrastructure. Therefore, enabling this behaviour will come at a higher cost.

Concerning (1) above, the TF learned that Dataverse and Zenodo had already started implementing FAIR Signposting at this level. In the case of Dataverse, the currently deployed public codebase includes it while it is on the deployment path for Zenodo. The other repositories indicated it was also on their implementation pathway. Given adequate time and resources, they expressed considerable interest and enthusiasm to do so, which will depend on the repository developers' prioritisation. Concerning (2), several GREI members indicated that support for user-provided metadata was on their development pathway and that a clear standard for referring to it (i.e., via Signposting) was helpful in these efforts.

Knowing that Dataverse had implemented Signposting before the start of the two hackathon events, TF participants used the FAIR Signposting benchmarks created at the earlier events to test their implementation. Several “bugs” were discovered and reported to the Dataverse developers, which were rapidly corrected. This provides anecdotal evidence that the hackathon events are producing assessment tooling that is effective and useful. With this in mind, we have offered to provide GREI participants full (early) access to these benchmark tests and instructions on conducting self-assessment to assist their adoption of the specification.

The FAIR-IMPACT project launched a support action for Enabling FAIR Signposting and RO-Crate for content/metadata discovery and consumption, where 15 funded organisations and individuals across Europe are participating, including adding Signposting to eurac’s Environmental Data Platform, University of Novi Sad’s CRIS UNS, InvenioRDM, DRI, FAIRPoints, FAIRDOM-SEEK, and CKAN. Several of these participants were Dataverse users and have now deployed and are testing the latest Signposting support, others were new to FAIR and are making their first structured metadata representations in RO-Crate while deploying Signposting.

Overall, the feedback shows that it is relatively easy to retrofit Signposting if the data provider already has the other ingredients (e.g., RDF metadata or DOIs). However, for newcomers, the learning curve of such elements of the FAIR stack can still be daunting. It was tempting for them to add instead additional custom signposting (e.g., rel="https://schema.org/affiliation" from an author to an organisation), which we accept is valid but advise against.

Beyond the repository community, we also see the adoption of FAIR Signposting by tool-builders. For example, a Chrome extension has recently been published that will report when it discovers Signposting metadata in a Web page [Rogers 2023]. In addition, Signposting was a project theme at the BioHackathon Europe 2023 event [Soiland-Reyes 2024], where efforts were made to improve the tooling around Signposting and find convergence points between Signposting and the FAIR Digital Object specifications.

TF Outreach & Emergent Models for Governance

Shortly after the publication of our earlier report to EOSC on FAIR Assessment governance [Wilkinson 2022b], the FAIR-IMPACT project authored a response document [Verburg 2023], which was in part supportive but expressed some additional concerns and disagreements.

Given that the objective of the latest two hackathon events was to engender harmonization between the assessment tools, the participants also took time to “observe the process.”

In particular, the mechanisms for reaching agreement on the appropriate metrics, their associated testing code, quality assurance around these, and how this could be replicated in the future as more specialized (e.g., domain-specific) FAIR metrics are designed. The objective was to gather evidence for how FAIR assessment governance could be established and maintained. Of note, we observed that creating a benchmark environment was a critical aspect of designing and harmonizing test software, and we anticipate that this will become a primary activity of any governance process.

We have planned meetings around a joint TF/FAIR-IMPACT workshop where FAIR assessment governance will be discussed, and the various stakeholders will present their preferred models. The event is expected to take place in late November.

In addition, we will continue discussing the role of standards registries such as FAIRsharing, where claims of use of community metadata standards can be validated via API calls against the records describing these standards instead of being hard-coded into the FAIR assessment tools, for example, FAIRsharing already follows the advice of the EOSC TF on Persistent Identifiers and includes registrations of the properties and schema for these entities.

Conclusions & Recommendations

FAIR Signposting is a standards-compliant, straightforward, and unambiguous design pattern for (meta)data publication that fits well with existing Web publication behaviours and creates no new technology standard or infrastructure. Its predictability and consistency will dramatically improve the ability of agents to find and reuse data on the EOSC, providing much-needed harmonisation for EOSC tooling.

The TF has emphasized professionalism in creating this specification and its associated compliance tooling to engender confidence in both the users of assessment tools and those being assessed. Implementation of Signposting by repositories and other EOSC resources and its use by FAIR assessment tools will help solve the problem of inconsistent FAIR tests, moreover, the suite of benchmarks and a governance mechanism that similarly requires benchmarks for all future tests will help ensure new assessment tools do not recreate the current problem.

Finally, we can expect additional benefits as repositories increase their support for user-provided metadata - the critical, rich, domain-specific metadata largely invisible to data discovery agents. FAIR Signposting provides a way to immediately maximize the benefit of this evolution in scholarly publishing, giving additional incentive to hasten its implementation.

Our recommendations to the EOSC as a result of these series of workshops and hackathons are as follows:

  1. As a result of the professionalism of the documentation and the existence of an extensive reference environment for ensuring compliance with associated tools, the EOSC can be confident in their recommendation of Signposting as a FAIR-enabling design pattern for EOSC resources
  2. Signposting is not intended to exclude other metadata publishing options, for example, embedded Schema.org metadata is still encouraged to improve search engine discovery.
  3. While Signposting offers some freedom in, for example, the minting of novel link-relation types, the EOSC should discourage this since it interferes with the ability of agents to interpret the discovered metadata.
  4. EOSC should encourage the registration of community standards in standards registries, such as FAIRsharing, to both advertise the existence of (and commitment to) such a standard and as a mechanism for FAIR assessment tools to validate them.

Acknowledgments

Participants of the six meetings who are not members of the FAIR Metrics and Data Quality Task Force but without whom none of this would have been achieved: Herbert Van de Sompel, Philippe Rocca-Serra, Avi Ma’ayan, Carole Goble, Ceilyn Boyd, Kristian Garza, Peter Doorn, Alban Gaignard, Thomas Rosnet, Stian Soiland-Reyes, Antonis Lempesis, Andreas Czerniak, Luiz Bonino, Michel Dumontier, Vincent Emonet, Barbara Magagna, Marie-Dominique Devignes, Wilko Steinhoff.

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