Mark D. WilkinsonpersName, Michel DumontierpersName, IJsbrand Jan AalbersbergpersName, Gabrielle AppletonpersName, Myles AxtonpersName, Arie BaakpersName, Niklas BlombergpersName, Jan-Willem BoitenpersName, Luiz Bonino da Silva SantospersName, Philip E. BournepersName, Jildau BouwmanpersName, Anthony J. BrookespersName, Tim ClarkpersName, Mercè CrosaspersName, Ingrid DillopersName, Olivier DumonpersName, Scott EdmundspersName, Chris T. EvelopersName, Richard FinkerspersName, Alejandra Gonzalez-BeltranpersName, Alasdair J.G. GraypersName, Paul GrothpersName, Carole GoblepersName, Jeffrey S. GrethepersName, Jaap HeringapersName, Peter A.C ’t HoenpersName, Rob HooftpersName, Tobias KuhnpersName, Ruben KokpersName, Joost KokpersName, Scott J. LusherpersName, Maryann E. MartonepersName, Albert MonspersName, Abel L. PackerpersName, Bengt PerssonpersName, Philippe Rocca-SerrapersName, Marco RoospersName, Rene van SchaikpersName, Susanna-Assunta SansonepersName, Erik SchultespersName, Thierry SengstagpersName, Ted SlaterpersName, George StrawnpersName, Morris A. SwertzpersName, Mark ThompsonpersName, Johan van der LeipersName, Erik van MulligenpersName, Jan VelteroppersName, Andra WaagmeesterpersName, Peter WittenburgpersName, Katherine WolstencroftpersName, Jun ZhaopersName, Barend MonspersName (2016date). “The FAIR Guiding Principles for scientific data management and stewardship.” Scientific Datatitle·j.
Object of study — the FAIR Guiding Principlesterm and machine-actionable stewardship of scholarly digital research objectsterm
Research question — which minimal, domain-independent principles let people and machines find, access, integrate, and reuse scholarly digital objectsterm
Contribution — the first formal publication of the FAIR Principlesterm, their rationale, implementation boundaries, and exemplar community implementations
phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | data discovery, integration, reuse, and machine actionability in a diverse scholarly data ecosystem — “Questions such as these highlight some of the barriers to data discovery and reuse, not only for humans, but even more so for machines; yet it is precisely these kinds of deeply and broadly integrative analyses that constitute the bulk of contemporary e-Science. The reason that we often need several weeks (or months) of specialist technical effort to gather the data necessary to answer such research questions is not the lack of appropriate technology; the reason is, that we do not pay our valuable digital objects the careful attention they deserve when we create and preserve them. Overcoming these barriers, therefore, necessitates that all stakeholders—including researchers, special-purpose, and general-purpose repositories—evolve to meet the emergent challenges described above. The goal is for scholarly digital objects of all kinds to become ‘first class citizens’ in the scientific publication ecosystem, where the quality of the publication—and more importantly, the impact of the publication—is a function of its ability to be accurately and appropriately found, re-used, and cited over time, by all stakeholders, both human and mechanical.” | |
| claim-type | existence — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | |
| method — evidence | — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | |
| object of study — evidence | — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | |
| research question — evidence | — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | |
| contribution — evidence | — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | |
| mechanism | long-term care Collection, annotation, archival, and continuing care keep digital assets discoverable and reusable for downstream work. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | mechanisms[0] |
| mechanism | computational agents Autonomous agents compensate for human limits of scale and speed in data discovery and integration. — “The emphasis placed on FAIRness being applied to both human-driven and machine-driven activities, is a specific focus of the FAIR Guiding Principles that distinguishes them from many peer initiatives (discussed in the subsequent section). Humans and machines often face distinct barriers when attempting to find and process data on the Web. Humans have an intuitive sense of ‘semantics’ (the meaning or intent of a digital object) because we are capable of identifying and interpreting a wide variety of contextual cues, whether those take the form of structural/visual/iconic cues in the layout of a Web page, or the content of narrative notes. As such, we are less likely to make errors in the selection of appropriate data or other digital objects, although humans will face similar difficulties if sufficient contextual metadata is lacking. The primary limitation of humans, however, is that we are unable to operate at the scope, scale, and speed necessitated by the scale of contemporary scientific data and complexity of e-Science. It is for this reason that humans increasingly rely on computational agents to undertake discovery and integration tasks on their behalf. This necessitates machines to be capable of autonomously and appropriately acting when faced with the wide range of types, formats, and access-mechanisms/protocols that will be encountered during their self-guided exploration of the global data ecosystem. It also necessitates that the machines keep an exquisite record of provenance such that the data they are collecting can be accurately and adequately cited. Assisting these agents, therefore, is a critical consideration for all participants in the data management and stewardship process—from researchers and data producers to data repository hosts.” | mechanisms[1] |
| mechanism | contextual metadata Metadata lets an agent identify an unfamiliar object's type, purpose, utility, and use constraints. — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | mechanisms[2] |
| mechanism | general-purpose, open technologies Generalized standards make previously unseen data types more actionable without bespoke parsers. — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | mechanisms[3] |
| mechanism | incremental adherence Independent principles can be adopted in any combination as publishing environments evolve. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | mechanisms[4] |
| mechanism | rich metadata Public descriptions and explicit access rules preserve discovery for sensitive data even when content stays restricted. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | mechanisms[5] |
| mechanism | persistent identifiers A DOI or Handle resolves users and machines to searchable metadata, files, terms, licenses, and versions. — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | mechanisms[6] |
| mechanism | access token A token grants controlled access to restricted Dataverse files while metadata remains public. — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | mechanisms[7] |
| mechanism | RDF RDF representations and shared vocabularies provide machine-readable semantics and interoperability. — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | mechanisms[8] |
| mechanism | mappings service Multiple entity URLs are mapped to a canonical URL so information can be integrated across sources. — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | mechanisms[9] |
| mechanism | cross-references Database links and explicit ontology types enable automated retrieval and citation across UniProt resources. — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | mechanisms[10] |
| mechanism | shared, common goals Coordinated implementation by producers and publishers gradually makes community data FAIR. — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | mechanisms[11] |
| builds-on | Concept Web Alliance — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[0] |
| builds-on | Joint Declaration of Data Citation Principles — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[1] |
| complements | Data Seal of Approval — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[2] |
| complements | Data Citation Implementation Group — “In addition to, and in support of, communities and resources that are already pursuing FAIR objectives, the Data Citation Implementation Group of Force11 has published specific technical recommendations for how to implement many of the principles 27 , with a particular focus on identifiers and their resolution, persistence, and metadata accessibility especially related to citation. In addition, the ‘Skunkworks’ group that emerged from the Lorentz Workshop has been creating software supporting infrastructures 28 that are, end-to-end, compatible with FAIR principles, and can be implemented over existing repositories. These code modules have a particular focus on metadata publication and searchability, compatibility in cases of strict privacy considerations, and the extremely difficult problem of data and metadata interoperability (manuscript in preparation). Finally, there are several emergent projects, some listed in Box 3 , for which FAIR is a key objective. These projects may provide valuable advice and guidance for those wishing to become more FAIR.” | claim_relations[3] |
| sense | FAIR as four high-level, separable desiderata rather than a technical standard — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | senses[0] |
| sense | FAIRness as an incremental degree attainable in combinations — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | senses[1] |
| sense | machine actionability as a continuum for unfamiliar digital objects — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | senses[2] |
| sense | data stewardship as long-term care beyond collection and archival — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | senses[3] |
| sense | metadata-level FAIRness for restricted or personally identifiable data — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | senses[4] |
| sense | FAIR scope as data plus algorithms, tools, workflows, and other research objects — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | senses[5] |
| sense | findability as persistent identification and searchable metadata — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | senses[6] |
| sense | accessibility as resolvable interfaces with explicit authorization — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | senses[7] |
| sense | interoperability as shared machine-readable formats, vocabularies, and mappings — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | senses[8] |
| sense | reusability as licensed, cited, provenance-rich downstream use — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | senses[9] |
| sense | general-purpose repositories as broad in format but weakly harmonized — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | senses[10] |
| sense | FAIR implementation as technology-neutral evaluation of local choices — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | senses[11] |
| note | Concept Web Alliance — The paper says FAIR reflects, combines, builds upon, and extends this work. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[0] |
| weight | Concept Web Alliance — 0.95 — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[0] |
| note | Joint Declaration of Data Citation Principles — The paper situates FAIR as extending earlier data-citation principles. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[1] |
| weight | Joint Declaration of Data Citation Principles — 0.95 — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[1] |
| note | Data Seal of Approval — The source explicitly calls FAIR complementary to the Data Seal of Approval. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[2] |
| weight | Data Seal of Approval — 0.95 — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | claim_relations[2] |
| note | Data Citation Implementation Group — Its technical recommendations implement many FAIR principles, especially identifiers and metadata access. — “In addition to, and in support of, communities and resources that are already pursuing FAIR objectives, the Data Citation Implementation Group of Force11 has published specific technical recommendations for how to implement many of the principles 27 , with a particular focus on identifiers and their resolution, persistence, and metadata accessibility especially related to citation. In addition, the ‘Skunkworks’ group that emerged from the Lorentz Workshop has been creating software supporting infrastructures 28 that are, end-to-end, compatible with FAIR principles, and can be implemented over existing repositories. These code modules have a particular focus on metadata publication and searchability, compatibility in cases of strict privacy considerations, and the extremely difficult problem of data and metadata interoperability (manuscript in preparation). Finally, there are several emergent projects, some listed in Box 3 , for which FAIR is a key objective. These projects may provide valuable advice and guidance for those wishing to become more FAIR.” | claim_relations[3] |
| weight | Data Citation Implementation Group — 0.9 — “In addition to, and in support of, communities and resources that are already pursuing FAIR objectives, the Data Citation Implementation Group of Force11 has published specific technical recommendations for how to implement many of the principles 27 , with a particular focus on identifiers and their resolution, persistence, and metadata accessibility especially related to citation. In addition, the ‘Skunkworks’ group that emerged from the Lorentz Workshop has been creating software supporting infrastructures 28 that are, end-to-end, compatible with FAIR principles, and can be implemented over existing repositories. These code modules have a particular focus on metadata publication and searchability, compatibility in cases of strict privacy considerations, and the extremely difficult problem of data and metadata interoperability (manuscript in preparation). Finally, there are several emergent projects, some listed in Box 3 , for which FAIR is a key objective. These projects may provide valuable advice and guidance for those wishing to become more FAIR.” | claim_relations[3] |
| note | FAIR Principles —distinct-from→ peer initiatives — Flat explicit distinction; gradable relation strength is below categorical 1.0. — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | concept_edges[0] |
| relation | FAIR Principles —distinct-from→ peer initiatives — The FAIR Principles are distinct from peer initiatives focused on the human scholar. — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | concept_edges[0] |
| weight | FAIR Principles —distinct-from→ peer initiatives — 0.95 — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | concept_edges[0] |
| effect direction | good data management —causes→ knowledge discovery and innovation — increases — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concept_edges[1] |
| note | good data management —causes→ knowledge discovery and innovation — Flat positive pathway claim. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concept_edges[1] |
| relation | good data management —causes→ knowledge discovery and innovation — Good data management is the key conduit leading to knowledge discovery and innovation. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concept_edges[1] |
| weight | good data management —causes→ knowledge discovery and innovation — 0.95 — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concept_edges[1] |
| note | long-term care —part-of→ data stewardship — Explicit containment statement. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concept_edges[2] |
| relation | long-term care —part-of→ data stewardship — Data stewardship includes the notion of long-term care of valuable digital assets. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concept_edges[2] |
| note | FAIR Guiding Principles —distinct-from→ standard — Flat explicit negative identity; distinct-from remains a gradable edge class. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concept_edges[3] |
| relation | FAIR Guiding Principles —distinct-from→ standard — The FAIR Guiding Principles are not themselves a standard. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concept_edges[3] |
| weight | FAIR Guiding Principles —distinct-from→ standard — 0.95 — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concept_edges[3] |
| note | FAIR Guiding Principles —distinct-from→ specification — Flat explicit negative identity; distinct-from remains a gradable edge class. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concept_edges[4] |
| relation | FAIR Guiding Principles —distinct-from→ specification — The FAIR Guiding Principles are not themselves a specification. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concept_edges[4] |
| weight | FAIR Guiding Principles —distinct-from→ specification — 0.95 — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concept_edges[4] |
| note | Dataverse —is-a→ open-source data repository software — Direct categorical definition. — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concept_edges[5] |
| relation | Dataverse —is-a→ open-source data repository software — Dataverse is an open-source data repository software. — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concept_edges[5] |
| note | metadata —part-of→ Deposits — Explicit container-first inclusion. — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concept_edges[6] |
| relation | metadata —part-of→ Deposits — Dataverse deposits include metadata. — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concept_edges[6] |
| note | ISA —is-a→ community-driven metadata tracking framework — Direct categorical definition. — “ISA 16 : is a community-driven metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of life science datasets. ISA provides progressively FAIR structured metadata to Nature Scientific Data’s Data Descriptor articles, and many GigaScience data papers, and underpins the EBI MetaboLights database among other data resources. At the heart is a general-purpose, extensible ISA model, originally only available as a tabular representation but subsequently enhanced as an RDF-based representation 17 , and JSON serializations to enable the ‘I’ and ‘R’, becoming ‘FAIR’ when published as linked data ( http://elixir-uk.org/node-events/201cisa-as-a-fair-research-object201d-hack-the-spec-event-1 ) and complementing other research objects 18 .” | concept_edges[7] |
| relation | ISA —is-a→ community-driven metadata tracking framework — ISA is a community-driven metadata tracking framework. — “ISA 16 : is a community-driven metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of life science datasets. ISA provides progressively FAIR structured metadata to Nature Scientific Data’s Data Descriptor articles, and many GigaScience data papers, and underpins the EBI MetaboLights database among other data resources. At the heart is a general-purpose, extensible ISA model, originally only available as a tabular representation but subsequently enhanced as an RDF-based representation 17 , and JSON serializations to enable the ‘I’ and ‘R’, becoming ‘FAIR’ when published as linked data ( http://elixir-uk.org/node-events/201cisa-as-a-fair-research-object201d-hack-the-spec-event-1 ) and complementing other research objects 18 .” | concept_edges[7] |
| note | Open PHACTS —is-a→ data integration platform — Direct categorical definition. — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | concept_edges[8] |
| relation | Open PHACTS —is-a→ data integration platform — Open PHACTS is a data integration platform. — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | concept_edges[8] |
| note | wwPDB —is-a→ special-purpose, intensively-curated data archive — Direct categorical definition. — “wwPDB 4 , 21 : wwPDB is a special-purpose, intensively-curated data archive that hosts information about experimentally-determined 3D structures of proteins and nucleic acids. All wwPDB entries are stably hosted on an FTP server (‘A’) and represented in machine-readable formats (text and XML); the latter are machine-actionable using the metadata provided by the wwPDB conforming to the Macromolecular Information Framework (mmCIF 22 ), a data standard of the International Union of Crystallography (IUCr) (‘F’,‘I’ for humans, ‘F’,‘I’ for IUCr-aware machines). The wwPDB metadata contains cross-references to common identifiers such as PubMed and NCBI Taxonomy, and their wwPDB metadata are described in data dictionaries and schema documents ( http://mmcif.wwpdb.org and http://pdbml.wwpdb.org ) which conform to the IUCr data standard for the chemical and structural biology domains (‘R’). A variety of software tools are available to interpret both wwPDB data and meta-data (‘I’,‘R’ for humans, ‘I’,‘R’ for machines with this software). Each entry is represented by a DOI (‘F’, ‘A’ for humans and machines). The DOI resolves to a zipped file which requires special software for further interrogation/interpretation. Other wwPDB access points 23–25 provide access to wwPDB records through URLs that are likely to be stable in the long-term (‘F’), and all data and metadata is searchable through one or more of the wwPDB-affiliated websites (‘F’)” | concept_edges[9] |
| relation | wwPDB —is-a→ special-purpose, intensively-curated data archive — wwPDB is a special-purpose, intensively-curated data archive. — “wwPDB 4 , 21 : wwPDB is a special-purpose, intensively-curated data archive that hosts information about experimentally-determined 3D structures of proteins and nucleic acids. All wwPDB entries are stably hosted on an FTP server (‘A’) and represented in machine-readable formats (text and XML); the latter are machine-actionable using the metadata provided by the wwPDB conforming to the Macromolecular Information Framework (mmCIF 22 ), a data standard of the International Union of Crystallography (IUCr) (‘F’,‘I’ for humans, ‘F’,‘I’ for IUCr-aware machines). The wwPDB metadata contains cross-references to common identifiers such as PubMed and NCBI Taxonomy, and their wwPDB metadata are described in data dictionaries and schema documents ( http://mmcif.wwpdb.org and http://pdbml.wwpdb.org ) which conform to the IUCr data standard for the chemical and structural biology domains (‘R’). A variety of software tools are available to interpret both wwPDB data and meta-data (‘I’,‘R’ for humans, ‘I’,‘R’ for machines with this software). Each entry is represented by a DOI (‘F’, ‘A’ for humans and machines). The DOI resolves to a zipped file which requires special software for further interrogation/interpretation. Other wwPDB access points 23–25 provide access to wwPDB records through URLs that are likely to be stable in the long-term (‘F’), and all data and metadata is searchable through one or more of the wwPDB-affiliated websites (‘F’)” | concept_edges[9] |
| note | UniProt —is-a→ comprehensive resource — Direct categorical definition. — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | concept_edges[10] |
| relation | UniProt —is-a→ comprehensive resource — UniProt is a comprehensive resource. — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | concept_edges[10] |
| audit | FAIR Guiding Principles —contrasted-with→ Data Seal of Approval — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but FAIR is COMPLEMENTARY to the Data Seal of Approval; contrasted-with overstates. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | concept_edges[11] |
| note | FAIR Guiding Principles —contrasted-with→ Data Seal of Approval — Explicit focus contrast alongside an explicit complementarity claim. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | concept_edges[11] |
| relation | FAIR Guiding Principles —contrasted-with→ Data Seal of Approval — The Data Seal of Approval focuses on producer and repository conduct, while FAIR focuses on the data itself. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | concept_edges[11] |
| weight | FAIR Guiding Principles —contrasted-with→ Data Seal of Approval — 0.95 — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | concept_edges[11] |
| relation | machine-actionability → digital object — Machine-actionability is a graded property of a digital object. — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | unhoused_relations[0] |
| relation | FAIR Guiding Principles → Findability — Findability is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[1] |
| relation | FAIR Guiding Principles → Accessibility — Accessibility is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[2] |
| relation | FAIR Guiding Principles → Interoperability — Interoperability is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[3] |
| relation | FAIR Guiding Principles → Reusability — Reusability is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[4] |
| relation | FAIR Guiding Principles → algorithms, tools, and workflows — The principles apply to algorithms, tools, and workflows as well as conventional data. — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | unhoused_relations[5] |
| relation | general-purpose data repositories → discovery and re-usability problem — The growth of broad but weakly harmonized repositories exacerbates the discovery and reuse problem. — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | unhoused_relations[6] |
| weight | general-purpose data repositories → discovery and re-usability problem — 0.95 — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | unhoused_relations[6] |
| relation | minimal set of community-agreed guiding principles and practices → FAIR Guiding Principles — Workshop deliberations produced and refined the FAIR Guiding Principles. — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | unhoused_relations[7] |
| weight | minimal set of community-agreed guiding principles and practices → FAIR Guiding Principles — 0.95 — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | unhoused_relations[7] |
| relation | machine actionable → machine-actionability — The phrase machine actionable denotes a continuum of machine-actionability. — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | unhoused_relations[8] |
| relation | contextual metadata → machine-actionability — Contextual metadata forms one independent context of machine-actionability. — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | unhoused_relations[9] |
| relation | content of the digital object → machine-actionability — Object content forms a second independent context of machine-actionability. — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | unhoused_relations[10] |
| relation | generalized interoperability technologies and standards → machine-actionability — Generalized repository-level technologies assist machines in discovering and exploring unfamiliar data. — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | unhoused_relations[11] |
| weight | generalized interoperability technologies and standards → machine-actionability — 0.95 — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | unhoused_relations[11] |
| relation | rich metadata → highly sensitive or personally-identifiable data — Rich public metadata can support high FAIRness while sensitive data remain unpublished. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | unhoused_relations[12] |
| weight | rich metadata → highly sensitive or personally-identifiable data — 0.95 — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | unhoused_relations[12] |
| relation | analytical workflows → good Data Management and Stewardship practice — Formal publication of analytical workflows is necessary for transparency and reproducibility. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | unhoused_relations[13] |
| relation | FAIR Guiding Principles → implementation choices — The principles guide evaluation of implementation choices without prescribing a technology. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | unhoused_relations[14] |
| relation | FAIRDOM → FAIR data and model management facility — FAIRDOM integrates SEEK and openBIS to produce a FAIR data and model management facility. — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | unhoused_relations[15] |
| weight | FAIRDOM → FAIR data and model management facility — 0.95 — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | unhoused_relations[15] |
| relation | Open PHACTS → data integration platform — Access to Open PHACTS is mediated through a machine-accessible interface. — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | unhoused_relations[16] |
| relation | FAIR Guiding Principles → Concept Web Alliance — FAIR reflects, combines, builds upon, and extends Concept Web Alliance work. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | unhoused_relations[17] |
| weight | FAIR Guiding Principles → Concept Web Alliance — 0.95 — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | unhoused_relations[17] |
| relation | good data management → knowledge discovery and innovation — Good data management is a pre-condition supporting knowledge discovery and innovation. — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | unhoused_relations[18] |
| relation | FAIR Guiding Principles → good Data Management and Stewardship practice — The FAIR Principles provide mileposts guiding basic data-management and stewardship practice. — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | unhoused_relations[19] |
| weight | FAIR Guiding Principles → good Data Management and Stewardship practice — 0.95 — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | unhoused_relations[19] |
| no type for this | machine-actionability → digital object — Machine-actionability is a graded property of a digital object. — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | unhoused_relations[0] |
| no type for this | FAIR Guiding Principles → Findability — Findability is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[1] |
| no type for this | FAIR Guiding Principles → Accessibility — Accessibility is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[2] |
| no type for this | FAIR Guiding Principles → Interoperability — Interoperability is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[3] |
| no type for this | FAIR Guiding Principles → Reusability — Reusability is one of the four FAIR desiderata. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | unhoused_relations[4] |
| no type for this | FAIR Guiding Principles → algorithms, tools, and workflows — The principles apply to algorithms, tools, and workflows as well as conventional data. — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | unhoused_relations[5] |
| no type for this | general-purpose data repositories → discovery and re-usability problem — The growth of broad but weakly harmonized repositories exacerbates the discovery and reuse problem. — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | unhoused_relations[6] |
| no type for this | minimal set of community-agreed guiding principles and practices → FAIR Guiding Principles — Workshop deliberations produced and refined the FAIR Guiding Principles. — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | unhoused_relations[7] |
| no type for this | machine actionable → machine-actionability — The phrase machine actionable denotes a continuum of machine-actionability. — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | unhoused_relations[8] |
| no type for this | contextual metadata → machine-actionability — Contextual metadata forms one independent context of machine-actionability. — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | unhoused_relations[9] |
| no type for this | content of the digital object → machine-actionability — Object content forms a second independent context of machine-actionability. — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | unhoused_relations[10] |
| no type for this | generalized interoperability technologies and standards → machine-actionability — Generalized repository-level technologies assist machines in discovering and exploring unfamiliar data. — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | unhoused_relations[11] |
| no type for this | rich metadata → highly sensitive or personally-identifiable data — Rich public metadata can support high FAIRness while sensitive data remain unpublished. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | unhoused_relations[12] |
| no type for this | analytical workflows → good Data Management and Stewardship practice — Formal publication of analytical workflows is necessary for transparency and reproducibility. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | unhoused_relations[13] |
| no type for this | FAIR Guiding Principles → implementation choices — The principles guide evaluation of implementation choices without prescribing a technology. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | unhoused_relations[14] |
| no type for this | FAIRDOM → FAIR data and model management facility — FAIRDOM integrates SEEK and openBIS to produce a FAIR data and model management facility. — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | unhoused_relations[15] |
| no type for this | Open PHACTS → data integration platform — Access to Open PHACTS is mediated through a machine-accessible interface. — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | unhoused_relations[16] |
| no type for this | FAIR Guiding Principles → Concept Web Alliance — FAIR reflects, combines, builds upon, and extends Concept Web Alliance work. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | unhoused_relations[17] |
| no type for this | good data management → knowledge discovery and innovation — Good data management is a pre-condition supporting knowledge discovery and innovation. — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | unhoused_relations[18] |
| no type for this | FAIR Guiding Principles → good Data Management and Stewardship practice — The FAIR Principles provide mileposts guiding basic data-management and stewardship practice. — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | unhoused_relations[19] |
| limitation | The existing digital ecosystem prevents extraction of maximum value from scholarly-data investments. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | limitations[0] |
| limitation | Good data management is largely undefined and left to data or repository owners. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | limitations[1] |
| limitation | Many important low-throughput datasets do not fit special-purpose repository data models. — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | limitations[2] |
| limitation | General-purpose repositories often do not integrate or harmonize deposits and impose few descriptor requirements. — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | limitations[3] |
| limitation | Poorly prepared digital objects can require weeks or months of specialist effort for integrative analyses. — “Questions such as these highlight some of the barriers to data discovery and reuse, not only for humans, but even more so for machines; yet it is precisely these kinds of deeply and broadly integrative analyses that constitute the bulk of contemporary e-Science. The reason that we often need several weeks (or months) of specialist technical effort to gather the data necessary to answer such research questions is not the lack of appropriate technology; the reason is, that we do not pay our valuable digital objects the careful attention they deserve when we create and preserve them. Overcoming these barriers, therefore, necessitates that all stakeholders—including researchers, special-purpose, and general-purpose repositories—evolve to meet the emergent challenges described above. The goal is for scholarly digital objects of all kinds to become ‘first class citizens’ in the scientific publication ecosystem, where the quality of the publication—and more importantly, the impact of the publication—is a function of its ability to be accurately and appropriately found, re-used, and cited over time, by all stakeholders, both human and mechanical.” | limitations[4] |
| limitation | People cannot operate at the scope, scale, and speed required by contemporary scientific data. — “The emphasis placed on FAIRness being applied to both human-driven and machine-driven activities, is a specific focus of the FAIR Guiding Principles that distinguishes them from many peer initiatives (discussed in the subsequent section). Humans and machines often face distinct barriers when attempting to find and process data on the Web. Humans have an intuitive sense of ‘semantics’ (the meaning or intent of a digital object) because we are capable of identifying and interpreting a wide variety of contextual cues, whether those take the form of structural/visual/iconic cues in the layout of a Web page, or the content of narrative notes. As such, we are less likely to make errors in the selection of appropriate data or other digital objects, although humans will face similar difficulties if sufficient contextual metadata is lacking. The primary limitation of humans, however, is that we are unable to operate at the scope, scale, and speed necessitated by the scale of contemporary scientific data and complexity of e-Science. It is for this reason that humans increasingly rely on computational agents to undertake discovery and integration tasks on their behalf. This necessitates machines to be capable of autonomously and appropriately acting when faced with the wide range of types, formats, and access-mechanisms/protocols that will be encountered during their self-guided exploration of the global data ecosystem. It also necessitates that the machines keep an exquisite record of provenance such that the data they are collecting can be accurately and adequately cited. Assisting these agents, therefore, is a critical consideration for all participants in the data management and stewardship process—from researchers and data producers to data repository hosts.” | limitations[5] |
| limitation | A machine may identify a data type yet fail to parse an unknown format or determine its licensing requirements. — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | limitations[6] |
| limitation | The optimal state of full autonomous machine understanding may rarely be achieved. — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | limitations[7] |
| limitation | Building bespoke parsers for every data type, programming language, and analytical tool is unsustainable. — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | limitations[8] |
| limitation | Community vocabularies may lack attributes needed for rich annotation, forcing extensions or new FAIR vocabularies. — “Specific exemplar efforts that provide varying levels of FAIRness are detailed later in this document. Additional issues, however, remain to be addressed. First, when community-endorsed vocabularies or other (meta)data standards do not include the attributes necessary to achieve rich annotation, there are two possible solutions: either publish an extension of an existing, closely related vocabulary, or—in the extreme case—create and explicitly publish a new vocabulary resource, following FAIR principles (‘I2’). Second, to explicitly identify the standard chosen when more than one vocabulary or other (meta)data standard is available, and given that for instance in the life sciences there are over 600 content standards, the BioSharing registry ( https://biosharing.org/ ) can be of use as it describes the standards in detail, including versions where applicable.” | limitations[9] |
| limitation | The FAIR Principles deliberately do not choose a technology, standard, implementation, or specification. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | limitations[10] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | Existing scholarly-data infrastructure does not deliver the maximum benefit from research investments. — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | content_tags.findings[0] |
| finding | The FAIR Principles apply to data, algorithms, tools, workflows, and other scholarly digital research objects. — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | content_tags.findings[1] |
| finding | Computational agents are critical stakeholders because people cannot work at the scope, scale, and speed of contemporary data-intensive science. — “The emphasis placed on FAIRness being applied to both human-driven and machine-driven activities, is a specific focus of the FAIR Guiding Principles that distinguishes them from many peer initiatives (discussed in the subsequent section). Humans and machines often face distinct barriers when attempting to find and process data on the Web. Humans have an intuitive sense of ‘semantics’ (the meaning or intent of a digital object) because we are capable of identifying and interpreting a wide variety of contextual cues, whether those take the form of structural/visual/iconic cues in the layout of a Web page, or the content of narrative notes. As such, we are less likely to make errors in the selection of appropriate data or other digital objects, although humans will face similar difficulties if sufficient contextual metadata is lacking. The primary limitation of humans, however, is that we are unable to operate at the scope, scale, and speed necessitated by the scale of contemporary scientific data and complexity of e-Science. It is for this reason that humans increasingly rely on computational agents to undertake discovery and integration tasks on their behalf. This necessitates machines to be capable of autonomously and appropriately acting when faced with the wide range of types, formats, and access-mechanisms/protocols that will be encountered during their self-guided exploration of the global data ecosystem. It also necessitates that the machines keep an exquisite record of provenance such that the data they are collecting can be accurately and adequately cited. Assisting these agents, therefore, is a critical consideration for all participants in the data management and stewardship process—from researchers and data producers to data repository hosts.” | content_tags.findings[2] |
| finding | Machine actionability is a continuum rather than an all-or-nothing property. — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | content_tags.findings[3] |
| finding | Metadata and the content of a digital object can each be machine-actionable to different degrees. — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | content_tags.findings[4] |
| finding | Bespoke parsers for every data type, language, and analytical tool are not sustainable. — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | content_tags.findings[5] |
| finding | FAIR is domain-independent and applies to a wide range of scholarly outputs. — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | content_tags.findings[6] |
| finding | The four FAIR elements are related but independent, separable, combinable, and incrementally adoptable. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | content_tags.findings[7] |
| finding | Rich public metadata and access rules can make sensitive data highly FAIR even when the data themselves are not public. — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | content_tags.findings[8] |
| finding | The FAIR Principles precede implementation choices and are neither a standard nor a specification. — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | content_tags.findings[9] |
| finding | Dataverse keeps metadata public even when data are restricted or removed for privacy. — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | content_tags.findings[10] |
| finding | FAIRDOM uses persistent HTTP URLs, community metadata, RDF, and multiple representations for systems-biology assets. — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | content_tags.findings[11] |
| finding | Open PHACTS combines multiple access URLs, canonical response URLs, rich provenance, standardized descriptions, and machine-readable interfaces. — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | content_tags.findings[12] |
| finding | wwPDB is strongly machine-actionable for machines equipped with domain-specific IUCr software. — “wwPDB 4 , 21 : wwPDB is a special-purpose, intensively-curated data archive that hosts information about experimentally-determined 3D structures of proteins and nucleic acids. All wwPDB entries are stably hosted on an FTP server (‘A’) and represented in machine-readable formats (text and XML); the latter are machine-actionable using the metadata provided by the wwPDB conforming to the Macromolecular Information Framework (mmCIF 22 ), a data standard of the International Union of Crystallography (IUCr) (‘F’,‘I’ for humans, ‘F’,‘I’ for IUCr-aware machines). The wwPDB metadata contains cross-references to common identifiers such as PubMed and NCBI Taxonomy, and their wwPDB metadata are described in data dictionaries and schema documents ( http://mmcif.wwpdb.org and http://pdbml.wwpdb.org ) which conform to the IUCr data standard for the chemical and structural biology domains (‘R’). A variety of software tools are available to interpret both wwPDB data and meta-data (‘I’,‘R’ for humans, ‘I’,‘R’ for machines with this software). Each entry is represented by a DOI (‘F’, ‘A’ for humans and machines). The DOI resolves to a zipped file which requires special software for further interrogation/interpretation. Other wwPDB access points 23–25 provide access to wwPDB records through URLs that are likely to be stable in the long-term (‘F’), and all data and metadata is searchable through one or more of the wwPDB-affiliated websites (‘F’)” | content_tags.findings[13] |
| finding | UniProt combines stable identifiers, human- and machine-readable forms, shared ontologies, and extensive database links. — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | content_tags.findings[14] |
| finding | FAIR emphasizes properties of data, while the Data Seal of Approval emphasizes producer and repository conduct. — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | content_tags.findings[15] |
| finding | Good data management and stewardship are preconditions for knowledge discovery and innovation, not ends in themselves. — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | content_tags.findings[16] |
| quantity | four — foundational FAIR principles — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | content_tags.quantities[0] |
| quantity | 2014 — year of the Jointly Designing a Data Fairport workshop — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | content_tags.quantities[1] |
| quantity | two — machine-actionability contexts: contextual metadata and object content — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | content_tags.quantities[2] |
| quantity | over 600 — content standards in the life sciences — “Specific exemplar efforts that provide varying levels of FAIRness are detailed later in this document. Additional issues, however, remain to be addressed. First, when community-endorsed vocabularies or other (meta)data standards do not include the attributes necessary to achieve rich annotation, there are two possible solutions: either publish an extension of an existing, closely related vocabulary, or—in the extreme case—create and explicitly publish a new vocabulary resource, following FAIR principles (‘I2’). Second, to explicitly identify the standard chosen when more than one vocabulary or other (meta)data standard is available, and given that for instance in the life sciences there are over 600 content standards, the BioSharing registry ( https://biosharing.org/ ) can be of use as it describes the standards in detail, including versions where applicable.” | content_tags.quantities[3] |
| quantity | more than 60,000 datasets — size of Harvard Dataverse reported in the article — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | content_tags.quantities[4] |
| quantity | three levels — Dataverse metadata granularity — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | content_tags.quantities[5] |
| quantity | more than 150 different databases — number of databases linked from UniProt records — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | content_tags.quantities[6] |
| variable | amount of detail provided (position of a digital object along the machine-actionability continuum) — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | content_tags.variables[0] |
| variable | type of object (structural and intentional classification assessed by an autonomous agent) — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | content_tags.variables[1] |
| variable | license, consent, or other accessibility or use constraints (conditions determining whether an object is usable) — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | content_tags.variables[2] |
| variable | contextual metadata (machine-actionability of what a digital object is) — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | content_tags.variables[3] |
| variable | content of the digital object (machine-actionability of how an object can be processed or integrated) — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | content_tags.variables[4] |
| variable | persistent identifier (stable discovery and resolution mechanism) — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | content_tags.variables[5] |
| variable | community standards (shared formats and ontologies used for interoperability) — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | content_tags.variables[7] |
| variable | provenance (record required for accurate and adequate citation by computational agents) — “The emphasis placed on FAIRness being applied to both human-driven and machine-driven activities, is a specific focus of the FAIR Guiding Principles that distinguishes them from many peer initiatives (discussed in the subsequent section). Humans and machines often face distinct barriers when attempting to find and process data on the Web. Humans have an intuitive sense of ‘semantics’ (the meaning or intent of a digital object) because we are capable of identifying and interpreting a wide variety of contextual cues, whether those take the form of structural/visual/iconic cues in the layout of a Web page, or the content of narrative notes. As such, we are less likely to make errors in the selection of appropriate data or other digital objects, although humans will face similar difficulties if sufficient contextual metadata is lacking. The primary limitation of humans, however, is that we are unable to operate at the scope, scale, and speed necessitated by the scale of contemporary scientific data and complexity of e-Science. It is for this reason that humans increasingly rely on computational agents to undertake discovery and integration tasks on their behalf. This necessitates machines to be capable of autonomously and appropriately acting when faced with the wide range of types, formats, and access-mechanisms/protocols that will be encountered during their self-guided exploration of the global data ecosystem. It also necessitates that the machines keep an exquisite record of provenance such that the data they are collecting can be accurately and adequately cited. Assisting these agents, therefore, is a critical consideration for all participants in the data management and stewardship process—from researchers and data producers to data repository hosts.” | content_tags.variables[8] |
| variable | FAIRness (incremental degree to which a resource exhibits the four principles) — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | content_tags.variables[9] |
| definition | FAIR — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | content_tags.definitions[0] |
| definition | data stewardship — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | content_tags.definitions[1] |
| definition | computational stakeholders — “There are numerous and diverse stakeholders who stand to benefit from overcoming these obstacles: researchers wanting to share, get credit, and reuse each other’s data and interpretations; professional data publishers offering their services; software and tool-builders providing data analysis and processing services such as reusable workflows; funding agencies (private and public) increasingly concerned with long-term data stewardship; and a data science community mining, integrating and analysing new and existing data to advance discovery. To facilitate the reading of this manuscript by these diverse stakeholders, we provide definitions for common abbreviations in Box 1 . Humans, however, are not the only critical stakeholders in the milieu of scientific data. Similar problems are encountered by the applications and computational agents that we task to undertake data retrieval and analysis on our behalf. These ‘computational stakeholders’ are increasingly relevant, and demand as much, or more, attention as their importance grows. One of the grand challenges of data-intensive science, therefore, is to improve knowledge discovery through assisting both humans, and their computational agents, in the discovery of, access to, and integration and analysis of, task-appropriate scientific data and other scholarly digital objects.” | content_tags.definitions[2] |
| definition | machine actionable — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | content_tags.definitions[3] |
| definition | ultimate machine-actionability — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | content_tags.definitions[4] |
| definition | FAIR Guiding Principles — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | content_tags.definitions[5] |
| definition | Findability — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | content_tags.definitions[6] |
| definition | Accessibility — “We will consider the current approach to this problem from a variety of data discovery and integration perspectives. If the desired datasets existed, where might they have been published, and how would one begin to search for them, using what search tools? The desired search would need to filter based on specific species, specific tissues, specific types of data (Poly-A, microarray, NGS), specific conditions (infection), and specific genes—is that information (‘metadata’) captured by the repositories, and if so, what formats is it in, is it searchable, and how? Once the data is discovered, can it be downloaded? In what format(s)? Can that format be easily integrated with private in-house data (the local dataset of alternative polyadenylation sites) as well as other data publications from third-parties and with the community’s core gene/protein data repositories? Can this integration be done automatically to save time and avoid copy/paste errors? Does the researcher have permission to use the data from these third-party researchers, under what license conditions, and who should be cited if a data-point is re-used?” | content_tags.definitions[7] |
| definition | Interoperability — “We will consider the current approach to this problem from a variety of data discovery and integration perspectives. If the desired datasets existed, where might they have been published, and how would one begin to search for them, using what search tools? The desired search would need to filter based on specific species, specific tissues, specific types of data (Poly-A, microarray, NGS), specific conditions (infection), and specific genes—is that information (‘metadata’) captured by the repositories, and if so, what formats is it in, is it searchable, and how? Once the data is discovered, can it be downloaded? In what format(s)? Can that format be easily integrated with private in-house data (the local dataset of alternative polyadenylation sites) as well as other data publications from third-parties and with the community’s core gene/protein data repositories? Can this integration be done automatically to save time and avoid copy/paste errors? Does the researcher have permission to use the data from these third-party researchers, under what license conditions, and who should be cited if a data-point is re-used?” | content_tags.definitions[8] |
| definition | Reusability — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | content_tags.definitions[9] |
| definition | Dataverse — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | content_tags.definitions[10] |
| definition | FAIRDOM — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | content_tags.definitions[11] |
| definition | ISA — “ISA 16 : is a community-driven metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of life science datasets. ISA provides progressively FAIR structured metadata to Nature Scientific Data’s Data Descriptor articles, and many GigaScience data papers, and underpins the EBI MetaboLights database among other data resources. At the heart is a general-purpose, extensible ISA model, originally only available as a tabular representation but subsequently enhanced as an RDF-based representation 17 , and JSON serializations to enable the ‘I’ and ‘R’, becoming ‘FAIR’ when published as linked data ( http://elixir-uk.org/node-events/201cisa-as-a-fair-research-object201d-hack-the-spec-event-1 ) and complementing other research objects 18 .” | content_tags.definitions[12] |
| definition | Open PHACTS — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | content_tags.definitions[13] |
| definition | wwPDB — “wwPDB 4 , 21 : wwPDB is a special-purpose, intensively-curated data archive that hosts information about experimentally-determined 3D structures of proteins and nucleic acids. All wwPDB entries are stably hosted on an FTP server (‘A’) and represented in machine-readable formats (text and XML); the latter are machine-actionable using the metadata provided by the wwPDB conforming to the Macromolecular Information Framework (mmCIF 22 ), a data standard of the International Union of Crystallography (IUCr) (‘F’,‘I’ for humans, ‘F’,‘I’ for IUCr-aware machines). The wwPDB metadata contains cross-references to common identifiers such as PubMed and NCBI Taxonomy, and their wwPDB metadata are described in data dictionaries and schema documents ( http://mmcif.wwpdb.org and http://pdbml.wwpdb.org ) which conform to the IUCr data standard for the chemical and structural biology domains (‘R’). A variety of software tools are available to interpret both wwPDB data and meta-data (‘I’,‘R’ for humans, ‘I’,‘R’ for machines with this software). Each entry is represented by a DOI (‘F’, ‘A’ for humans and machines). The DOI resolves to a zipped file which requires special software for further interrogation/interpretation. Other wwPDB access points 23–25 provide access to wwPDB records through URLs that are likely to be stable in the long-term (‘F’), and all data and metadata is searchable through one or more of the wwPDB-affiliated websites (‘F’)” | content_tags.definitions[14] |
| definition | UniProt — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | content_tags.definitions[15] |
| concept | FAIR Principles — not defined in this paper's own words; principles for findable, accessible, interoperable, reusable digital objects — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | concepts[0] |
| concept | FAIR Data Principles — not defined in this paper's own words; formal name used for the principles — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | concepts[1] |
| concept | peer initiatives — not defined in this paper's own words; human-scholar-focused data initiatives contrasted with FAIR — “There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.” | concepts[2] |
| concept | good data management — not defined in this paper's own words; practices supporting discovery, integration, and reuse — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concepts[3] |
| concept | data stewardship — long-term care’ of valuable digital assets — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concepts[4] |
| concept | long-term care — not defined in this paper's own words; continuing preservation of digital assets — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concepts[5] |
| concept | knowledge discovery and innovation — not defined in this paper's own words; downstream outcome of managed and reusable data — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concepts[6] |
| concept | high quality digital publications — not defined in this paper's own words; outputs facilitating discovery, evaluation, and reuse — “Good data management is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardship includes the notion of ‘long-term care’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data management and stewardship, therefore, are high quality digital publications that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data management’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data management and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.” | concepts[7] |
| concept | Findability — not defined in this paper's own words; FAIR discovery dimension — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | concepts[8] |
| concept | Accessibility — not defined in this paper's own words; FAIR retrieval dimension — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | concepts[9] |
| concept | Interoperability — not defined in this paper's own words; FAIR integration dimension — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | concepts[10] |
| concept | Reusability — not defined in this paper's own words; FAIR downstream-use dimension — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | concepts[11] |
| concept | algorithms, tools, and workflows — not defined in this paper's own words; non-data digital research objects within FAIR's scope — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | concepts[12] |
| concept | scholarly digital research objects — not defined in this paper's own words; data and process components subject to FAIR — “This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.” | concepts[13] |
| concept | computational stakeholders — not defined in this paper's own words; applications and agents acting on behalf of researchers — “There are numerous and diverse stakeholders who stand to benefit from overcoming these obstacles: researchers wanting to share, get credit, and reuse each other’s data and interpretations; professional data publishers offering their services; software and tool-builders providing data analysis and processing services such as reusable workflows; funding agencies (private and public) increasingly concerned with long-term data stewardship; and a data science community mining, integrating and analysing new and existing data to advance discovery. To facilitate the reading of this manuscript by these diverse stakeholders, we provide definitions for common abbreviations in Box 1 . Humans, however, are not the only critical stakeholders in the milieu of scientific data. Similar problems are encountered by the applications and computational agents that we task to undertake data retrieval and analysis on our behalf. These ‘computational stakeholders’ are increasingly relevant, and demand as much, or more, attention as their importance grows. One of the grand challenges of data-intensive science, therefore, is to improve knowledge discovery through assisting both humans, and their computational agents, in the discovery of, access to, and integration and analysis of, task-appropriate scientific data and other scholarly digital objects.” | concepts[14] |
| concept | computational agents — not defined in this paper's own words; autonomous software for retrieval and analysis — “There are numerous and diverse stakeholders who stand to benefit from overcoming these obstacles: researchers wanting to share, get credit, and reuse each other’s data and interpretations; professional data publishers offering their services; software and tool-builders providing data analysis and processing services such as reusable workflows; funding agencies (private and public) increasingly concerned with long-term data stewardship; and a data science community mining, integrating and analysing new and existing data to advance discovery. To facilitate the reading of this manuscript by these diverse stakeholders, we provide definitions for common abbreviations in Box 1 . Humans, however, are not the only critical stakeholders in the milieu of scientific data. Similar problems are encountered by the applications and computational agents that we task to undertake data retrieval and analysis on our behalf. These ‘computational stakeholders’ are increasingly relevant, and demand as much, or more, attention as their importance grows. One of the grand challenges of data-intensive science, therefore, is to improve knowledge discovery through assisting both humans, and their computational agents, in the discovery of, access to, and integration and analysis of, task-appropriate scientific data and other scholarly digital objects.” | concepts[15] |
| concept | general-purpose data repositories — not defined in this paper's own words; repositories accepting diverse formats with few descriptor constraints — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | concepts[16] |
| concept | discovery and re-usability problem — not defined in this paper's own words; difficulty created by a diverse and poorly integrated data ecosystem — “For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDB 4 ), and UniProt 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositories, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverse 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders.” | concepts[17] |
| concept | first class citizens — not defined in this paper's own words; status sought for reusable and citable scholarly digital objects — “Questions such as these highlight some of the barriers to data discovery and reuse, not only for humans, but even more so for machines; yet it is precisely these kinds of deeply and broadly integrative analyses that constitute the bulk of contemporary e-Science. The reason that we often need several weeks (or months) of specialist technical effort to gather the data necessary to answer such research questions is not the lack of appropriate technology; the reason is, that we do not pay our valuable digital objects the careful attention they deserve when we create and preserve them. Overcoming these barriers, therefore, necessitates that all stakeholders—including researchers, special-purpose, and general-purpose repositories—evolve to meet the emergent challenges described above. The goal is for scholarly digital objects of all kinds to become ‘first class citizens’ in the scientific publication ecosystem, where the quality of the publication—and more importantly, the impact of the publication—is a function of its ability to be accurately and appropriately found, re-used, and cited over time, by all stakeholders, both human and mechanical.” | concepts[18] |
| concept | minimal set of community-agreed guiding principles and practices — not defined in this paper's own words; workshop strategy for lowering reuse barriers — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | concepts[19] |
| concept | FAIR Guiding Principles — not defined in this paper's own words; refined four-principle framework for machines and people — “With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practices, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIR) both for machines and for people. These are now referred to as the FAIR Guiding Principles. Subsequently, a dedicated FAIR working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.” | concepts[20] |
| concept | human-driven — not defined in this paper's own words; human discovery and reuse processes — “The emphasis placed on FAIRness being applied to both human-driven and machine-driven activities, is a specific focus of the FAIR Guiding Principles that distinguishes them from many peer initiatives (discussed in the subsequent section). Humans and machines often face distinct barriers when attempting to find and process data on the Web. Humans have an intuitive sense of ‘semantics’ (the meaning or intent of a digital object) because we are capable of identifying and interpreting a wide variety of contextual cues, whether those take the form of structural/visual/iconic cues in the layout of a Web page, or the content of narrative notes. As such, we are less likely to make errors in the selection of appropriate data or other digital objects, although humans will face similar difficulties if sufficient contextual metadata is lacking. The primary limitation of humans, however, is that we are unable to operate at the scope, scale, and speed necessitated by the scale of contemporary scientific data and complexity of e-Science. It is for this reason that humans increasingly rely on computational agents to undertake discovery and integration tasks on their behalf. This necessitates machines to be capable of autonomously and appropriately acting when faced with the wide range of types, formats, and access-mechanisms/protocols that will be encountered during their self-guided exploration of the global data ecosystem. It also necessitates that the machines keep an exquisite record of provenance such that the data they are collecting can be accurately and adequately cited. Assisting these agents, therefore, is a critical consideration for all participants in the data management and stewardship process—from researchers and data producers to data repository hosts.” | concepts[21] |
| concept | machine-driven activities — not defined in this paper's own words; computational discovery and reuse processes — “The emphasis placed on FAIRness being applied to both human-driven and machine-driven activities, is a specific focus of the FAIR Guiding Principles that distinguishes them from many peer initiatives (discussed in the subsequent section). Humans and machines often face distinct barriers when attempting to find and process data on the Web. Humans have an intuitive sense of ‘semantics’ (the meaning or intent of a digital object) because we are capable of identifying and interpreting a wide variety of contextual cues, whether those take the form of structural/visual/iconic cues in the layout of a Web page, or the content of narrative notes. As such, we are less likely to make errors in the selection of appropriate data or other digital objects, although humans will face similar difficulties if sufficient contextual metadata is lacking. The primary limitation of humans, however, is that we are unable to operate at the scope, scale, and speed necessitated by the scale of contemporary scientific data and complexity of e-Science. It is for this reason that humans increasingly rely on computational agents to undertake discovery and integration tasks on their behalf. This necessitates machines to be capable of autonomously and appropriately acting when faced with the wide range of types, formats, and access-mechanisms/protocols that will be encountered during their self-guided exploration of the global data ecosystem. It also necessitates that the machines keep an exquisite record of provenance such that the data they are collecting can be accurately and adequately cited. Assisting these agents, therefore, is a critical consideration for all participants in the data management and stewardship process—from researchers and data producers to data repository hosts.” | concepts[22] |
| concept | machine actionable — not defined in this paper's own words; degree to which an autonomous agent can interpret and act on an object — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | concepts[23] |
| concept | digital object — not defined in this paper's own words; data or other research object presented to a computational explorer — “Throughout this paper, we use the phrase ‘machine actionable’ to indicate a continuum of possible states wherein a digital object provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail provided—to have the capacity, when faced with a digital object never encountered before, to: a) identify the type of object (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadata and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraints, and d) take appropriate action, in much the same manner that a human would.” | concepts[24] |
| concept | contextual metadata — not defined in this paper's own words; information answering what an object is — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | concepts[25] |
| concept | content of the digital object — not defined in this paper's own words; information determining how an object can be processed — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | concepts[26] |
| concept | machine-actionability — not defined in this paper's own words; continuum toward autonomous correct operation on unfamiliar objects — “For example, a machine may be capable of determining the data-type of a discovered digital object, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital object—may rarely be achieved. Nevertheless, the FAIR principles provide ‘steps along a path’ toward machine-actionability; adopting, in whole or in part, the FAIR principles, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadata surrounding a digital object (‘what is it?’), and second, when referring to the content of the digital object itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.” | concepts[27] |
| concept | bespoke parsers — not defined in this paper's own words; type-specific software for interpreting particular formats — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | concepts[28] |
| concept | general-purpose, open technologies — not defined in this paper's own words; cross-domain technologies for unfamiliar data types — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | concepts[29] |
| concept | generalized interoperability technologies and standards — not defined in this paper's own words; repository-level support for machine exploration — “Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsers that understand life science wwPDB files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologies. To reiterate the earlier point—ultimate machine-actionability occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsers, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standards at the data/repository level, becomes a first-priority for good data stewardship.” | concepts[30] |
| concept | contemporary data publishing environments — not defined in this paper's own words; manual and automated settings governed by FAIR considerations — “Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principles—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIR implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principles describe distinct considerations for contemporary data publishing environments with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIR differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadata and data.” | concepts[31] |
| concept | data resources, tools, vocabularies and infrastructures — not defined in this paper's own words; classes expected to exhibit FAIR characteristics — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | concepts[32] |
| concept | rich metadata — not defined in this paper's own words; public descriptive information supporting discovery and access — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | concepts[33] |
| concept | highly sensitive or personally-identifiable data — not defined in this paper's own words; restricted-data case handled by metadata-level FAIRness — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | concepts[34] |
| concept | analytical workflows — not defined in this paper's own words; non-data research objects requiring formal publication — “The elements of the FAIR Principles are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructures should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIR is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRness’. Moreover, the modularity of the Principles, and their distinction between data and metadata, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable data, where publication of rich metadata to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRness’ even in the absence of FAIR publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflows, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principles can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.” | concepts[35] |
| concept | implementation choices — not defined in this paper's own words; technology decisions evaluated against FAIR — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concepts[36] |
| concept | standard — not defined in this paper's own words; normative specification that FAIR explicitly is not — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concepts[37] |
| concept | specification — not defined in this paper's own words; implementation prescription that FAIR explicitly is not — “These high-level FAIR Guiding Principles precede implementation choices, and do not suggest any specific technology, standard, or implementation-solution; moreover, the Principles are not, themselves, a standard or a specification. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choices are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIR using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIR structured metadata.” | concepts[38] |
| concept | Dataverse — open-source data repository software — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concepts[39] |
| concept | open-source data repository software — not defined in this paper's own words; software class instantiated by Dataverse — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concepts[40] |
| concept | Deposits — not defined in this paper's own words; Dataverse submissions containing metadata and files — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concepts[41] |
| concept | metadata — not defined in this paper's own words; public descriptive layer within a Dataverse deposit — “Dataverse 7 : Dataverse is an open-source data repository software installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverse, with more than 60,000 datasets, is the largest of the current Dataverse repositories, and is open to all researchers from all research fields. Dataverse generates a formal citation for each deposit, following the standard defined by Altman and King 13 . Dataverse makes the Digital Object Identifier (DOI), or other persistent identifiers (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadata, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Deposits include metadata, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadata is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadata is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principles: 1) data citation metadata, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadata, which when possible maps to metadata standards used within a scientific domain, and 3) file-level metadata, which can be deep and extensive for tabular data files (including column-level metadata). Finally, Dataverse provides public machine-accessible interfaces to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘A’).” | concepts[42] |
| concept | FAIRDOM — not defined in this paper's own words; integrated SEEK/openBIS facility — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | concepts[43] |
| concept | FAIR data and model management facility — not defined in this paper's own words; systems-biology facility produced by FAIRDOM — “FAIRDOM ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facility for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadata, using community standards, formats and ontologies (‘I’). The metadata is stored as RDF to enable interoperability and assets can be downloaded for reuse (‘R’).” | concepts[44] |
| concept | ISA — metadata tracking framework — “ISA 16 : is a community-driven metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of life science datasets. ISA provides progressively FAIR structured metadata to Nature Scientific Data’s Data Descriptor articles, and many GigaScience data papers, and underpins the EBI MetaboLights database among other data resources. At the heart is a general-purpose, extensible ISA model, originally only available as a tabular representation but subsequently enhanced as an RDF-based representation 17 , and JSON serializations to enable the ‘I’ and ‘R’, becoming ‘FAIR’ when published as linked data ( http://elixir-uk.org/node-events/201cisa-as-a-fair-research-object201d-hack-the-spec-event-1 ) and complementing other research objects 18 .” | concepts[45] |
| concept | community-driven metadata tracking framework — not defined in this paper's own words; framework class instantiated by ISA — “ISA 16 : is a community-driven metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of life science datasets. ISA provides progressively FAIR structured metadata to Nature Scientific Data’s Data Descriptor articles, and many GigaScience data papers, and underpins the EBI MetaboLights database among other data resources. At the heart is a general-purpose, extensible ISA model, originally only available as a tabular representation but subsequently enhanced as an RDF-based representation 17 , and JSON serializations to enable the ‘I’ and ‘R’, becoming ‘FAIR’ when published as linked data ( http://elixir-uk.org/node-events/201cisa-as-a-fair-research-object201d-hack-the-spec-event-1 ) and complementing other research objects 18 .” | concepts[46] |
| concept | Open PHACTS — not defined in this paper's own words; drug-discovery data integration service — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | concepts[47] |
| concept | data integration platform — not defined in this paper's own words; platform class instantiated by Open PHACTS — “Open PHACTS 19 : Open PHACTS is a data integration platform for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRness. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standard, with rich provenance (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specification (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).” | concepts[48] |
| concept | wwPDB — not defined in this paper's own words; curated structural biology archive — “wwPDB 4 , 21 : wwPDB is a special-purpose, intensively-curated data archive that hosts information about experimentally-determined 3D structures of proteins and nucleic acids. All wwPDB entries are stably hosted on an FTP server (‘A’) and represented in machine-readable formats (text and XML); the latter are machine-actionable using the metadata provided by the wwPDB conforming to the Macromolecular Information Framework (mmCIF 22 ), a data standard of the International Union of Crystallography (IUCr) (‘F’,‘I’ for humans, ‘F’,‘I’ for IUCr-aware machines). The wwPDB metadata contains cross-references to common identifiers such as PubMed and NCBI Taxonomy, and their wwPDB metadata are described in data dictionaries and schema documents ( http://mmcif.wwpdb.org and http://pdbml.wwpdb.org ) which conform to the IUCr data standard for the chemical and structural biology domains (‘R’). A variety of software tools are available to interpret both wwPDB data and meta-data (‘I’,‘R’ for humans, ‘I’,‘R’ for machines with this software). Each entry is represented by a DOI (‘F’, ‘A’ for humans and machines). The DOI resolves to a zipped file which requires special software for further interrogation/interpretation. Other wwPDB access points 23–25 provide access to wwPDB records through URLs that are likely to be stable in the long-term (‘F’), and all data and metadata is searchable through one or more of the wwPDB-affiliated websites (‘F’)” | concepts[49] |
| concept | special-purpose, intensively-curated data archive — not defined in this paper's own words; archive class instantiated by wwPDB — “wwPDB 4 , 21 : wwPDB is a special-purpose, intensively-curated data archive that hosts information about experimentally-determined 3D structures of proteins and nucleic acids. All wwPDB entries are stably hosted on an FTP server (‘A’) and represented in machine-readable formats (text and XML); the latter are machine-actionable using the metadata provided by the wwPDB conforming to the Macromolecular Information Framework (mmCIF 22 ), a data standard of the International Union of Crystallography (IUCr) (‘F’,‘I’ for humans, ‘F’,‘I’ for IUCr-aware machines). The wwPDB metadata contains cross-references to common identifiers such as PubMed and NCBI Taxonomy, and their wwPDB metadata are described in data dictionaries and schema documents ( http://mmcif.wwpdb.org and http://pdbml.wwpdb.org ) which conform to the IUCr data standard for the chemical and structural biology domains (‘R’). A variety of software tools are available to interpret both wwPDB data and meta-data (‘I’,‘R’ for humans, ‘I’,‘R’ for machines with this software). Each entry is represented by a DOI (‘F’, ‘A’ for humans and machines). The DOI resolves to a zipped file which requires special software for further interrogation/interpretation. Other wwPDB access points 23–25 provide access to wwPDB records through URLs that are likely to be stable in the long-term (‘F’), and all data and metadata is searchable through one or more of the wwPDB-affiliated websites (‘F’)” | concepts[50] |
| concept | UniProt — not defined in this paper's own words; protein sequence and annotation resource — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | concepts[51] |
| concept | comprehensive resource — not defined in this paper's own words; resource class instantiated by UniProt — “UniProt 26 : UniProt is a comprehensive resource for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadata (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProt Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProt record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProt Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.” | concepts[52] |
| concept | Concept Web Alliance — not defined in this paper's own words; earlier work on machine actionability and semantic harmonization — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | concepts[53] |
| concept | Joint Declaration of Data Citation Principles — not defined in this paper's own words; earlier principles for citable and reusable scholarly data — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | concepts[54] |
| concept | Data Seal of Approval — not defined in this paper's own words; complementary framework focused on producer and repository conduct — “The ideas within the FAIR Guiding Principles reflect, combine, build upon and extend previous work by both the Concept Web Alliance ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionability and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principles (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principles and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principles are also complementary to the ‘Data Seal of Approval’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIR focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.” | concepts[55] |
| concept | Data Citation Implementation Group — not defined in this paper's own words; group publishing identifier and metadata-access recommendations — “In addition to, and in support of, communities and resources that are already pursuing FAIR objectives, the Data Citation Implementation Group of Force11 has published specific technical recommendations for how to implement many of the principles 27 , with a particular focus on identifiers and their resolution, persistence, and metadata accessibility especially related to citation. In addition, the ‘Skunkworks’ group that emerged from the Lorentz Workshop has been creating software supporting infrastructures 28 that are, end-to-end, compatible with FAIR principles, and can be implemented over existing repositories. These code modules have a particular focus on metadata publication and searchability, compatibility in cases of strict privacy considerations, and the extremely difficult problem of data and metadata interoperability (manuscript in preparation). Finally, there are several emergent projects, some listed in Box 3 , for which FAIR is a key objective. These projects may provide valuable advice and guidance for those wishing to become more FAIR.” | concepts[56] |
| concept | data producers and publishers — not defined in this paper's own words; actors called to implement FAIR — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | concepts[57] |
| concept | good Data Management and Stewardship practice — not defined in this paper's own words; basic practice guided by FAIR mileposts — “The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data management and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovation. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principles provide a set of mileposts for data producers and publishers. They guide the implementation of the most basic levels of good Data Management and Stewardship practice, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishers to examine and implement these principles, and actively participate with the FAIR initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRness.” | concepts[58] |
Full text — tagged
The reference list is not part of the text we hold for this paper. Our copy was extracted from the publisher's page and the bibliography did not survive that extraction, so the article below ends before its references. Nothing has been removed by us.
The FAIR Guiding Principlesterm for scientific data management and stewardship Abstract There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principlesterm. The intent is that these may act as a guideline for those wishing to enhance the reusabilityterm of their data holdings. Distinct from peer initiativesterm that focus on the human scholar, the FAIR Principlesterm put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principlesterm, and includes the rationale behind them, and some exemplar implementations in the community.
Comment Supporting discovery through good data managementterm Good data managementterm is not a goal in itself, but rather is the key conduit leading to knowledge discovery and innovationterm, and to subsequent data and knowledge integration and reuse by the community after the data publication process. Unfortunately, the existing digital ecosystem surrounding scholarly data publication prevents us from extracting maximum benefit from our research investments (e.g., ref. 1 ). Partially in response to this, science funders, publishers and governmental agencies are beginning to require data management and stewardship plans for data generated in publicly funded experiments. Beyond proper collection, annotation, and archival, data stewardshipterm includes the notion of ‘long-term careterm’ of valuable digital assets, with the goal that they should be discovered and re-used for downstream investigations, either alone, or in combination with newly generated data. The outcomes from good data managementterm and stewardship, therefore, are high quality digital publicationsterm that facilitate and simplify this ongoing process of discovery, evaluation, and reuse in downstream studies. What constitutes ‘good data managementterm’ is, however, largely undefined, and is generally left as a decision for the data or repository owner. Therefore, bringing some clarity around the goals and desiderata of good data managementterm and stewardship, and defining simple guideposts to inform those who publish and/or preserve scholarly data, would be of great utility.
This article describes four foundational principles—Findabilityterm, Accessibilityterm, Interoperabilityterm, and Reusabilityterm—that serve to guide data producers and publishersterm as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflowsterm that led to that data. All scholarly digital research objectsterm 2 —from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusabilityterm.
There are numerous and diverse stakeholders who stand to benefit from overcoming these obstacles: researchers wanting to share, get credit, and reuse each other’s data and interpretations; professional data publishers offering their services; software and tool-builders providing data analysis and processing services such as reusable workflows; funding agencies (private and public) increasingly concerned with long-term data stewardshipterm; and a data science community mining, integrating and analysing new and existing data to advance discovery. To facilitate the reading of this manuscript by these diverse stakeholders, we provide definitions for common abbreviations in Box 1 . Humans, however, are not the only critical stakeholders in the milieu of scientific data. Similar problems are encountered by the applications and computational agentsterm that we task to undertake data retrieval and analysis on our behalf. These ‘computational stakeholdersterm’ are increasingly relevant, and demand as much, or more, attention as their importance grows. One of the grand challenges of data-intensive science, therefore, is to improve knowledge discovery through assisting both humans, and their computational agentsterm, in the discovery of, access to, and integration and analysis of, task-appropriate scientific data and other scholarly digital objectsterm.
For certain types of important digital objectsterm, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank 3 , Worldwide Protein Data Bank (wwPDBterm 4 ), and UniProtterm 5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/ ) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD 6 ) in the space sciences. These foundational and critical core resources are continuously curating and capturing high-value reference datasets and fine-tuning them to enhance scholarly output, provide support for both human and mechanical users, and provide extensive tooling to access their content in rich, dynamic ways. However, not all datasets or even data types can be captured by, or submitted to, these repositories. Many important datasets emerging from traditional, low-throughput bench science don’t fit in the data models of these special-purpose repositories, yet these datasets are no less important with respect to integrative research, reproducibility, and reuse in general. Apparently in response to this, we see the emergence of numerous general-purpose data repositoriesterm, at scales ranging from institutional (for example, a single university), to open globally-scoped repositories such as Dataverseterm 7 , FigShare ( http://figshare.com ), Dryad 8 , Mendeley Data ( https://data.mendeley.com/ ), Zenodo ( http://zenodo.org/ ), DataHub ( http://datahub.io ), DANS ( http://www.dans.knaw.nl/ ), and EUDat 9 . Such repositories accept a wide range of data types in a wide variety of formats, generally do not attempt to integrate or harmonize the deposited data, and place few restrictions (or requirements) on the descriptors of the data deposition. The resulting data ecosystem, therefore, appears to be moving away from centralization, is becoming more diverse, and less integrated, thereby exacerbating the discovery and re-usability problemterm for both human and computational stakeholdersterm.
A specific example of these obstacles could be imagined in the domain of gene regulation and expression analysis. Suppose a researcher has generated a dataset of differentially-selected polyadenylation sites in a non-model pathogenic organism grown under a variety of environmental conditions that stimulate its pathogenic state. The researcher is interested in comparing the alternatively-polyadenylated genes in this local dataset, to other examples of alternative-polyadenylation, and the expression levels of these genes—both in this organism and related model organisms—during the infection process. Given that there is no special-purpose archive for differential polyadenylation data, and no model organism database for this pathogen, where does the researcher begin?
We will consider the current approach to this problem from a variety of data discovery and integration perspectives. If the desired datasets existed, where might they have been published, and how would one begin to search for them, using what search tools? The desired search would need to filter based on specific species, specific tissues, specific types of data (Poly-A, microarray, NGS), specific conditions (infection), and specific genes—is that information (‘metadataterm’) captured by the repositories, and if so, what formats is it in, is it searchable, and how? Once the data is discovered, can it be downloaded? In what format(s)? Can that format be easily integrated with private in-house data (the local dataset of alternative polyadenylation sites) as well as other data publications from third-parties and with the community’s core gene/protein data repositories? Can this integration be done automatically to save time and avoid copy/paste errors? Does the researcher have permission to use the data from these third-party researchers, under what license conditions, and who should be cited if a data-point is re-used?
Questions such as these highlight some of the barriers to data discovery and reuse, not only for humans, but even more so for machines; yet it is precisely these kinds of deeply and broadly integrative analyses that constitute the bulk of contemporary e-Science. The reason that we often need several weeks (or months) of specialist technical effort to gather the data necessary to answer such research questions is not the lack of appropriate technology; the reason is, that we do not pay our valuable digital objectsterm the careful attention they deserve when we create and preserve them. Overcoming these barriers, therefore, necessitates that all stakeholders—including researchers, special-purpose, and general-purpose repositories—evolve to meet the emergent challenges described above. The goal is for scholarly digital objectsterm of all kinds to become ‘first class citizensterm’ in the scientific publication ecosystem, where the quality of the publication—and more importantly, the impact of the publication—is a function of its ability to be accurately and appropriately found, re-used, and cited over time, by all stakeholders, both human and mechanical.
With this goal in-mind, a workshop was held in Leiden, Netherlands, in 2014, named ‘Jointly Designing a Data Fairport’. This workshop brought together a wide group of academic and private stakeholders all of whom had an interest in overcoming data discovery and reuse obstacles. From the deliberations at the workshop the notion emerged that, through the definition of, and widespread support for, a minimal set of community-agreed guiding principles and practicesterm, all stakeholders could more easily discover, access, appropriately integrate and re-use, and adequately cite, the vast quantities of information being generated by contemporary data-intensive science. The meeting concluded with a draft formulation of a set of foundational principles that were subsequently elaborated in greater detail—namely, that all research objects should be Findable, Accessible, Interoperable and Reusable (FAIRterm·def) both for machines and for people. These are now referred to as the FAIR Guiding Principlesterm. Subsequently, a dedicated FAIRterm·def working group, established by several members of the FORCE11 community 10 fine-tuned and improved the Principles. The results of these efforts are reported here.
The significance of machines in data-rich research environments The emphasis placed on FAIRnessterm·var being applied to both human-driventerm and machine-driven activitiesterm, is a specific focus of the FAIR Guiding Principlesterm that distinguishes them from many peer initiativesterm (discussed in the subsequent section). Humans and machines often face distinct barriers when attempting to find and process data on the Web. Humans have an intuitive sense of ‘semantics’ (the meaning or intent of a digital objectterm) because we are capable of identifying and interpreting a wide variety of contextual cues, whether those take the form of structural/visual/iconic cues in the layout of a Web page, or the content of narrative notes. As such, we are less likely to make errors in the selection of appropriate data or other digital objectsterm, although humans will face similar difficulties if sufficient contextual metadataterm is lacking. The primary limitation of humans, however, is that we are unable to operate at the scope, scale, and speed necessitated by the scale of contemporary scientific data and complexity of e-Science. It is for this reason that humans increasingly rely on computational agentsterm to undertake discovery and integration tasks on their behalf. This necessitates machines to be capable of autonomously and appropriately acting when faced with the wide range of types, formats, and access-mechanisms/protocols that will be encountered during their self-guided exploration of the global data ecosystem. It also necessitates that the machines keep an exquisite record of provenanceterm·var such that the data they are collecting can be accurately and adequately cited. Assisting these agents, therefore, is a critical consideration for all participants in the data management and stewardship process—from researchers and data producers to data repository hosts.
Throughout this paper, we use the phrase ‘machine actionableterm’ to indicate a continuum of possible states wherein a digital objectterm provides increasingly more detailed information to an autonomously-acting, computational data explorer. This information enables the agent—to a degree dependent on the amount of detail providedterm·var—to have the capacity, when faced with a digital objectterm never encountered before, to: a) identify the type of objectterm·var (with respect to both structure and intent), b) determine if it is useful within the context of the agent’s current task by interrogating metadataterm and/or data elements, c) determine if it is usable, with respect to license, consent, or other accessibility or use constraintsterm·var, and d) take appropriate action, in much the same manner that a human would.
For example, a machine may be capable of determining the data-type of a discovered digital objectterm, but not capable of parsing it due to it being in an unknown format; or it may be capable of processing the contained data, but not capable of determining the licensing requirements related to the retrieval and/or use of that data. The optimal state—where machines fully ‘understand’ and can autonomously and correctly operate-on a digital objectterm—may rarely be achieved. Nevertheless, the FAIR principlesterm provide ‘steps along a path’ toward machine-actionabilityterm; adopting, in whole or in part, the FAIR principlesterm, leads the resource along the continuum towards this optimal state. In addition, the idea of being machine-actionable applies in two contexts—first, when referring to the contextual metadataterm surrounding a digital objectterm (‘what is it?’), and second, when referring to the content of the digital objectterm itself (‘how do I process it/integrate it?’). Either, or both of these may be machine-actionable, and each forms its own continuum of actionability.
Finally, we wish to draw a distinction between data that is machine-actionable as a result of specific investment in software supporting that data-type, for example, bespoke parsersterm that understand life science wwPDBterm files or space science Space Physics Archive Search and Extract (SPASE) files, and data that is machine-actionable exclusively through the utilization of general-purpose, open technologiesterm. To reiterate the earlier point—ultimate machine-actionabilityterm·def occurs when a machine can make a useful decision regarding data that it has not encountered before. This distinction is important when considering both (a) the rapidly growing and evolving data environment, with new technologies and new, more complex data-types continuously being developed, and (b) the growth of general-purpose repositories, where the data-types likely to be encountered by an agent are unpredictable. Creating bespoke parsersterm, in all computer languages, for all data-types and all analytical tools that require those data-types, is not a sustainable activity. As such, the focus on assisting machines in their discovery and exploration of data through application of more generalized interoperability technologies and standardsterm at the data/repository level, becomes a first-priority for good data stewardshipterm.
The FAIR Guiding Principlesterm in detail Representatives of the interested stakeholder-groups, discussed above, coalesced around four core desiderata—the FAIR Guiding Principlesterm—and limited elaboration of these, which have been refined ( Box 2 ) from the meeting’s original draft, available at ( https://www.force11.org/node/6062 ). A separate document that dynamically addresses community discussion relating to clarifications and explanations of the principles, and detailed guidelines for and examples of FAIRterm·def implementations, is currently being constructed ( http://datafairport.org/fair-principles-living-document-menu ). The FAIR Guiding Principlesterm describe distinct considerations for contemporary data publishing environmentsterm with respect to supporting both manual and automated deposition, exploration, sharing, and reuse. While there have been a number of recent, often domain-focused publications advocating for specific improvements in practices relating to data management and archival 1 , 11 , 12 , FAIRterm·def differs in that it describes concise, domain-independent, high-level principles that can be applied to a wide range of scholarly outputs. Throughout the Principles, we use the phrase ‘(meta)data’ in cases where the Principle should be applied to both metadataterm and data.
The elements of the FAIR Principlesterm are related, but independent and separable. The Principles define characteristics that contemporary data resources, tools, vocabularies and infrastructuresterm should exhibit to assist discovery and reuse by third-parties. By minimally defining each guiding principle, the barrier-to-entry for data producers, publishers and stewards who wish to make their data holdings FAIRterm·def is purposely maintained as low as possible. The Principles may be adhered to in any combination and incrementally, as data providers’ publishing environments evolve to increasing degrees of ‘FAIRnessterm·var’. Moreover, the modularity of the Principles, and their distinction between data and metadataterm, explicitly support a wide range of special circumstances. One such example is highly sensitive or personally-identifiable dataterm, where publication of rich metadataterm to facilitate discovery, including clear rules regarding the process for accessing the data, provides a high degree of ‘FAIRnessterm·var’ even in the absence of FAIRterm·def publication of the data itself. A second example involves the publication of non-data research objects. Analytical workflowsterm, for example, are a critical component of the scholarly ecosystem, and their formal publication is necessary to achieve both transparency and scientific reproducibility. The FAIR principlesterm can equally be applied to these non-data assets, which need to be identified, described, discovered, and reused in much the same manner as data.
Specific exemplar efforts that provide varying levels of FAIRnessterm·var are detailed later in this document. Additional issues, however, remain to be addressed. First, when community-endorsed vocabularies or other (meta)data standardsterm do not include the attributes necessary to achieve rich annotation, there are two possible solutions: either publish an extension of an existing, closely related vocabulary, or—in the extreme case—create and explicitly publish a new vocabulary resource, following FAIR principlesterm (‘I2’). Second, to explicitly identify the standardterm chosen when more than one vocabulary or other (meta)data standardterm is available, and given that for instance in the life sciences there are over 600 content standardsterm, the BioSharing registry ( https://biosharing.org/ ) can be of use as it describes the standardsterm in detail, including versions where applicable.
The Principles precede implementation These high-level FAIR Guiding Principlesterm precede implementation choicesterm, and do not suggest any specific technology, standardterm, or implementation-solution; moreover, the Principles are not, themselves, a standardterm or a specificationterm. They act as a guide to data publishers and stewards to assist them in evaluating whether their particular implementation choicesterm are rendering their digital research artefacts Findable, Accessible, Interoperable, and Reusable. We anticipate that these high level principles will enable a broad range of integrative and exploratory behaviours, based on a wide range of technology choices and implementations. Indeed, many repositories are already implementing various aspects of FAIRterm·def using a variety of technology choices and several examples are detailed in the next section; examples include Scientific Data itself and how narrative data articles are anchored to a progressively FAIRterm·def structured metadataterm.
Examples of FAIRnessterm·var, and the resulting value-added Dataverseterm 7 : Dataverseterm is an open-source data repository softwareterm installed in dozens of institutions globally to support public community repositories or institutional research data repositories. Harvard Dataverseterm, with more than 60,000 datasets, is the largest of the current Dataverseterm repositories, and is open to all researchers from all research fields. Dataverseterm generates a formal citation for each depositterm, following the standardterm defined by Altman and King 13 . Dataverseterm makes the Digital Objectterm Identifier (DOI), or other persistent identifiersterm·var (Handles), public when the dataset is published (‘F’). This resolves to a landing page, providing access to metadataterm, data files, dataset terms, waivers or licenses, and version information, all of which is indexed and searchable (‘F’, ‘A’, and ‘R’). Depositsterm include metadataterm, data files, and any complementary files (such as documentation or code) needed to understand the data and analysis (‘R’). Metadataterm is always public, even if the data are restricted or removed for privacy issues (‘F’, ‘A’). This metadataterm is offered at three levels, extensively supporting the ‘I’ and ‘R’ FAIR principlesterm: 1) data citation metadataterm, which maps to DataCite schema or Dublin Core Terms, 2) domain-specific metadataterm, which when possible maps to metadataterm standardsterm used within a scientific domain, and 3) file-level metadataterm, which can be deep and extensive for tabular data files (including column-level metadataterm). Finally, Dataverseterm provides public machine-accessible interfaces to search the data, access the metadataterm and download the data files, using a token to grant access when data files are restricted (‘A’).
FAIRDOMterm ( http://fair-dom.org/about ): integrates the SEEK 14 and openBIS 15 platforms to produce a FAIR data and model management facilityterm for Systems Biology. Individual research assets (or aggregates of data and models) are identified with unique and persistent HTTP URLs, which can be registered with DOIs for publication (‘F’). Assets can be accessed over the Web in a variety of formats appropriate for individuals and/or their computers (RDF, XML) (‘I’). Research assets are annotated with rich metadataterm, using community standardsterm·var, formats and ontologies (‘I’). The metadataterm is stored as RDF to enable interoperabilityterm and assets can be downloaded for reuse (‘R’).
ISAterm 16 : is a community-driven metadata tracking frameworkterm to facilitate standards-compliant collection, curation, management and reuse of life science datasets. ISAterm provides progressively FAIRterm·def structured metadataterm to Nature Scientific Data’s Data Descriptor articles, and many GigaScience data papers, and underpins the EBI MetaboLights database among other data resources. At the heart is a general-purpose, extensible ISAterm model, originally only available as a tabular representation but subsequently enhanced as an RDF-based representation 17 , and JSON serializations to enable the ‘I’ and ‘R’, becoming ‘FAIRterm·def’ when published as linked data ( http://elixir-uk.org/node-events/201cisa-as-a-fair-research-object201d-hack-the-spec-event-1 ) and complementing other research objects 18 .
Open PHACTSterm 19 : Open PHACTSterm is a data integration platformterm for information pertaining to drug discovery. Access to the platform is mediated through a machine-accessible interface 20 which provides multiple representations that are both human (HTML) and machine readable (RDF, JSON, XML, CSV, etc), providing the ‘A’ facet of FAIRnessterm·var. The interface allows multiple URLs to be used to access information about a particular entity through a mappings service (‘F’ and ‘A’). Thus, a user can provide a ChEMBL URL to retrieve information sourced from, for example, Chemspider or DrugBank. Each call provides a canonical URL in its response (‘A’ and ‘I’). All data sources used are described using standardized dataset descriptions, following the global VoID standardterm, with rich provenanceterm·var (‘R’ and ‘I’). All interface features are described using RDF following the Linked Data API specificationterm (‘A’). Finally, a majority of the datasets are described using community agreed upon ontologies (‘I’).
wwPDBterm 4 , 21 : wwPDBterm is a special-purpose, intensively-curated data archiveterm that hosts information about experimentally-determined 3D structures of proteins and nucleic acids. All wwPDBterm entries are stably hosted on an FTP server (‘A’) and represented in machine-readable formats (text and XML); the latter are machine-actionable using the metadataterm provided by the wwPDBterm conforming to the Macromolecular Information Framework (mmCIF 22 ), a data standardterm of the International Union of Crystallography (IUCr) (‘F’,‘I’ for humans, ‘F’,‘I’ for IUCr-aware machines). The wwPDBterm metadataterm contains cross-references to common identifiers such as PubMed and NCBI Taxonomy, and their wwPDBterm metadataterm are described in data dictionaries and schema documents ( http://mmcif.wwpdbterm.org and http://pdbml.wwpdbterm.org ) which conform to the IUCr data standardterm for the chemical and structural biology domains (‘R’). A variety of software tools are available to interpret both wwPDBterm data and meta-data (‘I’,‘R’ for humans, ‘I’,‘R’ for machines with this software). Each entry is represented by a DOI (‘F’, ‘A’ for humans and machines). The DOI resolves to a zipped file which requires special software for further interrogation/interpretation. Other wwPDBterm access points 23–25 provide access to wwPDBterm records through URLs that are likely to be stable in the long-term (‘F’), and all data and metadataterm is searchable through one or more of the wwPDB-affiliated websites (‘F’) UniProtterm 26 : UniProtterm is a comprehensive resourceterm for protein sequence and annotation data. All entries are uniquely identified by a stable URL, that provides access to the record in a variety of formats including a web page, plain-text, and RDF (‘F’ and ‘A’). The record contains rich metadataterm (‘F’) that is both human-readable (HTML) and machine-readable (text and RDF), where the RDF formatted response utilizes shared vocabularies and ontologies such as UniProtterm Core, FALDO, and ECO (‘I’). Interlinking with more than 150 different databases, every UniProtterm record has extensive links into, for example, PubMed, enabling rich citation. These links are machine-actionable in the RDF representation (‘R’). Finally, in the RDF representation, the UniProtterm Core Ontology explicitly types all records, leaving no ambiguity—neither for humans nor machines—about what the data represents (‘R’), enabling fully-automated retrieval of records and cross-referencing information.
In addition to, and in support of, communities and resources that are already pursuing FAIRterm·def objectives, the Data Citation Implementation Groupterm of Force11 has published specific technical recommendations for how to implement many of the principles 27 , with a particular focus on identifiers and their resolution, persistence, and metadataterm accessibilityterm especially related to citation. In addition, the ‘Skunkworks’ group that emerged from the Lorentz Workshop has been creating software supporting infrastructures 28 that are, end-to-end, compatible with FAIR principlesterm, and can be implemented over existing repositories. These code modules have a particular focus on metadataterm publication and searchability, compatibility in cases of strict privacy considerations, and the extremely difficult problem of data and metadataterm interoperabilityterm (manuscript in preparation). Finally, there are several emergent projects, some listed in Box 3 , for which FAIRterm·def is a key objective. These projects may provide valuable advice and guidance for those wishing to become more FAIRterm·def.
FAIRnessterm·var is a prerequisite for proper data management and data stewardshipterm The ideas within the FAIR Guiding Principlesterm reflect, combine, build upon and extend previous work by both the Concept Web Allianceterm ( https://conceptweblog.wordpress.com/ ) partners, who focused on machine-actionabilityterm and harmonization of data structures and semantics, and by the scientific and scholarly organizations that developed the Joint Declaration of Data Citation Principlesterm (JDDCP 29 ), who focused on primary scholarly data being made citable, discoverable and available for reuse, so as to be capable of supporting more rigorous scholarship. An attempt to define the similarities and overlaps between the FAIR Principlesterm and the JDDCP is provided at ( https://www.force11.org/node/6062 ). The FAIR Principlesterm are also complementary to the ‘Data Seal of Approvalterm’ (DSA) ( http://datasealofapproval.org/media/filer_public/2013/09/27/guidelines_2014-2015.pdf ) in that they share the general aim to render data re-usable for users other than those who originally generated them. While the DSA focuses primarily on the responsibilities and conduct of data producers and repositories, FAIRterm·def focuses primarily on the data itself. Clearly, the broader community of stakeholders is coalescing around a set of common, dovetailed visions spanning all facets of the scholarly data publishing ecosystem.
The end result, when implemented, will be more rigorous management and stewardship of these valuable digital resources, to the benefit of the entire academic community. As stated at the outset, good data managementterm and stewardship is not a goal in itself, but rather a pre-condition supporting knowledge discovery and innovationterm. Contemporary e-Science requires data to be Findable, Accessible, Interoperable, and Reusable in the long-term, and these objectives are rapidly becoming expectations of agencies and publishers. We demonstrate, therefore, that the FAIR Data Principlesterm provide a set of mileposts for data producers and publishersterm. They guide the implementation of the most basic levels of good Data Management and Stewardship practiceterm, thus helping researchers adhere to the expectations and requirements of their funding agencies. We call on all data producers and publishersterm to examine and implement these principles, and actively participate with the FAIRterm·def initiative by joining the Force11 working group. By working together towards shared, common goals, the valuable data produced by our community will gradually achieve the critical goals of FAIRnessterm·var.
Additional Information How to cite this article: WilkinsonpersName, M. D. et al. The FAIR Guiding Principlesterm for scientific data management and stewardship. Sci. Data 3:160018 doi: 10.1038/sdata.2016.18 (2016).