The FAIR Principles explicitly require the use of FAIR vocabularies, but what precisely constitutes a FAIR vocabulary remains unclear. Here we provide de nitions for FAIR vocabularies, examine the application of the FAIR Principles to vocabularies, align their requirements with the Open Biomedical Ontologies (OBO) Principles, and propose FAIR Vocabulary Features (FVFs). We also design assessment approaches for FAIR vocabularies by mapping the FVFs with existing FAIR assessment indicators. Finally, we demonstrate how FVFs can be used for evaluating and improving vocabularies using exemplar biomedical vocabularies.
The Findable, Accessible, Interoperable and Reusable (FAIR) Principles [
†To whom correspondence should be addressed.
Copyright © 2022 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0). data, which are usually generated, annotated and used by di erent groups of researchers. FAIR vocabularies promote biomedical data FAIRness throughout the data life cycle, during the data generation, curation, and distribution processes, and support data exchange and integration across data resources.
Multiple e orts have been made to develop standards for FAIR
vocabularies. The FAIRsFAIR recommendations provide guidance[
Garijo and Poveda-Villalon[
Researchers have also developed approaches to assess the FAIR level of digital
objects both manually and automatically; FAIRsharing hosts FAIR indicators
for automated tests in their FAIR Maturity Evaluation Service[
Therefore, in this paper, we distinguish the concepts of FAIR data, FAIR data
resources, and FAIR vocabularies, and propose a set of general FAIR Vocabulary
Features (FVFs) as a set of satis able features for vocabularies. We also adapted
the RDA indicators to measure the FAIR level of vocabularies. Further, we
provide example assessments based on selected ontologies available from the
EMBL-EBI Ontology Lookup Service (OLS)[
FAIR Data and FAIR Vocabulary In the execution of this work, we note the distinction between FAIR data and FAIR capable data resources. In our analysis, data can be FAIR, to a greater or lesser extent, and data resources and data vocabularies are capable of supporting FAIRness (FAIR capable) at di erent levels. Data vocabularies are designed to support FAIR data, and they can also be considered as FAIR data resources.
The orthogonality of these concepts is an important context for this work when determining the features of a FAIR vocabulary. We must also determine whether a vocabulary itself is 1) FAIR in terms of its application to FAIR data 2) FAIR in the context of FAIR capable resources 3) FAIR in the context of other vocabularies. A FAIR vocabulary has a set of FAIR features and have a list of associated FAIR indicators. It is usable for annotation, analysis and presentation of data, and is deployable in the context of a FAIR capable data resource or tools. It also serves 'aggregation' use cases where data originates from di erent domain, and enables data interoperability where di erent vocabularies are used.
Vocabularies come in di erent forms, such as lists, thesaurus, taxonomies,
and ontologies; each at di erent levels of semantic maturity and FAIR
requirements. The International Classi cation of Diseases (ICD-11)[
Existing Vocabulary Standards
In determining features of FAIR vocabularies, we considered previous
standardisation work by the Open Biomedical Ontology (OBO) community to determine
whether the OBO Principles[
The OBO Principles aim to coordinate the development of biomedical ontologies, which focus speci cally on ontologies, covering both the development of ontologies and ontology themselves. Despite the OBO principles predating the FAIR principles, a comparison of the two aided us in de ning FVFs. Table 1 summarises the key points of the OBO Foundry principles, and assesses their suitability as FVFs. We also noted that not all the OBO principles possess the same level of maturity or granularity, and therefore some were unmappable and excluded from the comparison. As a result, this analysis did not include OBO Principle 1, 4, 6, 9 - 12 and 20. The rationale for suitability as FVFs is discussed in detail below and further in Supplemental Table 1. 4
FAIR Vocabulary Features Based on the analysis of OBO foundry practices and our previous experience working with and developing ontologies, we propose eleven features for FAIR vocabulary in Table 2, covering requirements for identi ers, access protocols, knowledge representation, etc. Supplementary Table 2 shows the relationship among FAIR Vocabulary Features, the FAIR principles and requirements for FAIR vocabularies.
Table 2also provides examples for each FAIR feature, but does not exhaustively cover all current practices across the various vocabularies; each feature is represented in di erent formats and at varying FAIRness levels amongst those vocabularies. For example, for FVF-6: versioning and persistent vocabularies, of all ontologies indexed and updated in OLS, 59.3%§ of vocabularies use a date format of "yyyy-mm-dd" in the "versionIRI", such as "http://purl.obolibrary.org/
§See details in Supplementary Material 3 ID OBO Principle Summary Suitable as FAIR Vocabulary Feature? Principle 1: Open The ontology MUST be openly available to be used by No all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed in altered form under the original name or with the same identi ers.
Principle 2: Com- The ontology is made available in a common formal lan- Yes mon Format guage in an accepted concrete syntax.
Principle 3: Each class and relation (property) in the ontology must Yes URI/Identi er have a unique URI identi er.
Space Principle 4: Ver- The ontology provider has documented procedures for ver- No sioning sioning the ontology, and di erent versions of ontology are
marked, stored, and o cially released.
Principle 5: Scope The scope of an ontology is the extent of the domain or Yes subject matter it intends to cover. The ontology must have a clearly speci ed scope and content that adheres to that scope.
Principle 6: Tex- The ontology has textual de nitions for the majority of No tual De nitions its classes and for top level terms in particular Principle 7: Rela- Relations should be reused from the Relations Ontology Yes tions (RO).
Principle 8: Docu- The owners of the ontology should strive to provide Yes mentation as much documentation as possible. The documentation should detail the di erent processes speci c to an ontology life cycle and target various audiences (users or developers).
Principle 9: Docu- The ontology developers should document that the ontol- No mented Plurality ogy is used by multiple independent people or organizaof Users tions.
Principle 10: OBO Foundry ontology development, in common with Yes Commitment to many other standards-oriented scienti c activities, should Collaboration be carried out in a collaborative fashion.
Principle 11: Lo- There should be a person who is responsible for communi- No cus of Authority cations between the community and the ontology developers, for communicating with the Foundry on all Foundryrelated matters, for mediating discussions involving maintenance in the light of scienti c advance, and for ensuring that all user feedback is addressed.
Principe 12: Nam- Naming conventions are used No ing Conventions Principle 16: The ontology needs to re ect changes in scienti c consen- Yes Maintenance sus to remain accurate over time.
Principle 20: Re- Ontology developers MUST o er channels for community No sponsiveness participation and SHOULD be responsive to requests. -obo/scdo/releases/2021-04-15/scdo.owl". 2.51% of vocabularies use semantic versioning (x.x.x) such as "http://www.ebi.ac.uk/efo/releases/v3.34.0/efo.owl" or other forms of numeric versioning, such as http://www.orpha.net/version3.2. 31.66% of vocabularies do not provide valid machine-readable versioned IRIs. For FVF-1: identi ers, 74% of vocabularies use OBO-format PURLs, identi er.org, w3id.org identi ers, as well as other domain-speci c identi ers. For FVF-5: accessible using standard protocols, of all 199 selected ontologies, only one ontology used the HTTPS protocol; the rest use HTTP protocols. 5
FAIR Vocabulary Feature Indicators FAIR vocabulary Features outline general characteristics of a FAIR vocabulary, however, those features need to be objectively quanti ed to be useful in vocabulary selection, development and assessment. Hence, we propose aligning FVFs with FAIR indicators to enable computation of a discrete FAIR score, with the aim to o er an objective quantitative evaluation of vocabularies and to guide subsequent improvements.
We mapped the RDA indicators to FAIR Vocabulary Features, ltered out indicators that do not apply to vocabularies (see details in Supplementary Table 4, speci ed the digital object which the indicator refers to, and identi ed within each indicator the relevant standards used in corresponding domains. It is worth noting that when mapping the RDA indicators on datasets, metadata refers to the metadata to which the vocabulary can be applied, while in the context of vocabularies, metadata and data refer to the description of the vocabulary and the vocabulary information. Therefore, we combined the indicators evaluating data and metadata in the mapping, wherever possible. The FVFs, associated with selected indicators, can be used as indicators for FAIR Vocabulary as shown in Table 3. 6
Assessment against Indicators for FAIR Vocabulary
Features We tested the FAIR Vocabulary Features and corresponding indicators on three representative vocabularies, GO, EFO and ICD-11, as shown in Table 4. For each FVF, three compliance levels are assigned; if a vocabulary meets the requirements of all indicators, full compliance is achieved. Otherwise, depending on the scoring within each FVF, partial compliance or no compliance results are given. The percentages of full compliance, partial compliance and no compliance features are also calculated. Supplementary Table 5-7 provide the assessment details.
From the assessment results, both the Gene Ontology and Experimental Factor Ontology are vocabularies of high FAIR level, with over 80% FVFs ful lled.
The Gene Ontology only partially complies with `FVF-6: Vocabularies and their terms are persistent over time and are appropriately versioned ', with a Fail in
FVF-4: Vocabularies and their terms are reg- RDA-F4-01M istered or indexed in a searchable engine or a resource.
FVF-5: Vocabularies and their terms are retrievable using a standardised communications protocol, preferably open, free and universally RDA-A1-04M implementable protocols. and allows for authentication and authorisation, where necessary.
FVF-6: Vocabularies and their terms are persistent over time and are appropriately versioned.
FVF-7: Vocabularies and their terms use a formal, accessible and broadly applicable, and preferably machine-understandable language for knowledge representation.
FVF-8: Vocabularies and terms use quali ed RDA-I3-02D references to other vocabularies.
FVF-9: Vocabularies and terms are described RDA-R1-01M with a plurality of accurate and relevant attributes.
FVF-10: Vocabularies are released with a standard data usage licence, preferably machine- RDA-R1.1-01M readable licence.
FVF-11: Vocabularies meet domain relevant community standards.
RDA ID RDA-F1-01D RDA-F1-02M RDA-A1-02M RDA-A1-02D RDA-A1-03M RDA-A1-03D RDA-A1-05D RDA-A1-04D RDA-A1.1-01M RDA-A1.1-01D RDA-A1.2-01D RDA-A2-01M RDA-R1.2-01M RDA-R1.2-02M RDA-I1-01M RDA-I1-01D RDA-I1-02M RDA-I1-02D RDA-I3-03M RDA-R1.1-02M RDA-R1.1-03M RDA-R1.3-01M RDA-R1.3-01D RDA-R1.3-02M RDA-R1.3-02D
Metadata is identi ed by a persistent identi er
Data is identi ed by a persistent identi er
Metadata is identi ed by a globally unique
identi er
Data is identi ed by a globally unique identi er
Rich metadata is provided to allow discovery
Metadata contains information to enable the
user to get access to the data
Metadata can be accessed manually (i.e. with
human intervention)
Data can be accessed manually (i.e. with
human intervention)
Metadata identi er resolves to a metadata
record
Data identi er resolves to a digital object
Data can be accessed automatically (i.e. by a
computer program)
Metadata is o ered in such a way that it can
be harvested and indexed
Metadata is accessed through standardised
protocol
Data is accessible through standardised
protocol
Metadata is accessible through a free access
protocol
Data is accessible through a free access protocol
Data is accessible through an access protocol
that supports authentication and authorisation
Metadata is guaranteed to remain available
after data is no longer available
Metadata includes provenance information
according to community-speci c standards
Metadata includes provenance information
according to a cross-community language
Metadata uses knowledge representation
expressed in standardised format
Data uses knowledge representation expressed
in standardised format
Metadata uses machine-understandable
knowledge representation
Data uses machine-understandable knowledge
representation
Data includes quali ed references to other data
Metadata includes quali ed references to other
metadata
Plurality of accurate and relevant attributes
are provided to allow reuse
Metadata includes information about the
licence under which the data can be reused
Metadata refers to a standard reuse licence
Metadata refers to a machine-understandable
reuse licence
Metadata complies with a community standard
Data complies with a community standard
Metadata is expressed in compliance with a
machine-understandable community standard
Data is expressed in compliance with a
machine-understandable community standard
`Indicator RDA-R1.2-02M: Metadata includes provenance information according
to a cross-community language '. `FVF-2: Vocabularies and their terms have rich
metadata' was not complied with since no general description of the ontology is
provided in the released artefact. Compared with the ontologies, the taxonomy,
ICD-11, fully complies with 18.18% FVFs, and partially complies with 36.36%
FVFs. This is because ICD-11 neither refers to other vocabularies, nor adheres
to other community standards, such as vocabulary formats. ICD-11 was selected
for this evaluation as it already o ers signi cant FAIR improvements over
ICD10[
The FAIR Vocabulary Features we propose integrate multiple FAIR vocabulary requirements and can be used as FAIR vocabulary standards to guide the development and maintenance of vocabularies. Each FVF is associated with indicators enabling its quanti able, objective assessment. Those indicators can be connected to related standards and extended to existing or emerging standards in other domains. For example, FVF-8: cross-referencing other vocabularies can be linked to the ontology cross-reference standards, MIREOT. We focused on how FVFs can be applied to ontologies, and demonstrated the potential for using them across other forms of vocabularies; for example, with the ICD-11, assessment would inform authors on the means to enrich their resources. Because of our expertise and requirements, this manuscript focuses on the biomedical domain; however, we anticipate this framework could be reused in other domains.
Integrating the FAIR vocabulary features with FAIR indicators makes it possible to assess the FAIR level of vocabularies, identify progressive ontology development use cases, and improve those vocabularies. We selected the RDA indicators as it has proven to be useful in many datasets and has been referenced by other assessment approaches in FAIRassist.org; yet, FVFs could alternatively be aligned to other FAIR-principle based indicators which would similarly re ect the guiding principles proposed by Wilkinson et al. Besides manual assessment, quanti able formal indicators are also amenable to becoming machine actionable.
Some e orts already exist, and reusing shared indicators will make it possible to perform automated FAIR vocabulary assessments.
The indicators were proposed to objectively measure the FAIR level of ontologies, yet this score does not re ect an absolute FAIR level for the vocabulary. Indeed, depending on the purpose and requirements of the vocabulary, some FVFs can be more or less important than other features. For example, for internal vocabularies which are used and shared within an institution, having global identi ers (FVF-1) is not a mandatory requirement. Instead of comparing the FAIR score of di erent vocabularies to nd the `FAIRer' one, we propose the FAIR score should be used to measure and guide the evolution of FAIR vocabularies by successively comparing the FAIR levels of iteratively developed versions. For example, compared to ICD-10, its successor, ICD-11 has incorporated many features to make it FAIRer, such as providing APIs for easier access, having a machine-readable license, etc.
From the assessment results of the two ontologies and ICD-11, ontology-based
vocabularies follow stricter semantics and therefore fared better in the scoring of
FAIR features. For example, many ontology-related standards have been
established, including formats, such as OWL, guidelines such as the OBO principles,
minimum information standards, such as MIBBI[
The FAIR Vocabulary features and assessments provide insights on how to improve vocabularies. For example, based on the EFO assessments, the FAIR level of EFO could easily be improved by adding a description of the aim and function of EFO. This way, di erent vocabulary management services can harvest the information.
Acknowledgements This work is funded by the IMI-FAIRplus project (Grant number 802750) and the European Molecular Biology Laboratory - European Bioinformatics Institute core funds. 8 Supplementary Table 1: The suitability of OBO principles used as FAIR
OBO-1: The ontology MUST be openly available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and Suitable as FAIR subsequently redistributed in altered form under the Vocabulary Feature? original name or with the same identifiers. No While it is highly desirable to have open source semantic artefacts, as it is to have open source code and ultimately open research. This is not a prerequisite for vocabularies to be FAIR, nor is it well aligned with the FAIR principles which require licensing information to be provided but do not mandate it be open source.
OBO-2: The ontology is made available in a common formal language in an accepted concrete syntax.
Common formats define minimum standards for accessing an ontology, support using ontologies in a FAIR capable resource, and are the foundation of interoperable vocabulary. Many common formal languages have been proposed during the development history of ontologies. OWL format is currently used as a W3C standard. OBO-3: Each class and relation (property) in the ontology must have a unique URI identifier.
Identifiability is a core FAIR principle, and in order to be fulfilled, all elements of the ontology, such as classes and relationships, should be clearly and uniquely identified. OBO-4: The ontology provider has documented procedures for versioning the ontology, and different versions of ontology are marked, stored, and officially released.
Proper versioning improves the findability and reusability of the vocabulary. We proposed a corresponding FVF to cover this aspect. Yet, this principle evaluates the development, especially the documentation process, of the ontology rather than FAIR vocabulary.
OBO-5: The scope of an ontology is the extent of the domain or subject matter it intends to cover. The ontology must have a clearly specified scope and content that adheres to that scope.
Users must be able to determine which ontologies meet their needs in order to implement these in FAIR capable resources and to be interoperable with other vocabularies. A clear specification of this aids in FAIR implementation; vocabularies do not exist in isolation. OBO-6: The ontology has textual definitions for the majority of its classes and for top level terms in particular While textual definitions provide human-readable content and are generally desirable, this is not essential as an FVF as ontology content has definitions in terms of logical axioms (e.g., position in the hierarchy) and term labels.
OBO-7: Relations should be reused from the Relations Ontology (RO).
Relation standards promote interoperability across different ontologies. This principle focuses on the relationships within and across ontologies. It can be adapted and used in a broader range of FAIR vocabularies. OBO-8: The owners of the ontology should strive to provide as much documentation as possible. The documentation should detail the different processes specific to an ontology life cycle and target various audiences (users or developers). Rich metadata of the vocabulary, such as the purpose and status of the ontology, promotes the reuse of the ontology.
OBO-9: The ontology developers should document that the ontology is used by multiple independent people or organizations. Usage of vocabularies depends on the content and there are strategies for interoperating ontologies in what is anyway a crowded semantic space. Evidence that an ontology is highly used - when measurable - assumes a level of maturity that is unlikely for some starting communities, and would not reflect fairness of the resource. OBO-10: OBO Foundry ontology development, in common with many other standards-oriented scientific activities, should be carried out in a collaborative fashion.
Vocabularies should be implementable in FAIR data resources and should reflect community needs. Responsiveness to community needs comes via collaboration and development should therefore be collaborative.
OBO-11: There should be a person who is responsible for communications between the community and the ontology developers, for communicating with the Foundry on all Foundry-related matters, for mediating discussions involving maintenance in the light of scientific advance, and for ensuring that all user feedback is addressed.
Having a designed contact is important for the community to provide feedback and ensures someone is having an ongoing editorial responsibility for the ontology. While it does pertain to sustainability of the resource and its possible evolution, it doesn’t directly speak to its level of fairness.
OBO-12: Naming conventions are used Consistency of naming is a best practice feature of ontologies but does not detract from deployment in support of the FAIR principles.
OBO-16: The ontology needs to reflect changes in scientific consensus to remain accurate over time.
Vocabularies codify knowledge. To fulfil one of their primary functions, they must evolve. Dead ontologies fail to support FAIR capable resources to interoperate. OBO-20: Ontology developers MUST offer channels for community participation and SHOULD be responsive to requests. Having communication channels to collect and respond to community requirements supports the maintenance and evolution of the ontology. However, it is not directly linked to the FAIRness of the vocabulary. Supplementary Table 2: FAIR Vocabulary Features mapped to FAIR principles and FAIR vocabulary requirements
Findability Accessibility Interoperability Reusability FAIR in terms of application to FAIR data.
FAIR in terms of serving as a FAIR data resource.
FAIR in the context of interacting with other vocabularies.
FVF-1 FVF-4 FVF-6
FVF-3 FVF-5 FVF-10
FVF-11 FVF-7 FVF-8
FVF-2 FVF-6 FVF-9 FVF-10 FVF-11 FVF-2 FVF-6 FVF-7 FVF-9 Supplementary Materials 3: VersionIRI analysis We fetched ontologies indexed in the OLS repository and selected those that are successfully loaded and up-to-date. OLS contains 266 biomedical ontologies by the time we access the database (https://www.ebi.ac.uk/ols/api/ontologies). We filtered out ontologies which could not be indexed automatically (without a valid loaded timestamp), and removed inactive ontologies based on the date information in the versionIRI section. 200 ontologies are selected based on these criteria.
We recognise the limitations of the ontology selection approaches. The filtering relys on the metadata collected by OLS instead of the ontology itself, and therefore might not correctly reflect the ontology status. We filted out some inactive ontologies based on the loading time (only ontologies with a loading timestamp after 2019-01-01 are choosen) and date information in the versioneIRI (ontologies with date before 2019-01-01 in the verionIRI are removed). But these criterias does not ensure all vocabularies selected are up-to-date. For example, for ontologies using semantic versioning format where no date information is provided in the versionIRI, or some update information are collected in other metadata fields such as 'annotation' 'editor comments', etc.
Despite the constraints of the analysis, it still provides enough information to showcase the status of current vocabularies. A complete list of selected ontologies are provided in the table below.
RDA-F3-01M Metadata includes the identifier for the data RDA-I2-01M Metadata uses FAIR-compliant vocabularies RDA-I2-01D Data uses FAIR-compliant vocabularies RDA-I3-01M Metadata includes references to other metadata RDA-I3-01D Data includes references to other data RDA-I3-02M Metadata includes references to other data
RDA-I3-04M Metadata include qualified references to other data Supplementary Table 5: FAIR assessment results of Gene ontology https://github.com/geneontology/go-ontology and http://geneontology.org/ FAIR vocabulary feature summary FVF, full compliance FVF, partial compliance RDA-F1- Metadata is identified by 01M a persistent identifier RDA-F1- Data is identified by a 01D persistent identifier
Metadata is identified by RDA-F1- a globally unique identifier 1 1 FVF-1: Vocabulary and 02M 1 their terms are assigned Full http://purl.obolibrary.org/ globally unique and RDA-F1- Data is identified by a Complia obo/go.owl is globally persistent identifiers. 02D globally unique identifier 1 nce unique identifier.
Assessment details Metadata are provided in http://geneontology.org/ docs/ontology-documen tation/. It can also be found in the OBO foundry repository https://github.com/OBO Foundry/OBOFoundry.g ithub.io/edit/master/onto logy/go.md. But they are not standard persistent identifiers.
Gene ontology uses PURL identifiers http://purl.obolibrary.org/ obo/go.owl http://geneontology.org/ docs/ontology-documen tation/ is globally unique identifier.
Metadata contains information to enable RDA-A1- the user to get access 01M to the data
Metadata can be accessed manually (i.e.
RDA-A1- with human 02M intervention)
Data can be accessed RDA-A1- manually (i.e. with 02D human intervention)
Metadata identifier RDA-A1- resolves to a metadata 03M record FVF-3: Vocabularies and their terms can be 03D
accessed using the identifiers, preferably by both human and machine.
RDA-A1- Data identifier resolves to a digital object
Data can be accessed RDA-A1- automatically (i.e. by a 05D computer program)
Data can be Full downloaded using
Complia command line tools, 1 nce such as curl, wget, etc.
Gene ontology has been indexed by EMBL OLS, BioPortal and other semantic Full repositories. Also it is
Complia indexed in Google 1 nce search.
Descriptive text is provided in http://geneontology.org.
Rich metadata for indexing and reuse is provided in https://github.com/OBO Full Foundry/OBOFoundry.g
Complia ithub.io/edit/master/onto 1 nce logy/go.md.
The metadata includes data download links http://geneontology.org/ docs/download-ontology /.
The metadata can be accessed from the gene ontology website.
Data can be downloaded from http://geneontology.org/ docs/download-ontology / http://geneontology.org/ docs/ontology-documen tation// is resolvable and directs to the metadata.
The vocabulary identifier http://purl.obolibrary.org/ obo/go.owl resolves to the ontology source files. Identifiers such as http://purl.obolibrary.org/ obo/GO_0098743 resolves to ontology terms. 1 1 1 1 1 FVF-5: Vocabularies and their terms are retrievable using a
standardised communications protocol, preferably open, free and
universally implementable protocols. and allows for authentication and authorisation, where necessary.
Data is accessible RDA-A1- through standardised 04D protocol
Metadata is accessible RDA-A1. through a free access 1-01M protocol
Data is accessible RDA-A1. through a free access 1-01D protocol
Data is accessible through an access protocol that supports RDA-A1. authentication and 2-01D authorisation
Metadata is guaranteed to remain available after RDA-A2- data is no longer 01M available
Metadata includes provenance information according to RDA-R1. community-specific 2-01M standards FVF-6: Vocabularies and their terms are persistent over time and are appropriately versioned.
Metadata includes provenance information according to a RDA-R1. cross-community 2-02M language
Partial
Complia 0 nce Metadata uses knowledge representation
RDA-I1- expressed in FVF-7: Vocabularies 01M standardised format and their terms use a formal, accessible and broadly applicable, and
preferably machine-understandabl 01D e language for
knowledge representation.
Data uses knowledge representation RDA-I1- expressed in standardised format
Metadata uses RDA-I1- machine-understandabl 02M e knowledge
The metadata can be accessed through the HTTP protocol.
Data can be accessed through HTTP protocol.
HTTP is a free access protocol.
HTTP is a free access protocol.
Metadata and data can be found in version controlled repositories on Github.
The metadata includes links to access different snapshots of the ontology. The snapshots are in owl/obo format and has PURL identifiers.
The metadata is provided in a standard format and can be harvested by major vocabulary serivices, such as OLS and BioPortal.
The data uses OWL and OBO standards.
HTTP HTTP allows access control. But authentication and Full authorisation are not
Complia required by Gene NA nce Ontology.
Full
Complia Basic metadata is 1 nce provided in OWL. 1 1 1 1 1 1 1 1
FVF-8: Vocabularies and terms use qualified references to other
vocabularies.
FVF-9: Vocabularies and terms are described with a plurality of accurate and relevant attributes.
FVF-10: Vocabularies are released with a standard data usage licence, preferably machine-readable
licence.
representation
Plurality of accurate and RDA-R1 relevant attributes are -01M provided to allow reuse
Metadata includes information about the RDA-R1. licence under which the 1-01M data can be reused RDA-R1. Metadata refers to a 1-02M standard reuse licence
Metadata refers to a RDA-R1. machine-understandabl 1-03M e reuse licence RDA-R1. Metadata complies with 3-01M a community standard RDA-R1. Data complies with a 3-01D community standard
Metadata is expressed in compliance with a RDA-R1. machine-understandabl 3-02M e community standard 1 1 1 1 1 1 1 1 1 1
The GO data uses OWL and OBO formats, which are machine-readable community formats.
The Gene ontology cross reference policy is here: http://geneontology.org/ docs/download-mappin gs/ Data from other vocabularies are provided as 'xref'/ The Gene ontology cross reference policy is provided here: Full http://geneontology.org/ Complia docs/download-mappin nce gs/
Gene Ontology includes sufficient term Full attributes.
Complia http://geneontology.org/ nce docs/GO-term-elements
Gene Ontology Consortium data and data products are licensed under the Creative Commons Attribution 4.0 Unported
License. 1 FAIR vocabulary Feature RDA-F1- Metadata is identified by 01M a persistent identifier RDA-F1- Data is identified by a 01D persistent identifier
Metadata is identified by FVF-1: Vocabulary and RDA-F1- a globally unique their terms are assigned 02M identifier 1 globally unique and RDA-F1- Data is identified by a persistent identifiers. 02D globally unique identifier 1 Supplementary Table 6: FAIR assessment results of Experimental Factor
FAIR vocabulary feature summary
FVF-3: Vocabularies and their terms can be accessed using the FVF-4: Vocabularies and their terms are Metadata is offered in registered or indexed in such a way that it can a searchable engine or RDA-F4- be harvested and a resource. 01M indexed FVF-5: Vocabularies and their terms are retrievable using a standardised communications protocol, preferably open, free and universally implementable protocols. and allows for authentication and authorisation, where necessary.
Metadata is accessed RDA-A1- through standardised 04M protocol
Data is accessible RDA-A1- through standardised 04D protocol
Metadata is accessible RDA-A1. through a free access 1-01M protocol
Data is accessible RDA-A1. through a free access 1-01D protocol
Data is accessible through an access protocol that supports RDA-A1. authentication and 2-01D authorisation
Metadata is guaranteed to remain available after RDA-A2- data is no longer 01M available 1 1 1 1 1 1 1 1 1 1
The metadata is provided in OWL format Full and has been harvested Complia by both OLS and nce BioPortal
EFO can be accessed using HTTP protocol, and it is an open-acess ontology.
EFO follows vocabulary release guidelines, and its versioned copies can be found on Github. But it doesn't strictly follows Partial cross community Complia language standards, nce such as rdfs, xmls FVF-7: Vocabularies and their terms use a formal, accessible and broadly applicable, and preferably machine-understandabl e language for knowledge representation.
FVF-8: Vocabularies and terms use qualified references to other vocabularies.
FVF-9: Vocabularies and terms are described with a plurality of accurate and relevant attributes.
FVF-10: Vocabularies are released with a standard data usage licence, preferably machine-readable RDA-I3- Data includes qualified 02D references to other data 1
Metadata includes RDA-I3- qualified references to 03M other metadata
Plurality of accurate and RDA-R1 relevant attributes are -01M provided to allow reuse
Metadata includes information about the RDA-R1. licence under which the 1-01M data can be reused 1 0 1 1 1 1 1 1
Full Complia nce Full Complia nce Full Complia nce
EFO can be downloaded in OWL and OBO, which are standardised format and machine-understandabl e.
EFO reuses terms from other vocabularies and provides suffient reference, such as source of the external term.
FVF-11: Vocabularies meet domain relevant community standards.
Metadata refers to a RDA-R1. machine-understandabl 1-03M e reuse licence RDA-R1. Metadata complies with 3-01M a community standard RDA-R1. Data complies with a 3-01D community standard
Metadata is expressed in compliance with a RDA-R1. machine-understandabl 3-02M e community standard
Data is expressed in compliance with a RDA-R1. machine-understandabl 3-02D e community standard 1 1 1 1 1
Full Complia nce
EFO uses the standard OWL format, complies with OBO principles and imports terms following the MIREOT standards.
Supplementary Table 7: FAIR assessment results of ICD-11 FAIR vocabulary feature summary 05/2021 ICD-11 browser and ICD11 print version:https://icd.who.int/en print version:https://icd.who.int/browse11/Downloads/Download? fileName=print_en.zip FAIR vocabulary Feature RDA-F1- Metadata is identified by 01M a persistent identifier RDA-F1- Data is identified by a 01D persistent identifier
Metadata is identified by RDA-F1- a globally unique 02M identifier FVF-1: Vocabulary and their terms are assigned globally unique and persistent identifiers.
RDA-F1- Data is identified by a 02D globally unique identifier 0
Metadata is accessed RDA-A1- through standardised 04M protocol
Data is accessible RDA-A1- through standardised 04D protocol
Metadata is accessible RDA-A1. through a free access 1-01M protocol
Data is accessible RDA-A1. through a free access 1-01D protocol
Data is accessible through an access protocol that supports RDA-A1. authentication and 2-01D authorisation 1 1 1 0 1 1 0 1 1 1 1 FVF-3: Vocabularies and their terms can be accessed using the identifiers, preferably by both human and machine.
FVF-4: Vocabularies and their terms are Metadata is offered in registered or indexed in such a way that it can a searchable engine or RDA-F4- be harvested and a resource. 01M indexed FVF-5: Vocabularies and their terms are retrievable using a standardised communications protocol, preferably open, free and universally implementable protocols. and allows for authentication and authorisation, where necessary.
ICD-11 uses HTTPS protocol.https://icd.who.i nt/browse11/l-m/en#http %3a%2f%2fid.who.int% 2ficd%2fentity%2f91170 7612
Metadata includes provenance information according to RDA-R1. community-specific 2-01M standards
Metadata uses knowledge representation RDA-I1- expressed in 01M standardised format
Data uses knowledge representation RDA-I1- expressed in 01D standardised format
Metadata uses machine-understandabl RDA-I1- e knowledge 02M representation
Data uses machine-understandabl RDA-I1- e knowledge 02D representation RDA-I3- Data includes qualified 02D references to other data 0
Metadata includes RDA-I3- qualified references to 03M other metadata 1 1 0 0 0 0 0 1
FVF-8: Vocabularies and terms use qualified references to other vocabularies.
Previous versions of ICD-11 can access at https://icd.who.int/brows e11/l-m/en/releases.
However, the versioning style does not follow common community standards.
ICD-11 is published mainly as a pdf document and doesn't use standard vocabulary formats.
No Complia nce
Terms in ICD-11 doesn't refer to other terms.
Partial The ICD-11 description Complia refers to other projects nce and publications.
Plurality of accurate and RDA-R1 relevant attributes are -01M provided to allow reuse
ICD-11 contains only a minimum description of each disease.
FVF-10: Vocabularies are released with a standard data usage licence, preferably machine-readable licence. RDA-R1. Metadata refers to a 1-02M standard reuse licence 1
Metadata refers to a RDA-R1. machine-understandabl 1-03M e reuse licence
Data is expressed in compliance with a RDA-R1. machine-understandabl 3-02D e community standard 0