Table 2 Potential suitability of TBox and ABox semantic graphs for meeting the FAIR Guiding Principles, using Semantic Phenotypes and Phenotype Knowledge Graphs as examples (criteria taken from [7], criteria for reusability not shown)
FINDABLE | ||
F1 | (meta) data are assigned a globally unique and persistent identifier | |
 Semantic Phenotype | ✓ | Semantic Phenotypes reference ontology classes through their URIs, including the class defining the phenotype. Ontologies provide persistent identifiers for kind terms and their associated universal statements. |
 Phenotype Knowledge Graph | ✓✓ | Phenotype Knowledge Graphs not only reference ontology classes like Semantic Phenotypes do, but also provide URIs for every particular descriptive statement, described part, property, quality, and relation and thus for kind terms, universal statements, proper names, and assertional statements. |
F2. | data are described with rich metadata | |
 Semantic Phenotype | ✓ | Metadata can be associated with a phenotype description as a whole, but not with each of the individual descriptive statements it comprises. |
 Phenotype Knowledge Graph | ✓✓ | Due to the possibility to organize a Phenotype Knowledge Graph into a set of named graphs, each of which documenting an individual descriptive statement, metadata can be associated on the fine granular level of particular descriptive statements of a phenotype description, in addition to the description as a whole. |
F3. | metadata clearly and explicitly include the identifier of the data it describes | |
 Semantic Phenotype | ✓ | Metadata can include an identifier that refers to the description as a whole, but not to individual descriptive statements. |
 Phenotype Knowledge Graph | ✓✓ | Metadata can include an identifier that refers to the description as a whole, but also identifiers that refer to each individual descriptive statement. |
F4. | (meta) data are registered or indexed in a searchable resource | |
 Semantic Phenotype | ✓✓ | Metadata can be expressed as TBox or ABox semantic graphs and stored in a tuple store. |
 Phenotype Knowledge Graph | ✓✓ | |
ACCESSIBLE | ||
A1. | (meta) data are retrievable by their identifier using a standardized communication protocol | |
 Semantic Phenotype | ✓ | Semantic Phenotypes and their metadata can be stored in a tuple store and queried with SPARQL. |
 Phenotype Knowledge Graph | ✓✓ | Phenotype Knowledge Graphs and their metadata can be stored in a tuple store and queried with SPARQL. Because particular descriptive statements, described parts, properties, qualities, and relations have their own URIs, they can be individually accessed. |
A1.1 | the protocol is open, free, and universally implementable | |
 Semantic Phenotype | ✓ | SPARQL |
 Phenotype Knowledge Graph | ✓ | |
A1.2 | the protocol allows for an authentication and authorization procedure, where necessary | |
 Semantic Phenotype | – | This depends on the application employing the concept of Semantic Phenotypes or Phenotype Knowledge Graphs. |
 Phenotype Knowledge Graph | – | |
A2. | metadata are accessible, even when the data are no longer available | |
 Semantic Phenotype | – | This depends on the application employing the concept of Semantic Phenotypes or Phenotype Knowledge Graphs. |
 Phenotype Knowledge Graph | – | |
INTEROPERABLE | ||
I1. | (meta) data use a formal, accessible, shared, and broadly applicable language for knowledge representation | |
 Semantic Phenotype | ✓ | Semantic Phenotypes and Phenotype Knowledge Graphs both can be represented in RDF/OWL. |
 Phenotype Knowledge Graph | ✓ | |
I2. | (meta) data use vocabularies that follow FAIR principles | |
 Semantic Phenotype | ✓ | Semantic Phenotypes and Phenotype Knowledge Graphs both use ontologies and other controlled vocabularies that provide URIs for their terms. |
 Phenotype Knowledge Graph | ✓ | |
I3. | (meta) data include qualified references to other (meta)data | |
 Semantic Phenotype | ✓ | This depends on how and which (meta) data are provided, but Semantic Phenotypes and their associated metadata can include cross-references and inter-relationships to other Semantic Phenotypes and their metadata. |
 Phenotype Knowledge Graph | ✓✓ | This depends on how and which (meta) data are provided, but Phenotype Knowledge Graphs and their associated metadata can include cross-references and inter-relationships to other Phenotype Knowledge Graphs and their metadata and that to a finer degree of granularity than Semantic Phenotypes due to the fact that they provide URIs to individual descriptive statements and to each described part, property, quality, and relation. |