Table 1 Potential suitability of TBox and ABox semantic graphs for meeting eScience-compliant data and metadata standards, using Semantic Phenotypes and Phenotype Knowledge Graphs as examples
TERMINOLOGY | ||
Concept standard | What is the meaning of a concept? What do we know of the corresponding kind? | |
 Semantic Phenotype | ✓✓ | Reference to ontology terms provides machine- and human-readable specifications of the meaning of concepts used in data (i.e., phenotype descriptions) and metadata statements. |
 Phenotype Knowledge Graph | ✓✓ | |
Nomenclatural standard | Which words or symbols are used for referring to a specific kind? | |
 Semantic Phenotype | ✓ | URIs, preferred labels, and synonyms provide unambiguous reference of a kind term to its underlying class definition. However, entities (i.e., parts, properties, qualities, relations) mentioned in class axioms are referenced only anonymously. |
 Phenotype Knowledge Graph | ✓✓ | Same as with Semantic Phenotypes, with the addition that each particular descriptive statement, described part, property, quality, and relation of data and metadata statements of Phenotype Knowledge Graphs possess their own URI and can be individually referenced. |
ASSERTIONS | ||
Format standard | Which syntax and file format must be used? | |
 Semantic Phenotype | ✓ | Semantic Phenotypes can be documented in RDF/OWL, which provides a machine-actionable syntax and format. SPARQL can be used for querying, but querying is computationally more difficult than querying Phenotype Knowledge Graphs. |
 Phenotype Knowledge Graph | ✓✓ | Phenotype Knowledge Graphs can be documented in RDF/OWL, which provides a machine-actionable syntax and format. SPARQL can be used for querying. Querying Phenotype Knowledge Graphs is computationally less difficult than querying Semantic Phenotypes. |
Content standard | Which information is relevant? How must it be modeled? | |
 Semantic Phenotype | ✓ | The use of domain-specific semantic data models in Semantic Phenotypes provides a basic categorization and classification of contents relevant for a given domain. |
 Phenotype Knowledge Graph | ✓✓ | The use of domain-specific semantic data models in Phenotype Knowledge Graphs provides a basic categorization and classification of contents relevant for a given domain. With the identification of individual descriptive statements, parts, properties, qualities, and relations, Phenotype Knowledge Graphs can be categorized and classified at various levels of granularity, including levels finer than it is possible with Semantic Phenotypes. |