Core model SIO
- Identifier: Base rdf:type sio:identifier: a label that specifically refers to (identifies) an entity (instance/type).
- Entity: Base rdf:type sio:object: An object is an entity that is wholly identifiable at any instant of time during which it exists. The entity may be a Person or a Machine. The entity MUST be involved in a Process via it's Role node.
- Role: Base rdf:type sio:role: describes behaviours, rights and obligations of an entity in some particular circumstance.
- Process: Base rdf:type sio:process: identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists.
- Quality: Base rdf:type sio:quality: an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary.
- Measurement value OR quality OR phenotype:
- specific type for quantitative rdf:type sio:measurement-value: a quantitative description that reflects the magnitude of some attribute.
- specific base type for qualitative rdf:type sio:object-quality
- e.g. sio:phenotype: an observable characteristic of an individual.
- Every beige node must have a unique identifier
- We recommend using the base URI of the overall document, followed by a document-fragment, followed by some unique id
- Regarding the re-use of nodes, we have the following advice:
- Every measurement value or phenotype MUST have a novel unique identifier
- Quality node URIs MAY be re-used to refer to the same quality of the same individual over multiple observations; however, distinct URIs MUST be anticipated by agents
- (this recognizes that it will not always be possible for a data entry process to look-up the URI of the Quality node from a previous observation, or from another location where this Quality was observed)
- Role node URIs MAY be re-used to refer to the same role of the same individual over multiple processes; however, distinct URIs MUST be anticipated by agents
- (this recognizes that it will not always be possible for a data entry process to look-up the URI of the Role node from a previous observation, or from another location where this Role was manifest)
- Process node URIs MUST NOT be re-used
- Entity node URIs MAY be distinct; the identification of the same entity occurs via the Identifier node
- Identifier node URIs MAY be distinct; the identification of the same identifier is the combination of identifier type and value (i.e. the id within a specific identifier namespace)
- Quality is an optional node, for a specific role/process
- for example, the process of consent-taking is not measuring an "intrinsic attribute" of a Person
- The SIO Ontology currently cannot adequately represent qualitative observations/measurements. As such, we are modelling this using "has phenotype --> some phenotype/object-quality". As such, this aspect of the model will likely change over the next few months.