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meta.yaml
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meta.yaml
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id: https://w3id.org/biolink/biolinkml/meta
title: Biolink Schema Metamodel
name: metamodel
description: A metamodel for defining biolink related schemas
license: https://creativecommons.org/publicdomain/zero/1.0/
version: 1.7.0
prefixes:
meta: https://w3id.org/biolink/biolinkml/meta/
biolinkml: https://w3id.org/biolink/biolinkml/
skos: http://www.w3.org/2004/02/skos/core#
OIO: http://www.geneontology.org/formats/oboInOwl#
pav: http://purl.org/pav/
oslc: http://open-services.net/ns/core#
schema: http://schema.org/
bibo: http://purl.org/ontology/bibo/
default_prefix: meta
default_range: string
default_curi_maps:
- semweb_context
emit_prefixes:
- meta
- rdf
- rdfs
- xsd
- skos
- dcterms
- OIO
- owl
- pav
imports:
- biolinkml:types
- biolinkml:mappings
- biolinkml:extensions
- biolinkml:annotations
subsets:
owl:
description: Set of slots that appear in the OWL representation of a model
#==================================
# Slots #
#==================================
slots:
# -----------------------------------
# Common metadata shared by all elements
# -----------------------------------
name:
domain: element
identifier: true
description: >-
the unique name of the element within the context of the schema. Name is combined with the default prefix to
form the globally unique subject of the target class.
slot_uri: rdfs:label
in_subset:
- owl
mappings:
- schema:name
see_also:
- https://en.wikipedia.org/wiki/Data_element_name
definition_uri:
domain: element
description: the "native" URI of the element
comments:
- Formed by combining the default_prefix with the mangled element
range: uriorcurie
readonly: filled in by the schema loader
id_prefixes:
domain: element
multivalued: true
range: ncname
description: >-
the identifier of this class or slot must begin with one of the URIs referenced by this prefix
description:
domain: element
description: a description of the element's purpose and use
slot_uri: skos:definition
in_subset:
- owl
aliases:
domain: element
range: string
multivalued: true
slot_uri: skos:altLabel
deprecated:
domain: element
range: string
description: Description of why and when this element will no longer be used
todos:
domain: element
range: string
description: Outstanding issue that needs resolution
multivalued: true
notes:
domain: element
multivalued: true
description: editorial notes about an element intended for internal consumption
slot_uri: skos:editorialNote
in_subset:
- owl
comments:
domain: element
multivalued: true
description: notes and comments about an element intended for external consumption
slot_uri: skos:note
in_subset:
- owl
in_subset:
domain: element
multivalued: true
range: subset_definition
description: >-
used to indicate membership of a term in a defined subset of biolink terms used for a particular domain
or application (e.g. the translator_minimal subset holding the minimal set of predicates used in a
translator knowledge graph)
slot_uri: OIO:inSubset
from_schema:
domain: element
range: uri
readonly: supplied by the schema loader
description: id of the schema that defined the element
notes:
- A stronger model would be range schema_definition, but this doesn't address the import model
slot_uri: skos:inScheme
imported_from:
domain: element
range: string
readonly: supplied by the schema loader
description: the imports entry that this element was derived from. Empty means primary source
see_also:
domain: element
multivalued: true
range: uriorcurie
description: a reference
slot_uri: rdfs:seeAlso
in_subset:
- owl
created_by:
domain: element
range: uriorcurie
description: agent that created the element
slot_uri: pav:createdBy
created_on:
domain: element
range: datetime
description: time at which the element was created
slot_uri: pav:createdOn
last_updated_on:
domain: element
range: datetime
description: time at which the element was last updated
slot_uri: pav:lastUpdatedOn
modified_by:
domain: element
range: uriorcurie
description: agent that modified the element
slot_uri: oslc:modifiedBy
status:
domain: element
range: uriorcurie
description: status of the element
slot_uri: bibo:status
examples:
- value: "bibo:draft"
# --------------------------------------------------------------
# Slots that are common to slot definition and class definition
# --------------------------------------------------------------
is_a:
domain: definition
range: definition
abstract: true
description: >-
specifies single-inheritance between classes or slots.
While multiple inheritance is not allowed, mixins can be provided effectively providing the same thing.
The semantics are the same when translated to formalisms that allow MI (e.g. RDFS/OWL). When translating to a SI
framework (e.g. java classes, python classes) then is a is used.
When translating a framework without polymorphism (e.g. json-schema, solr document schema) then is a and mixins
are recursively unfolded
abstract:
domain: definition
range: boolean
description: >-
an abstract class is a high level class or slot that is typically used to group common slots together and cannot
be directly instantiated.
mixin:
domain: definition
range: boolean
description: this slot or class can only be used as a mixin -- equivalent to abstract
mixins:
domain: definition
multivalued: true
range: definition
description: List of definitions to be mixed in. Targets may be any definition of the same type
apply_to:
domain: definition
multivalued: true
range: definition
description: >-
Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for
identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot
systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class,
and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class.
values_from:
domain: definition
multivalued: true
range: uriorcurie
description: >-
the identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot
# -----------------------------------
# Enum definition slots
# -----------------------------------
code_set:
domain: enum_definition
range: uriorcurie
description: >-
the identifier of an enumeration code set.
todos:
- this should be able to connect to an existing code set from TCCM
code_set_version:
domain: enum_definition
range: string
description: >-
the version identifier of the enumeration code set
comments:
- we assume that version identifiers lexically sort in temporal order. Recommend semver when possible
code_set_tag:
domain: enum_definition
range: string
description: >-
the version tag of the enumeration code set
comments:
- enum_definition cannot have both a code_set_tag and a code_set_version
pv_formula:
domain: enum_definition
range: pv_formula_options
description: >-
Defines the specific formula to be used to generate the permissible values.
comments:
- you cannot have BOTH the permissible_values and permissible_value_formula tag
- code_set must be supplied for this to be valid
permissible_values:
domain: enum_definition
range: permissible_value
multivalued: true
inlined: true
description: >-
A list of possible values for a slot range
# -----------------------------------
# Slots for permissible_value
# -----------------------------------
text:
domain: permissible_value
range: string
identifier: true
meaning:
domain: permissible_value
range: uriorcurie
description: >-
the value meaning (in the 11179 sense) of a permissible value
notes:
- we may want to change the range of this (and other) elements in the model to an entitydescription type construct
# -----------------------------------
# Schema definition slots
# -----------------------------------
id:
domain: schema_definition
range: uri
description: The official schema URI
required: true
emit_prefixes:
domain: schema_definition
multivalued: true
range: ncname
description: >-
a list of Curie prefixes that are used in the representation of instances of the model. All prefixes in
this list are added to the prefix sections of the target models.
title:
domain: schema_definition
description: the official title of the schema
slot_uri: dcterms:title
in_subset:
- owl
version:
domain: schema_definition
description: particular version of schema
slot_uri: pav:version
mappings:
- schema:schemaVersion
imports:
domain: schema_definition
range: uriorcurie
multivalued: true
description: other schemas that are included in this schema
license:
domain: schema_definition
description: license for the schema
slot_uri: dcterms:license
in_subset:
- owl
default_curi_maps:
domain: schema_definition
multivalued: true
description: ordered list of prefixcommon biocontexts to be fetched to resolve id prefixes and inline prefix variables
default_prefix:
domain: schema_definition
range: string
ifabsent: default_ns
description: default and base prefix -- used for ':' identifiers, @base and @vocab
default_range:
domain: schema_definition
range: type_definition
description: default slot range to be used if range element is omitted from a slot definition
notes:
- restricted to type definitions for the time being. Could be broadened if required
subsets:
domain: schema_definition
multivalued: true
range: subset_definition
inlined: true
description: list of subsets referenced in this model
types:
domain: schema_definition
range: type_definition
multivalued: true
inlined: true
description: data types used in the model
enums:
domain: schema_definition
range: enum_definition
multivalued: true
inlined: true
description: enumerated ranges
slot_definitions:
domain: schema_definition
multivalued: true
range: slot_definition
inlined: true
alias: slots
description: slot definitions
classes:
domain: schema_definition
range: class_definition
multivalued: true
inlined: true
description: class definitions
metamodel_version:
domain: schema_definition
readonly: supplied by the schema loader
description: Version of the metamodel used to load the schema
in_subset:
- owl
source_file:
domain: schema_definition
readonly: suppplied by the schema loader
description: name, uri or description of the source of the schema
in_subset:
- owl
source_file_date:
domain: schema_definition
range: datetime
readonly: supplied by the loader
description: modification date of the source of the schema
in_subset:
- owl
source_file_size:
domain: schema_definition
range: integer
readonly: supplied by the schema loader
description: size in bytes of the source of the schema
in_subset:
- owl
generation_date:
domain: schema_definition
range: datetime
readonly: supplied by the schema loader
description: date and time that the schema was loaded/generated
in_subset:
- owl
# -----------------------------------
# Class definition slots
# -----------------------------------
slots:
domain: class_definition
multivalued: true
range: slot_definition
description: list of slot names that are applicable to a class
comments:
- >-
This defines the set of slots that are allowed to be used for a given class.
The final list of slots for a class is the
combination of the parent (is a) slots, mixins slots, apply to slots minus the slot usage entries.
Formally,
slot_usage:
domain: class_definition
multivalued: true
range: slot_definition
inlined: true
description: the redefinition of a slot in the context of the containing class definition.
comments:
- >-
Many slots may be re-used across different classes, but the meaning of the slot may be refined by context.
For example, a generic association model may use slots subject/predicate/object with generic semantics and
minimal constraints. When this is subclasses, e.g. to disease-phenotype associations then slot usage may
specify both local naming (e.g. subject=disease) and local constraints
attributes:
domain: class_definition
multivalued: true
range: slot_definition
inlined: true
description: Inline definition of slots
comments:
- >-
attributes are an alternative way of defining new slots. An attribute adds a slot to the global space in the
form <class_name>__<slot_name> (lower case, double underscores). Attributes can be specialized via slot_usage.
class_uri:
domain: class_definition
range: uriorcurie
description: URI of the class in an RDF environment
ifabsent: class_curie
subclass_of:
domain: class_definition
range: uriorcurie
description: rdfs:subClassOf to be emitted in OWL generation
slot_uri: rdfs:subClassOf
defining_slots:
domain: class_definition
range: slot_definition
multivalued: true
inherited: true
description: >-
The combination of is a plus defining slots form a genus-differentia definition, or the set of
necessary and sufficient conditions that can be transformed into an OWL equivalence axiom
union_of:
domain: class_definition
range: class_definition
multivalued: true
description: indicates that the domain class consists exactly of the members of the classes in the range
notes:
- this only applies in the OWL generation
tree_root:
domain: class_definition
range: boolean
description: indicator that this is the root class in tree structures
# -----------------------------------
# Slot definition slots
# -----------------------------------
domain:
domain: slot_definition
range: class_definition
inherited: true
description: |
defines the type of the subject of the slot. Given the following slot definition
S1:
domain: C1
range: C2
the declaration
X:
S1: Y
implicitly asserts that X is an instance of C1
range:
domain: slot_definition
range: element
ifabsent: default_range
inherited: true
comments:
- range is underspecified, as not all elements can appear as the range of a slot.
description: |
defines the type of the object of the slot. Given the following slot definition
S1:
domain: C1
range: C2
the declaration
X:
S1: Y
implicitly asserts Y is an instance of C2
slot_uri:
domain: slot_definition
range: uriorcurie
ifabsent: slot_curie
description: predicate of this slot for semantic web application
multivalued:
domain: slot_definition
range: boolean
inherited: true
description: true means that slot can have more than one value
# ifabsent: False
inherited:
domain: slot_definition
range: boolean
inherited: true
description: true means that the *value* of a slot is inherited by subclasses
comments:
- Inherited applies to slot values. Parent *slots* are always inherited by subclasses
readonly:
domain: slot_definition
range: string
inherited: true
description: If present, slot is read only. Text explains why
ifabsent:
domain: slot_definition
range: string
inherited: true
description: >-
function that provides a default value for the slot. Possible values for this slot are defined in
biolink.utils.ifabsent_functions.default_library:
* [Tt]rue -- boolean True
* [Ff]alse -- boolean False
* int(value) -- integer value
* str(value) -- string value
* default_range -- schema default range
* bnode -- blank node identifier
* slot_uri -- URI for the slot
* class_curie -- CURIE for the containing class
* class_uri -- URI for the containing class
singular_name:
domain: slot_definition
description: a name that is used in the singular form
slot_uri: skos:altLabel
required:
domain: slot_definition
range: boolean
inherited: true
description: true means that the slot must be present in the loaded definition
inlined:
domain: slot_definition
range: boolean
inherited: true
description: >-
True means that keyed or identified slot appears in an outer structure by value. False means that only the key
or identifier for the slot appears within the domain, referencing a structure that appears elsewhere.
comments:
- classes without keys or identifiers are necessarily inlined as lists
inlined_as_list:
domain: slot_definition
range: boolean
inherited: true
description: >-
True means that an inlined slot is represented as a list of range instances. False means that an inlined slot
is represented as a dictionary, whose key is the slot key or identifier and whose value is the range instance.
comments:
- |-
The default loader will accept either list or dictionary form as input. This parameter controls internal
representation and output.
- |-
A keyed or identified class with one additional slot can be input in a third form, a dictionary whose key
is the key or identifier and whose value is the one additional element. This form is still stored according
to the inlined_as_list setting.
key:
domain: slot_definition
range: boolean
inherited: true
description: >-
True means that the key slot(s) uniquely identify the container. In future releases, it will be possible for there
to be compound keys, where several slots combine to produce a unique identifier
comments:
- key is inherited
- a given domain can have at most one key slot (restriction to be removed in the future)
- identifiers and keys are mutually exclusive. A given domain cannot have bot
- a key slot is automatically required. Keys cannot be optional
identifier:
domain: slot_definition
range: boolean
inherited: true
description: >-
True means that the key slot(s) uniquely identify the container. There can be at most one identifier or key per
container
aliases:
- primary key
- ID
- UID
- code
see_also:
- https://en.wikipedia.org/wiki/Identifier
comments:
- identifier is inherited
- a key slot is automatically required. Identifiers cannot be optional
- a given domain can have at most one identifier
- identifiers and keys are mutually exclusive. A given domain cannot have both
alias:
domain: slot_definition
range: string
description: >-
the name used for a slot in the context of its owning class. If present, this is used instead of the actual
slot name.
owner:
domain: slot_definition
range: definition
description: >-
the "owner" of the slot. It is the class if it appears in the slots list, otherwise the declaring slot
readonly: filled in by loader -- either class domain or slot domain
deprecated: Will be replaced by domain_of and eventually removed
domain_of:
domain: slot_definition
range: class_definition
description: the class(es) that reference the slot in a "slots" or "slot_usage" context
readonly: filled in by the loader
multivalued: true
is_usage_slot:
domain: slot_definition
deprecated: Replaced by usage_slot_name
range: boolean
description: True means that this slot was defined in a slot_usage situation
readonly: filled in by the loader
usage_slot_name:
domain: slot_definition
range: string
description: The name of the slot referenced in the slot_usage
readonly: filled in by the loader
subproperty_of:
domain: slot_definition
range: slot_definition
description: Ontology property which this slot is a subproperty of
slot_uri: rdfs:subPropertyOf
symmetric:
domain: slot_definition
range: boolean
description: True means that any instance of d s r implies that there is also an instance of r s d
inverse:
domain: slot_definition
range: slot_definition
description: indicates that any instance of d s r implies that there is also an instance of r s' d
slot_uri: owl:inverseOf
is_class_field:
domain: slot_definition
range: boolean
description: indicates that any instance, i, the domain of this slot will include an assert of i s range
role:
domain: slot_definition
range: string
description: the role played by the slot range
inherited: true
minimum_value:
domain: slot_definition
range: integer
description: for slots with ranges of type number, the value must be equal to or higher than this
inherited: true
maximum_value:
domain: slot_definition
range: integer
description: for slots with ranges of type number, the value must be equal to or lowe than this
inherited: true
pattern:
domain: slot_definition
range: string
description: the string value of the slot must conform to this regular expression
inherited: true
string_serialization:
domain: slot_definition
range: string
description: >-
Used on a slot that stores the string serialization of the containing object. The syntax follows python
formatted strings, with slot names enclosed in {}s. These are expanded using the values of those slots.
We call the slot with the serialization the s-slot, the slots used in the {}s are v-slots. If both
s-slots and v-slots are populated on an object then the value of the s-slot should correspond to the
expansion.
Implementations of frameworks may choose to use this property to either (a) PARSE: implement automated normalizations
by parsing denormalized strings into complex objects (b) GENERARE: implement automated to_string labeling of
complex objects
For example, a Measurement class may have 3 fields: unit, value, and string_value. The string_value slot
may have a string_serialization of {value}{unit} such that if unit=cm and value=2, the value of
string_value shouldd be 2cm
inherited: false
see_also:
- https://github.com/biolink/biolinkml/issues/128
# -----------------------------------
# Slots for type definition
# -----------------------------------
typeof:
domain: type_definition
range: type_definition
description: >-
Names a parent type
comments:
- the target type definition of the typeof slot is referred to as the "parent type"
- the type definition containing the typeof slot is referred to as the "child type"
- type definitions without a typeof slot are referred to as a "root type"
base:
domain: type_definition
description: python base type that implements this type definition
inherited: true
comments:
- every root type must have a base
- the base is inherited by child types but may be overriden. Base compatibility is not checked.
type_uri:
domain: type_definition
range: uriorcurie
alias: uri
inherited: true
description: The uri that defines the possible values for the type definition
comments:
- uri is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps)
- every root type must have a type uri
repr:
domain: type_definition
range: string
description: the name of the python object that implements this type definition
inherited: true
# -----------------------------------
# Slots for alt descripion
# -----------------------------------
alt_description_text:
domain: alt_description
range: string
required: true
description: text of an attributed description
alias: description
alt_description_source:
domain: alt_description
range: string
key: true
alias: source
description: the source of an attributed description
alt_descriptions:
domain: element
range: alt_description
multivalued: true
inlined: true
# -----------------------------------
# Slots for example
# -----------------------------------
value:
domain: example
description: example value
slot_uri: skos:example
value_description:
domain: example
alias: description
description: description of what the value is doing
examples:
domain: element
multivalued: true
range: example
inlined: true
description: example usages of an element
in_subset:
- owl
# -----------------------------------
# Slots for prefix
# -----------------------------------
prefix_prefix:
domain: prefix
range: ncname
key: true
description: the nsname (sans ':' for a given prefix)
prefix_reference:
domain: prefix
range: uri
required: true
description: A URI associated with a given prefix
prefixes:
domain: schema_definition
range: prefix
multivalued: true
inlined: true
description: prefix / URI definitions to be added to the context beyond those fetched from prefixcommons in id prefixes
# -----------------------------------
# Slots for local_name
# -----------------------------------
local_name_source:
domain: local_name
range: ncname
key: true
description: the ncname of the source of the name
local_name_value:
domain: local_name
range: string
required: true
description: a name assigned to an element in a given ontology
slot_uri: skos:altLabel
local_names:
domain: element
range: local_name
multivalued: true
inlined: true
#==================================
# Classes #
#==================================
classes:
element:
description: a named element in the model
abstract: true
mixins:
- extensible
- annotatable
slots:
- name
- id_prefixes
- definition_uri
- aliases
- local_names
- mappings
- description
- alt_descriptions
- deprecated
- todos
- notes
- comments
- examples
- in_subset
- from_schema
- imported_from
- see_also
- exact mappings
- close mappings
- related mappings
- narrow mappings
- broad mappings
- deprecated element has exact replacement
- deprecated element has possible replacement
see_also:
- https://en.wikipedia.org/wiki/Data_element
schema_definition:
description: "a collection of subset, type, slot and class definitions"
aliases:
- data dictionary
is_a: element
slots:
- id
- title
- version
- imports
- license
- prefixes
- emit_prefixes
- default_curi_maps
- default_prefix
- default_range
- subsets
- types
- enums
- slot_definitions
- classes
- metamodel_version
- source_file
- source_file_date
- source_file_size
- generation_date
see_also:
- https://en.wikipedia.org/wiki/Data_dictionary
slot_usage:
name:
range: ncname
# slot_usage:
# description:
# slot_uri: dcterms:description
type_definition:
description: A data type definition.
is_a: element
slots:
- typeof
- base
- type_uri
- repr
subset_definition:
description: the name and description of a subset
is_a: element
definition:
description: "base class for definitions"
abstract: true
is_a: element
slots:
- is_a
- abstract
- mixin
- mixins
- apply_to
- values_from
- created_by
- created_on
- last_updated_on
- modified_by
- status
see_also:
- https://en.wikipedia.org/wiki/Data_element_definition
enum_definition:
description: List of values that constrain the range of a slot
is_a: element
slots:
- code_set