Enum DefaultExtensions.SSSOM
java.lang.Object
java.lang.Enum<DefaultExtensions.SSSOM>
de.uni_mannheim.informatik.dws.melt.yet_another_alignment_api.DefaultExtensions.SSSOM
- All Implemented Interfaces:
Serializable
,Comparable<DefaultExtensions.SSSOM>
,java.lang.constant.Constable
- Enclosing class:
- DefaultExtensions
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Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum ConstantDescriptionLIST OF STRINGS: Identifies the persons or groups responsible for asserting the mappings.LIST OF STRINGS: A string identifying the author of this mapping.STRING Free text field containing either curator notes or text generated by tool providing additional informative information.Double: A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence.LIST OF STRINGS: Identifies the persons or groups responsible for the creation of the mapping.STRING A string identifying the creator of this mapping.LIST OF STRINGS: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping.LIST OF STRINGS: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping.MAP STRING TO STRING: Curie map which maps the short form (prefix) to its long form.STRING A url to the license of the mapping.SSSOMMappingCardinality
A string indicating whether this mapping is from a 1:1 (the subject_id maps to a single object_id), 1:n (the subject maps to more than one object_id), n:1, 1:0, 0:1 or n:n group.LocalDate: The date the mapping was asserted.STRING: A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable.STRING URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived.STRING A description of the mapping set.STRING: A globally unique identifier for the mapping set (not each individual mapping).LIST OF STRINGS: A mapping set or set of mapping set that was used to derive the mapping set.STRING The display name of a mapping set.STRING: A version string for the mapping.STRING: The mapping set this mapping was originally defined in.STRING A reference to the tool or algorithm that was used to generate the mapping.STRING Version string that denotes the version of the mapping tool used.LIST OF STRINGS: Strings that are shared by subj/obj.STRING: The conceptual category to which the subject belongs to.STRING: The ID of the object of the mapping.STRING: The label of object of the mappingLIST OF STRING A tuple of fields (term annotations on the object) that was used for the match.STRING Method of preprocessing applied to the fields of the object.STRING IRI of ontology source for the object.STRING Version IRI or version string of the source of the object term.SSSOMEntityType
The type of entity that is being mapped.STRING Pipe separated list of key value pairs for properties not part of the SSSOM spec.STRING: The ID of the predicate or relation that relates the subject and object of this match.STRING: The label of the predicate/relation of the mappingSSSOMPredicateModifier
A modifier for negating the prediate.LIST OF STRINGS: Identifies the persons or groups that reviewed and confirmed the mapping.LIST OF STRINGS: A string identifying the reviewer of this mapping.LIST OF STRING A URL specific for the mapping instance.STRING: The measure used for computing the the semantic similarity score.Double: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence.STRING: The conceptual category to which the subject belongs to.STRING: The ID of the subject of the mapping.STRING: The label of subject of the mappingLIST OF STRING A tuple of fields (term annotations on the subject) that was used for the match.STRING Method of preprocessing applied to the fields of the subject.STRING URI of ontology source for the subject.STRING Version IRI or version string of the source of the subject term.SSSOMEntityType
: The type of entity that is being mapped. -
Field Summary
Modifier and TypeFieldDescriptionstatic final String
private Class<?>
private boolean
private static final Map<String,
DefaultExtensions.SSSOM> private String
The URI of the extension label.private static final Map<String,
DefaultExtensions.SSSOM> -
Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionstatic DefaultExtensions.SSSOM
static DefaultExtensions.SSSOM
static DefaultExtensions.SSSOM
fromURLOrName
(String urlOrName) Class<?>
Return the name of the extension key as it should be used as a header in a TSV file.boolean
Return true, if the value of this key can have an abbreviated value which needs to be expanded.toString()
static DefaultExtensions.SSSOM
Returns the enum constant of this type with the specified name.static DefaultExtensions.SSSOM[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Details
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CREATOR_ID
LIST OF STRINGS: Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible. -
CREATOR_LABEL
STRING A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead. -
LICENSE
STRING A url to the license of the mapping. In absence of a license we assume no license. -
SUBJECT_TYPE
SSSOMEntityType
: The type of entity that is being mapped. -
SUBJECT_SOURCE
STRING URI of ontology source for the subject. -
SUBJECT_SOURCE_VERSION
STRING Version IRI or version string of the source of the subject term. -
OBJECT_TYPE
SSSOMEntityType
The type of entity that is being mapped. -
OBJECT_SOURCE
STRING IRI of ontology source for the object. Version IRI preferred. -
OBJECT_SOURCE_VERSION
STRING Version IRI or version string of the source of the object term. -
MAPPING_PROVIDER
STRING URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived. -
MAPPING_TOOL
STRING A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text. -
MAPPING_TOOL_VERSION
STRING Version string that denotes the version of the mapping tool used. -
MAPPING_DATE
LocalDate: The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file. -
SUBJECT_MATCH_FIELD
LIST OF STRING A tuple of fields (term annotations on the subject) that was used for the match. -
OBJECT_MATCH_FIELD
LIST OF STRING A tuple of fields (term annotations on the object) that was used for the match. -
SUBJECT_PREPROCESSING
STRING Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows. -
OBJECT_PREPROCESSING
STRING Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows. -
SEE_ALSO
LIST OF STRING A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability.Could also be a github issue URL that discussed a complicated alignment -
OTHER
STRING Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data. -
COMMENT
STRING Free text field containing either curator notes or text generated by tool providing additional informative information. -
MAPPING_SET_ID
STRING: A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable. -
MAPPING_SET_VERSION
STRING: A version string for the mapping. -
MAPPING_SET_SOURCE
LIST OF STRINGS: A mapping set or set of mapping set that was used to derive the mapping set. -
MAPPING_SET_TITLE
STRING The display name of a mapping set. -
MAPPING_SET_DESCRIPTION
STRING A description of the mapping set. -
CURIE_MAP
MAP STRING TO STRING: Curie map which maps the short form (prefix) to its long form. -
SUBJECT_ID
STRING: The ID of the subject of the mapping. -
SUBJECT_LABEL
STRING: The label of subject of the mapping -
SUBJECT_CATEGORY
STRING: The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases. -
PREDICATE_ID
STRING: The ID of the predicate or relation that relates the subject and object of this match. -
PREDICATE_LABEL
STRING: The label of the predicate/relation of the mapping -
PREDICATE_MODIFIER
SSSOMPredicateModifier
A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion -
OBJECT_ID
STRING: The ID of the object of the mapping. -
OBJECT_LABEL
STRING: The label of object of the mapping -
OBJECT_CATEGORY
STRING: The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases. -
MAPPING_JUSTIFICATION
STRING: A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable. -
AUTHOR_ID
LIST OF STRINGS: Identifies the persons or groups responsible for asserting the mappings. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible. -
AUTHOR_LABEL
LIST OF STRINGS: A string identifying the author of this mapping. In the spirit of provenance, consider to use author_id instead. -
REVIEWER_ID
LIST OF STRINGS: Identifies the persons or groups that reviewed and confirmed the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible. -
REVIEWER_LABEL
LIST OF STRINGS: A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use reviewer_id instead. -
MAPPING_SOURCE
STRING: The mapping set this mapping was originally defined in. mapping_source is used for example when merging multiple mapping sets or deriving one mapping set from another. -
MAPPING_CARDINALITY
SSSOMMappingCardinality
A string indicating whether this mapping is from a 1:1 (the subject_id maps to a single object_id), 1:n (the subject maps to more than one object_id), n:1, 1:0, 0:1 or n:n group. Note that this is a convenience field that should be derivable from the mapping set. -
CONFIDENCE
Double: A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence. -
CURATION_RULE
LIST OF STRINGS: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets. The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule. -
CURATION_RULE_TEXT
LIST OF STRINGS: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets. The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text. -
MATCH_STRING
LIST OF STRINGS: Strings that are shared by subj/obj. It is recommended to indicate the fields for the match using the object and subject_match_field slots. -
SEMANTIC_SIMILARITY_SCORE
Double: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence. -
SEMANTIC_SIMILARITY_MEASURE
STRING: The measure used for computing the the semantic similarity score. To make processing this field as unambiguous as possible, we recommend using wikidata identifiers, but wikipedia pages could also be acceptable.
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Field Details
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uri
The URI of the extension label. -
isEntityReference
private boolean isEntityReference -
clazz
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BASE_URI
- See Also:
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URL_MAP
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NAME_MAP
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Constructor Details
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SSSOM
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SSSOM
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SSSOM
private SSSOM(boolean isEntityReference) -
SSSOM
private SSSOM()
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Method Details
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values
Returns an array containing the constants of this enum type, in the order they are declared.- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
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toString
- Overrides:
toString
in classEnum<DefaultExtensions.SSSOM>
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isEntityReference
public boolean isEntityReference()Return true, if the value of this key can have an abbreviated value which needs to be expanded.- Returns:
- true, if the value of this key can have an abbreviated value which needs to be expanded.
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getDatatype
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getHeaderName
Return the name of the extension key as it should be used as a header in a TSV file.- Returns:
- just the name of the extension key.
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fromURL
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fromName
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fromURLOrName
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