Package de.uni_mannheim.informatik.dws.melt.yet_another_alignment_api

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

public static enum DefaultExtensions.SSSOM
extends Enum<DefaultExtensions.SSSOM>

SSSOM Extensions

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
AUTHOR_ID	LIST OF STRINGS: Identifies the persons or groups responsible for asserting the mappings.
AUTHOR_LABEL	LIST OF STRINGS: A string identifying the author of this mapping.
COMMENT	STRING Free text field containing either curator notes or text generated by tool providing additional informative information.
CONFIDENCE	Double: A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence.
CREATOR_ID	LIST OF STRINGS: Identifies the persons or groups responsible for the creation of the mapping.
CREATOR_LABEL	STRING A string identifying the creator of this mapping.
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_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.
CURIE_MAP	MAP STRING TO STRING: Curie map which maps the short form (prefix) to its long form.
LICENSE	STRING A url to the license of the mapping.
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.
MAPPING_DATE	LocalDate: The date the mapping was asserted.
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.
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_SET_DESCRIPTION	STRING A description of the mapping set.
MAPPING_SET_ID	STRING: A globally unique identifier for the mapping set (not each individual 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_VERSION	STRING: A version string for the mapping.
MAPPING_SOURCE	STRING: The mapping set this mapping was originally defined in.
MAPPING_TOOL	STRING A reference to the tool or algorithm that was used to generate the mapping.
MAPPING_TOOL_VERSION	STRING Version string that denotes the version of the mapping tool used.
MATCH_STRING	LIST OF STRINGS: Strings that are shared by subj/obj.
OBJECT_CATEGORY	STRING: The conceptual category to which the subject belongs to.
OBJECT_ID	STRING: The ID of the object of the mapping.
OBJECT_LABEL	STRING: The label of object of the mapping
OBJECT_MATCH_FIELD	LIST OF STRING A tuple of fields (term annotations on the object) that was used for the match.
OBJECT_PREPROCESSING	STRING Method of preprocessing applied to the fields of the object.
OBJECT_SOURCE	STRING IRI of ontology source for the object.
OBJECT_SOURCE_VERSION	STRING Version IRI or version string of the source of the object term.
OBJECT_TYPE	SSSOMEntityType The type of entity that is being mapped.
OTHER	STRING Pipe separated list of key value pairs for properties not part of the SSSOM spec.
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.
REVIEWER_ID	LIST OF STRINGS: Identifies the persons or groups that reviewed and confirmed the mapping.
REVIEWER_LABEL	LIST OF STRINGS: A string identifying the reviewer of this mapping.
SEE_ALSO	LIST OF STRING A URL specific for the mapping instance.
SEMANTIC_SIMILARITY_MEASURE	STRING: The measure used for computing the the semantic similarity score.
SEMANTIC_SIMILARITY_SCORE	Double: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence.
SUBJECT_CATEGORY	STRING: The conceptual category to which the subject belongs to.
SUBJECT_ID	STRING: The ID of the subject of the mapping.
SUBJECT_LABEL	STRING: The label of subject of the mapping
SUBJECT_MATCH_FIELD	LIST OF STRING A tuple of fields (term annotations on the subject) that was used for the match.
SUBJECT_PREPROCESSING	STRING Method of preprocessing applied to the fields of the subject.
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.
SUBJECT_TYPE	SSSOMEntityType: The type of entity that is being mapped.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BASE_URI
private Class<?>	clazz
private boolean	isEntityReference
private static final Map<String,DefaultExtensions.SSSOM>	NAME_MAP
private String	uri	The URI of the extension label.
private static final Map<String,DefaultExtensions.SSSOM>	URL_MAP

Constructor Summary

Constructors

Modifier	Constructor	Description
private	SSSOM()
private	SSSOM(boolean isEntityReference)
private	SSSOM(boolean isEntityReference, Class<?> clazz)
private	SSSOM(Class<?> clazz)

Method Summary

Modifier and Type	Method	Description
static DefaultExtensions.SSSOM	fromName(String name)
static DefaultExtensions.SSSOM	fromURL(String url)
static DefaultExtensions.SSSOM	fromURLOrName(String urlOrName)
Class<?>	getDatatype()
String	getHeaderName()	Return the name of the extension key as it should be used as a header in a TSV file.
boolean	isEntityReference()	Return true, if the value of this key can have an abbreviated value which needs to be expanded.
String	toString()
static DefaultExtensions.SSSOM	valueOf(String name)	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.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

CREATOR_ID

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM CREATOR_LABEL

STRING A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead.

LICENSE

public static final DefaultExtensions.SSSOM LICENSE

STRING A url to the license of the mapping. In absence of a license we assume no license.

SUBJECT_TYPE

public static final DefaultExtensions.SSSOM SUBJECT_TYPE

SSSOMEntityType: The type of entity that is being mapped.

SUBJECT_SOURCE

public static final DefaultExtensions.SSSOM SUBJECT_SOURCE

STRING URI of ontology source for the subject.

SUBJECT_SOURCE_VERSION

public static final DefaultExtensions.SSSOM SUBJECT_SOURCE_VERSION

STRING Version IRI or version string of the source of the subject term.

OBJECT_TYPE

public static final DefaultExtensions.SSSOM OBJECT_TYPE

SSSOMEntityType The type of entity that is being mapped.

OBJECT_SOURCE

public static final DefaultExtensions.SSSOM OBJECT_SOURCE

STRING IRI of ontology source for the object. Version IRI preferred.

OBJECT_SOURCE_VERSION

public static final DefaultExtensions.SSSOM OBJECT_SOURCE_VERSION

STRING Version IRI or version string of the source of the object term.

MAPPING_PROVIDER

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM MAPPING_TOOL_VERSION

STRING Version string that denotes the version of the mapping tool used.

MAPPING_DATE

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM SUBJECT_MATCH_FIELD

LIST OF STRING A tuple of fields (term annotations on the subject) that was used for the match.

OBJECT_MATCH_FIELD

public static final DefaultExtensions.SSSOM OBJECT_MATCH_FIELD

LIST OF STRING A tuple of fields (term annotations on the object) that was used for the match.

SUBJECT_PREPROCESSING

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM COMMENT

STRING Free text field containing either curator notes or text generated by tool providing additional informative information.

MAPPING_SET_ID

public static final DefaultExtensions.SSSOM MAPPING_SET_ID

STRING: A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable.

MAPPING_SET_VERSION

public static final DefaultExtensions.SSSOM MAPPING_SET_VERSION

STRING: A version string for the mapping.

MAPPING_SET_SOURCE

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM MAPPING_SET_TITLE

STRING The display name of a mapping set.

MAPPING_SET_DESCRIPTION

public static final DefaultExtensions.SSSOM MAPPING_SET_DESCRIPTION

STRING A description of the mapping set.

CURIE_MAP

public static final DefaultExtensions.SSSOM CURIE_MAP

MAP STRING TO STRING: Curie map which maps the short form (prefix) to its long form.

SUBJECT_ID

public static final DefaultExtensions.SSSOM SUBJECT_ID

STRING: The ID of the subject of the mapping.

SUBJECT_LABEL

public static final DefaultExtensions.SSSOM SUBJECT_LABEL

STRING: The label of subject of the mapping

SUBJECT_CATEGORY

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM PREDICATE_ID

STRING: The ID of the predicate or relation that relates the subject and object of this match.

PREDICATE_LABEL

public static final DefaultExtensions.SSSOM PREDICATE_LABEL

STRING: The label of the predicate/relation of the mapping

PREDICATE_MODIFIER

public static final DefaultExtensions.SSSOM PREDICATE_MODIFIER

SSSOMPredicateModifier A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion

OBJECT_ID

public static final DefaultExtensions.SSSOM OBJECT_ID

STRING: The ID of the object of the mapping.

OBJECT_LABEL

public static final DefaultExtensions.SSSOM OBJECT_LABEL

STRING: The label of object of the mapping

OBJECT_CATEGORY

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM 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

public static final DefaultExtensions.SSSOM SEMANTIC_SIMILARITY_SCORE

Double: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence.

SEMANTIC_SIMILARITY_MEASURE

public static final DefaultExtensions.SSSOM 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.

Field Details

uri

private String uri

The URI of the extension label.

isEntityReference

private boolean isEntityReference

clazz

private Class<?> clazz

BASE_URI

public static final String BASE_URI

See Also:

• Constant Field Values

URL_MAP

private static final Map<String,DefaultExtensions.SSSOM> URL_MAP

NAME_MAP

private static final Map<String,DefaultExtensions.SSSOM> NAME_MAP

Constructor Details

SSSOM

private SSSOM(Class<?> clazz)

SSSOM

private SSSOM(boolean isEntityReference,
 Class<?> clazz)

SSSOM

private SSSOM(boolean isEntityReference)

SSSOM

private SSSOM()

Method Details

values

public static DefaultExtensions.SSSOM[] 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

valueOf

public static DefaultExtensions.SSSOM valueOf(String name)

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 name

NullPointerException - if the argument is null

toString

public String toString()

Overrides:

toString in class Enum<DefaultExtensions.SSSOM>

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.

getDatatype

public Class<?> getDatatype()

getHeaderName

public String 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.

fromURL

public static DefaultExtensions.SSSOM fromURL(String url)

fromName

public static DefaultExtensions.SSSOM fromName(String name)

fromURLOrName

public static DefaultExtensions.SSSOM fromURLOrName(String urlOrName)