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>
  • 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

  • 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)