A semantic annotation is the attachment of semantic metadata to a resource. Semantic metadata provides a precise definition of concepts and clarifies the relationships between concepts. Although the process of semantic annotation may seem tedious, the payoff is enhanced information retrieval and discovery. For example, if a dataset is annotated as being about "carbon dioxide flux" and another annotated with "CO2 flux" the information system should recognize that the datasets are about equivalent concepts. In another example, if a user performs a search for datasets about "litter" (as in "plant litter"), the system will disambiguate the term from other meanings of "litter" (as in garbage, the group of animals born at the same time, etc.). Yet another example is if a user searches for datasets about "carbon flux", then datasets about "carbon dioxide flux" will also be returned because "carbon dioxide flux" is considered a type of "carbon flux".
A semantic annotation follows the Resource Description Framework (RDF) data model and uses semantic triples. A semantic triple is composed of a subject, object property (predicate), and object. In general, the subject and object can be thought of as nouns in a sentence and the object property is akin to a verb or relationship that connects the subject and object. The semantic triple expresses a statement about the associated resource. Ideally, these components should be globally unique and should be resolvable uniform resource identifiers (URIs) from controlled vocabularies so that users can look up the definitions and relationships of the terms to other terms. An example is "http://purl.obolibrary.org/obo/ENVO_01001357", which resolves to the term "desert" in the Environment Ontology (ENVO) when entered into an address bar in a web browser. Users can find the definition for "desert" and determine its relationship to other terms in the ontology.
- Additional background information on the RDF data model: https://www.w3.org/TR/WD-rdf-syntax-971002/
In EML 2.2.0 there are 5 kinds of semantic annotations that can be made in an EML document: dataset-level, entity-level, attribute-level, annotations element and additionalMetadata element annotations.
Semantic annotations made at the dataset-level, entity-level, and attribute-level follow the same pattern. An annotation made at any of these levels involves inserting an annotation element containing a propertyURI element and a valueURI element within the appropriate element. The subject of this annotation is the containing element. It is recommended to give the subject element an id attribute and make the subject the value of the id. The propertyURI is the object property and the valueURI is the object of the annotation. For example, an attribute-level annotation involves an attribute element. Within the attribute element are propertyURI and valueURI elements. The URIs should ideally point to terms in controlled vocabularies.
Multiple annotation elements may be embedded in the same dataset, entity-level or attribute element to assert multiple semantic statements as shown in the generic example below.
<dataset or entity-level or attribute> <- subject
<annotation>
<propertyURI>http://www.w3.org/1999/02/22-rdf-syntax-ns#type</propertyURI> <- object property 1 is "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"
<valueURI>https://schema.org/Person</valueURI> <- object 1 is "https://schema.org/Person"
</annotation>
<annotation>
<propertyURI>http://www.w3.org/1999/02/22-rdf-syntax-ns#type</propertyURI> <- object property 2 is "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"
<valueURI>http://semanticscience.org/resource/SIO_000404</valueURI> <- object 2 is "http://semanticscience.org/resource/SIO_000404"
</annotation>
</dataset or entity-level or attribute>
A dataset is defined as all of the information describing a data collection event. This event may take place over some period of time and include many actual collections (e.g. a time series or remote sensing application) or it could be just one actual collection (e.g. a day in the field). The dataset element encompasses all information about a single dataset. It is intended to provide overview information about the dataset: broad information such as the title, abstract, keywords, contacts, maintenance history, purpose, and distribution of the data themselves. A dataset can be (and often is) composed of a series of data entities (see 'entity-level annotation' section below) that are linked together by particular integrity constraints. Further information about datasets may be found in chapter 5.3.
A dataset-level annotation represents a precisely-defined semantic statement that applies to a dataset. This semantic statement is used to associate precise measurement semantics with the dataset. A dataset-level annotation element is embedded in a containing dataset element. The subject of the semantic statement is the dataset element that contains the annotation. If the dataset element contains an id attribute, then the subject should be the value of the id attribute. Each annotation consists of a propertyURI element and valueURI element, which respectively define a property and a value (object) that apply to the dataset. The associated labels can be used to display the property and value in a more readable format to users. Each URI should be resolvable to a controlled vocabulary that provides a precise definition, relationships to other terms, and multiple labels for displaying the statement.
In the following dataset-level annotation (Example 1), the subject of the semantic statement is the dataset element's id attribute value, "dataset-01". The object property of the statement is http://purl.org/dc/elements/1.1/subject. Finally, the value (object) in the semantic statement is http://purl.obolibrary.org/obo/ENVO_01000177, which resolves to the "grassland biome" term in the ENVO ontology (http://www.obofoundry.org/ontology/envo.html). Taken together, the semantic statement could be read as "the dataset with the id 'dataset-01' is about the subject grassland biome".
- Example 1: dataset-level annotation
<dataset id="dataset-01">
<title>Data from Cedar Creek LTER on productivity and species richness for use in a workshop titled
"An Analysis of the Relationship between Productivity and Diversity using Experimental Results from
the Long-Term Ecological Research Network" held at NCEAS in September 1996.</title>
<creator id="clarence.lehman">
<individualName>
<salutation>Mr.</salutation>
<givenName>Clarence</givenName>
<surName>Lehman</surName>
</individualName>
</creator>
...
<annotation>
<propertyURI label="Subject">http://purl.org/dc/elements/1.1/subject</propertyURI>
<valueURI label="grassland biome">http://purl.obolibrary.org/obo/ENVO_01000177</valueURI>
</annotation>
</dataset>
The entity-level elements include the dataTable, spatialRaster, spatialVector, storedProcedure, view, and otherEntity EML elements, in addition to custom modules. Entities are usually tables of data (dataTable). Data tables may be ascii text files, relational database tables, spreadsheets or other type of tabular data with a fixed logical structure. Related to data tables are views (view) and stored procedures (storedProcedure). Views and stored procedures are produced by a relational database management system or related system. Other types of data such as raster (spatialRaster), vector (spatialVector) or spatialReference image data are also data entities. An otherEntity element should be used to describe types of entities that are not described by any other entity type. The entity-level EML elements are nested under dataset elements. Further information about entities may be found in chapter 6.1.
An entity-level annotation represents a precisely-defined semantic statement that applies to an entity. This semantic statement is used to associate precise measurement semantics with the entity. An entity-level annotation element is embedded in a containing entity-level element. The subject of the semantic statement is the entity-level element that contains the annotation. If the entity-level element contains an id attribute, then the subject should be the value of the id attribute. Each annotation consists of a propertyURI element and valueURI element, which respectively define a property and a value (object) that apply to the entity. The associated labels can be used to display the property and value in a more readable format to users. Each URI should be resolvable to a controlled vocabulary that provides a precise definition, relationships to other terms, and multiple labels for displaying the statement.
In the following entity-level annotation (Example 2), the subject of the semantic statement is the otherEntity element's id attribute value, "urn:uuid:9f0eb128-aca8-4053-9dda-8e7b2c43a81b". The object property of the statement is http://purl.org/dc/elements/1.1/subject. Finally, the value (object) in the semantic statement is http://purl.obolibrary.org/obo/NCBITaxon_40674, which resolves to the "Mammalia" term in the NCBITaxon ontology (http://www.ontobee.org/ontology/NCBITaxon). Taken together, the semantic statement indicates that "the entity with the id 'urn:uuid:9f0eb128-aca8-4053-9dda-8e7b2c43a81b' is about the subject Mammalia".
- Example 2: entity-level annotation
<otherEntity id="urn:uuid:9f0eb128-aca8-4053-9dda-8e7b2c43a81b" scope="document">
<entityName>DBO_MMWatch_SWL2016_MooreGrebmeierVagle.xlsx</entityName>
<entityDescription>Data contained in the file DBO_MMWatch_SWL2016_MooreGrebmeierVagle.xlsx are marine mammal observations and observation conditions from CCGS Sir Wilfrid Laurier July 10-20, 2016. Data observations and locations are part of the Distributed Biological Observatory (DBO).</entityDescription>
<physical scope="document">
<objectName>DBO_MMWatch_SWL2016_MooreGrebmeierVagle.xlsx</objectName>
<size unit="bytes">24635</size>
</physical>
<entityType>Other</entityType>
<annotation>
<propertyURI label="Subject">http://purl.org/dc/elements/1.1/subject</propertyURI>
<valueURI label="Mammalia">http://purl.obolibrary.org/obo/NCBITaxon_40674</valueURI>
<annotation>
</otherEntity>
An attribute is a characteristic that describes a 'field' or 'variable' in a data entity, such as a column name in a spreadsheet. An attribute annotation represents a precisely-defined semantic statement that applies to an attribute. This semantic statement is used to associate precise measurement semantics with the attribute, such as the property being measured, the entity being measured, and the measurement standard for interpreting values for the attribute. attribute elements may be nested in entity-level elements, including the dataTable, spatialRaster, spatialVector, storedProcedure, view, or otherEntity elements, in addition to custom modules. Refer to chapter 6.2 for additional information about attributes.
A typical attribute annotation involves an annotation element that is embedded in a containing attribute element. The subject of the semantic statement is the attribute element that contains the annotation. If the attribute element contains an id attribute, then the subject should be the value of the id attribute. Each annotation consists of a propertyURI element and valueURI element that respectively define the property and value (object) of the semantic statement. The associated labels can be used to display the property and value in a more readable format to users. Each URI should be resolvable to a controlled vocabulary that provides a precise definition, relationships to other terms, and multiple labels for displaying the statement. Note that when annotating attributes that are measurements contained in tabular formats the preferred "default" object property is "contains measurements of type" from the OBOE ontology (http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType).
In the following attribute annotation (Example 3), the subject of the semantic statement is the attribute element's id attribute value, "att.4". The object property of the statement is http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType. Note that the URI for the object property resolves to a specific term in the OBOE ontology (https://github.com/NCEAS/oboe). Finally, the value (object) in the semantic statement is http://purl.dataone.org/odo/ECSO_00001197, which resolves to the "Plant Cover Percentage" term in the ECSO Ontology (https://github.com/DataONEorg/sem-prov-ontologies/tree/master/observation). Taken together, the semantic statement indicates that "att.4 contains measurements of type plant cover percentage".
- Example 3: attribute-level annotation
<attribute id="att.4">
<attributeName>pctcov</attributeName>
<attributeLabel>percent cover</attributeLabel>
<attributeDefinition>The percent ground cover on the field</attributeDefinition>
<annotation>
<propertyURI label="contains measurements of type">http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType</propertyURI>
<valueURI label="Plant Cover Percentage">http://purl.dataone.org/odo/ECSO_00001197</valueURI>
</annotation>
</attribute>
Semantic annotations may also be inserted in the annotations element that is nested under the eml root element. This type of semantic annotation involves an annotation element that has a references attribute. What is listed in the references attribute is the subject of the semantic annotation. Within the annotation element are propertyURI and valueURI elements. The propertyURI is the object property and the valueURI is the object of the annotation. The URIs should ideally point to terms in controlled vocabularies.
Multiple annotation elements can be used to create multiple annotations about the same or different subjects.
<eml>
...
<annotations>
<annotation references="john_doe"> <- subject 1 is "john_doe"
<propertyURI>http://www.w3.org/1999/02/22-rdf-syntax-ns#type</propertyURI> <- object property 1 is "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"
<valueURI>https://schema.org/Person</valueURI> <- object 1 is "https://schema.org/Person"
</annotation>
<annotation references="john_doe"> <- subject 2 is "john_doe" (same as subject 1)
<propertyURI>http://schema.org/hasOccupation</propertyURI> <- object property 2 is "http://schema.org/hasOccupation"
<valueURI>http://semanticscience.org/resource/SIO_000404</valueURI> <- object 2 is "http://semanticscience.org/resource/SIO_000404"
</annotation>
</annotations>
...
</eml>
The annotations element is nested under the eml root element and contains a list of annotations defining precise semantic statements for parts of a resource. An annotation represents a precisely-defined semantic statement that applies to the resource. This statement is used to associate precise semantics with a particular element in the EML document. For additional details, refer to [insert link]
The annotations element contains a set of annotation elements. Each annotation element has a references attribute that points to the id attribute of the element being annotated. The id of the element being annotated is listed in the references attribute, and must point to a unique id within the EML document. In the semantic statement, the subject is implicitly the id that is referenced. Each annotation also consists of a propertyURI element and valueURI element that respectively define a property and value (object) that apply to the resource. The associated labels can be used to display the statement in a more readable format to users. Each URI should resolve to a controlled vocabulary that provides a definition, relationships to other terms, and multiple labels for displaying the statement.
The following annotations element example (Example 4) has 3 different annotations. For the first annotation, the subject of the semantic statement is "CDF-biodiv-table", which is the id of another element in the EML document. The object property of the statement is http://purl.org/dc/elements/1.1/subject. Finally, the value (object) in the semantic statement is http://purl.obolibrary.org/obo/ENVO_01000177, which resolves to the "grassland biome" term in the ENVO ontology (http://www.obofoundry.org/ontology/envo.html). Taken together, the first semantic statement could be read as "CDR-biodiv-table is about the subject grassland biome".
The second semantic statement contains the subject "adam.shepherd", the object property http://www.w3.org/1999/02/22-rdf-syntax-ns#type and the value (object) https://schema.org/Person. This statement can be interpreted as "adam.shepherd is a person".
The third semantic statement also has the subject "adam.shepherd". The object property is "https://schema.org/memberOf" and the value (object) is "https://doi.org/10.17616/R37P4C". This statement can be read as "adam.shepherd is a member of BCO-DMO".
- Example 4:
annotationselement annotation
<eml>
<dataset id="dataset-01">
<title>Data from Cedar Creek LTER on productivity and species richness for use in a workshop titled "An Analysis of the Relationship between Productivity and Diversity using Experimental Results from the Long-Term Ecological Research Network" held at NCEAS in September 1996.</title>
<creator id="adam.shepherd">
<individualName>
<salutation>Mr.</salutation>
<givenName>Adam</givenName>
<surName>Shepherd</surName>
</individualName>
</creator>
<dataTable id="CDR-biodiv-table">
<entityName>CDR LTER-patterns among communities.txt</entityName>
...
</dataTable
</dataset>
...
<annotations>
<annotation references="CDR-biodiv-table">
<propertyURI label="Subject">http://purl.org/dc/elements/1.1/subject</propertyURI>
<valueURI label="grassland biome">http://purl.obolibrary.org/obo/ENVO_01000177</valueURI>
</annotation>
<annotation references="adam.shepherd">
<propertyURI label="is a">http://www.w3.org/1999/02/22-rdf-syntax-ns#type</propertyURI>
<valueURI label="Person">https://schema.org/Person</valueURI>
</annotation>
<annotation references="adam.shepherd">
<propertyURI label="member of">https://schema.org/memberOf</propertyURI>
<valueURI label="BCO-DMO">https://doi.org/10.17616/R37P4C</valueURI>
</annotation>
</annotations>
</eml>
Semantic annotations may also be inserted in the additionalMetadata element that is nested under the eml root element. This type of semantic annotation has a describes element and a metadata element containing the annotation. The metadata element has an annotation element. The content of the describes element is the subject of the semantic annotation. Within the annotation element are propertyURI and valueURI elements. The propertyURI is the object property and the valueURI is the object of the annotation. The URIs should ideally point to terms in controlled vocabularies.
Multiple annotation elements may be embedded in the same metadata element to assert multiple semantic statements about the same subject. Annotating different subjects requires using additional describes elements.
<eml>
...
<additionalMetadata>
<describes>john.smith</describes> <- subject is "john.smith"
<metadata>
<annotation>
<propertyURI>http://www.w3.org/1999/02/22-rdf-syntax-ns#type</propertyURI> <- object property 1 is "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"
<valueURI>https://schema.org/Person</valueURI> <- object 1 is "https://schema.org/Person"
</annotation>
<annotation>
<propertyURI>http://schema.org/hasOccupation</propertyURI> <- object property 2 is "http://schema.org/hasOccupation"
<valueURI>http://purl.obolibrary.org/obo/RoleO_0000248</valueURI> <- object 2 is "http://purl.obolibrary.org/obo/RoleO_0000248"
</annotation>
</metadata>
</additionalMetadata>
...
</eml>
The additionalMetadata element is nested under the eml root element and contains metadata that is not suitable for other parts of the EML document. It is intended to extend EML to include metadata that is not already available in another part of the EML specification, or to include site- or system-specific extensions that are needed beyond the core metadata. The content of this field is any well-formed XML fragment. Additional information may be found in chapter 8.2.
The additionalMetadata element contains describes elements, metadata elements, and annotation elements. The describes element has a pointer to the id attribute for the sub-portion of the resource that is described by the additional metadata. It is the metadata element that holds the additional metadata to be included in the document. This metadata field describes the element referenced in the describes element preceding it. Nested under the metadata element is the annotation element. An annotation is a precisely-defined semantic statement about an element in the EML document. The subject of the semantic statement is the id being referenced in the describes element that precedes the metadata element. Each annotation element consists of a propertyURI element and valueURI element that respectively define the property and value (object) of the semantic statement. The associated labels can be used to display the property and value in a more readable format to users. Each URI should be resolvable to a controlled vocabulary that provides a precise definition, relationships to other terms, and multiple labels for displaying the statement.
The following additionalMetadata annotation (Example 5) describes a semantic statement having the subject "adam.shepherd", which is the id of another element in the EML document. The object property of the statement is https://schema.org/memberOf. Finally, the value (object) in the semantic statement is https://doi.org/10.17616/R37P4C. Taken together, the semantic statement could be read as "adam.shepherd is a member of BCO-DMO".
- Example 5:
additionalMetadataelement annotation
<eml>
<dataset id="dataset-01">
<title>Data from Cedar Creek LTER on productivity and species richness for use in a workshop titled "An Analysis of the Relationship between Productivity and Diversity using Experimental Results from the Long-Term Ecological Research Network" held at NCEAS in September 1996.</title>
<creator id="adam.shepherd">
<individualName>
<salutation>Mr.</salutation>
<givenName>Adam</givenName>
<surName>Shepherd</surName>
</individualName>
</creator>
<dataTable id="CDR-biodiv-table">
<entityName>CDR LTER-patterns among communities.txt</entityName>
...
</dataTable
</dataset>
...
<additionalMetadata>
<describes>adam.shepherd</describes>
<metadata>
<annotation>
<propertyURI label="member of">https://schema.org/memberOf</propertyURI>
<valueURI label="BCO-DMO">https://doi.org/10.17616/R37P4C</valueURI>
</annotation>
</metadata>
</additionalMetadata>
...
</eml>