update semantics in EML 2.2.0 section

Updated the semantics in EML 2.2.0 section.

docs/eml-semantic-annotations-primer.md

@@ -6,22 +6,40 @@ A semantic annotation is the attachment of semantic metadata to a resource. Sema
 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**. Ideally, these components should be globally unique and should be resolvable uniform resource identifiers (URI) 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. 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.
 
 * Additional background information on the RDF data model: https://www.w3.org/TR/WD-rdf-syntax-971002/
-* The Ecosystem Ontology (ECSO): https://github.com/DataONEorg/sem-prov-ontologies/tree/master/observation
 
 
 ## Semantic Annotations in EML 2.2.0
 A general introduction to creating semantic annotations in an EML document is made here. Users can find additional explanations and examples for each kind of annotation listed in the appropriate section below.   
 
 In **EML 2.2.0** there are 5 kinds of semantic annotations that can be made in an EML document. The first 3 kinds are at the **dataset-level**, **entity-level**, and **attribute-level**. Semantic annotations may also be inserted in the `annotations` and `additionalMetadata` elements that are nested under the `eml` root element (**/eml/annotations** and **/eml/additionalMetadata**). 
 
+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. 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. 
+
+Multiple `annotation` elements may be embedded in the same dataset, entity-level or attribute element to assert multiple semantic statements.
+```
+<dataset or entity-level or attribute>          <- subject 
+    <annotation>
+        <propertyURI></propertyURI>             <- object property 1
+        <valueURI></valueURI>                   <- object 1
+    </annotation>
+    <annotation>
+        <propertyURI></propertyURI>             <- object property 2
+        <valueURI></valueURI>                   <- object 2
+    </annotation>
+</dataset or entity-level or attribute>
+```
+
+
+Semantic annotations made for **/eml/annotations** involve 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.  
+
 
 
 
 ### Dataset-level annotation
 
 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 at:[insert link].
 
-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 is embedded in a containing `dataset` element. The subject of the semantic statement is the `dataset` element that contains the annotation. 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.
+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` elemetn is embedded in a containing `dataset` element. The subject of the semantic statement is the `dataset` element that contains the annotation. 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".
 
@@ -52,7 +70,7 @@ In the following dataset-level annotation (Example 1), the subject of the semant
 
 Entities are usually tables of data (EML element `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 (EML element `view`) and stored procedures (EML element `storedProcedure`). Views and stored procedures are produced by an RDBMS or related system. Other types of data such as: raster (EML element `spatialRaster`), vector (EML element `spatialVector`) or spatialReference image data are also data entities. An `otherEntity` element would be used to describe types of entities that are not described by any other entity type. Entity-level EML elements are nested under `dataset` elements. Further information about entities may be found at: [insert link].
 
-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 is embedded in a containing entity-level element. The subject of the semantic statement is the entity-level element that contains the annotation. 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.
+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. 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".
 
@@ -79,9 +97,9 @@ In the following entity-level annotation (Example 2), the subject of the semanti
 
 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` EML elements, in addition to custom modules. Refer to the Data Structures Modules documentation for additional information about attributes [insert link].  
 
-A typical attribute annotation is embedded in a containing `attribute` element. The subject of the semantic statement is the `attribute` element that contains the annotation. 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 for annotating attributes that are measurements contained in tabular formats the preferred "default" object property is "contains measurements of type" (`http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType`).
+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. 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 for annotating attributes that are measurements contained in tabular formats the preferred "default" object property is "contains measurements of type" (`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".
+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