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Update eml-semantic-annotation-primer.md
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split two FAQs into multiple paras.  added a note about DC
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mobb committed Jul 31, 2019
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Expand Up @@ -590,7 +590,9 @@ A: Within the context of semantic annotation, "dereferencing" refers to the proc

<a name="URIvsURL"></a>

A: The distinctions among URIs (Uniform Resource Identifiers), URLs (Uniform Resource Locators), and URNs (Uniform Resource Names), relate to differentiating the functionalities of identifying a Resource, as opposed to locating a Resource, or doing both. URLs are all URIs (with some edge case exceptions subject to argument), and URNs are also URIs. In many cases, URIs serve both to name and locate a Resource. Within the vision of the Semantic Web, URIs are ideally unique, persistent URNs identifying some Web Resource, that can also serve to locate and retrieve (dereference) a representation of that Resource (URLs). The formal specification for these terms and what they mean is found in the IETF's RFC 3986, section 1.1.3 (https://tools.ietf.org/html/rfc3986#section-1.1.3). Another acronym one may encounter with increasing frequency is IRI (Internationalized Resource Identifier) that simply extends the concept of a URI to include full Unicode character set, rather than just ASCII in its construction (https://tools.ietf.org/html/rfc3987).
A: The distinctions among URIs (Uniform Resource Identifiers), URLs (Uniform Resource Locators), and URNs (Uniform Resource Names), relate to differentiating the functionalities of identifying a Resource, as opposed to locating a Resource, or doing both. URLs are all URIs (with some edge case exceptions subject to argument), and URNs are also URIs. In many cases, URIs serve both to name and locate a Resource.

Within the vision of the Semantic Web, URIs are ideally unique, persistent URNs identifying some Web Resource, that can also serve to locate and retrieve (dereference) a representation of that Resource (URLs). The formal specification for these terms and what they mean is found in the IETF's RFC 3986, section 1.1.3 (https://tools.ietf.org/html/rfc3986#section-1.1.3). Another acronym one may encounter with increasing frequency is IRI (Internationalized Resource Identifier) that simply extends the concept of a URI to include full Unicode character set, rather than just ASCII in its construction (https://tools.ietf.org/html/rfc3987).


**Q: What is SKOS?**
Expand All @@ -599,11 +601,13 @@ A: SKOS (Simple Knowledge Management System) is a W3C recommendation for organiz

**Q: What is RDFS?**

A: RDFS (Resource Description Framework Schema; https://www.w3.org/TR/rdf-schema/) is a W3C recommendation that extends the formal vocabulary for describing Resources expressed in an RDF data model (i.e., in a graph). "Base" RDF https://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/ provides a set of concepts for creating a graph model of data-- consisting of one or more triples relating a subject, predicate, and object. RDFS adds to the base RDF model by specifying a number of well-defined concepts and properties, such as rdfs:Class and rdfs:subClassOf. These and other RDFS classes and properties, enable data and knowledge modellers to express many relationships between the Subject and Object of a Triple. In the context of the Semantic Web, the RDF model relies extensively on dereferenceable URIs in the subject and predicate positions, and URIs or literals in the object position (there are small formal exceptions to this not immediately relevant here). RDF triples can be expressed in several syntaxes, including XML, JSON-LD, and Turtle, among others. RDFS then can be used to enrich the precision and expressivity of the components of a triple, as well as clarify the relationships among these.
A: RDFS (Resource Description Framework Schema; https://www.w3.org/TR/rdf-schema/) is a W3C recommendation that extends the formal vocabulary for describing Resources expressed in an RDF data model (i.e., in a graph). "Base" RDF https://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/ provides a set of concepts for creating a graph model of data-- consisting of one or more triples relating a subject, predicate, and object. RDFS adds to the base RDF model by specifying a number of well-defined concepts and properties, such as rdfs:Class and rdfs:subClassOf. These and other RDFS classes and properties, enable data and knowledge modellers to express many relationships between the Subject and Object of a Triple.

In the context of the Semantic Web, the RDF model relies extensively on dereferenceable URIs in the subject and predicate positions, and URIs or literals in the object position (there are small formal exceptions to this not immediately relevant here). RDF triples can be expressed in several syntaxes, including XML, JSON-LD, and Turtle, among others. RDFS then can be used to enrich the precision and expressivity of the components of a triple, as well as clarify the relationships among these.

**Q: Can you provide an example of a controlled vocabulary with a rdfs:label or skos:label?**

A: Most Semantic Web vocabularies make extensive use of rdfs:label or SKOS label properties. For example, this URI: http://purl.dataone.org/odo/ECSO_00000536 is from the ECSO ontology, under development by NSF's DataONE and Arctic Data Center. Within that ontology, the URI is associated with an rdfs:label of "Carbon Dioxide Flux", and a skos:altLabel of "CO2 flux". If you dereference the URI, you will see how the BioPortal ontology repository displays this information-- providing a human-readable representation of the underlying RDF/OWL language in which the ontology is stored.
A: Most Semantic Web vocabularies make extensive use of rdfs:label or SKOS label properties. For example, this URI: http://purl.dataone.org/odo/ECSO_00000536 is from the ECSO ontology, under development at NCEAS by NSF's DataONE and Arctic Data Center. Within that ontology, the URI is associated with an rdfs:label of "Carbon Dioxide Flux", and a skos:altLabel of "CO2 flux". If you dereference the URI, you will see how the BioPortal ontology repository displays this information-- providing a human-readable representation of the underlying RDF/OWL language in which the ontology is stored.

**Q: An image of an RDF Graph: is great, but a computer doesn't parse that. What does the RDF look like?**

Expand All @@ -625,7 +629,7 @@ that asserts:

"World Wide Web"(Subject) "creator"(Predicate) "Timothy Berners Lee"(Object) .

...although some semantic purists might question whether the Dublin Core property "Creator" can be used in this way as an RDF predicate, since it is not semantically defined-- would its rdfs:label be "creatorOf" or "hasCreator"?. Regardless of the formal semantic well-formedness of this Triple, however, one can see the expressive power of the RDF data model, and the value of dereferenceable URIs.
...although some semantic purists might question whether the Dublin Core property "Creator" can be used in this way as an RDF predicate, since it is not semantically defined-- would its rdfs:label be "creatorOf" or "hasCreator"? (Dublin Core does not say!). Regardless of the formal semantic well-formedness of this Triple, however, one can see the expressive power of the RDF data model, and the value of dereferenceable URIs.

A better solution would be to use the semantically defined term from SIO (the Semantic Science Integrated Ontology) http://semanticscience.org/resource/SIO_000364 as the predicate, with an rdfs:label "has creator"

Expand All @@ -643,7 +647,7 @@ https://orcid.org/0000-0003-1279-3709 http://semanticscience.org/resource/SIO_00

Within the SIO ontology, SIO_000364 and SIO_000365 are defined as inverses of one another. This enables one to ask both questions-- "who created the Web?" (A: Tim Berners Lee), and "what did Tim Berners Lee create" (A: the Web)-- even though you only asserted one of the Triples.

Finally, it is worth noting that one's choice of which Ontologies to use is important. Within the Ecological and Environmental sciences, there are several highly-recommended vocabularies, including those from the OBO Foundry (e.g. ChEBI, EnvO), as well as SIO. Specifically for annotating scientific measurements, the Arctic Data Center and DataONE are developing an Ontology for Ecosystem Measurements, ECSO.
Finally, it is worth noting that one's choice of which Ontologies to use is important. Within the Ecological and Environmental sciences, there are several highly-recommended vocabularies, including those from the OBO Foundry (e.g. ChEBI, EnvO), as well as SIO. Specifically for annotating scientific measurements, the Arctic Data Center and DataONE are developing an Ontology for Ecosystem Measurements, ECSO. We have used all these in the examples.

**Q: Are there tools are available to help data managers select subjects, predicates, and objects to annotate with?**

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