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Removed the Q's relating to semantics because they were outside the scope of this FAQ. The Q's and A's have been transferred to the semantic annotation primer.
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stevenchong committed Jul 30, 2019
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Expand Up @@ -412,90 +412,3 @@ That page also contains instructions for using the transformation
stylesheet that comes with EML2.1.0 to convert v2.0.0/1 documents to
v2.1.0.


**Q:**

**A:**


**Q:** What does ‘dereferenced’ mean? (context: a URI in an annotation)

**A:** Within the context of semantic annotation, "dereferencing" refers to the process of interpreting a URI, and providing "useful information" back about the Resource of interest. The phrase "resolving a URI" is often used synonymously with "dereferencing", but technically "resolution" refers to the process of determining HOW and WHAT to do with the URI, whereas "dereferencing" is explicitly about the action taken and its result, which is typically retrieving a representation of the Resource of interest. The formal specification for these terms and what they mean is found in the IETF's (Internet Engineering Task Force) RFC (Request for Comments) 3986 (<https://tools.ietf.org/html/rfc3986>).


**Q:** Explain the difference between an URI and a URL. (context: sample URIs look a lot like a URL. What makes it a URI?)

**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 (URL) and retrieve (dereference) a representation of that Resource. 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:** oveeview (“When are ID’s required in the EML”) - context: annotations

**A:**


**Q:** What is SKOS?

**A:** SKOS (Simple Knowledge Management System) is a W3C recommendation for organizing a vocabulary in thesauri, taxonomies, and other classification schemes. SKOS provides a set of concepts and properties, that, when expressed in a formal RDF-compatible syntax, can assist with interpreting the relationship of terms with one another, such as defining some category as *broader than* another. For example, one could state in SKOS syntax, that "animals" is a *broader concept than* "mammals". Definitive specification of SKOS can be found at <https://www.w3.org/TR/2009/REC-skos-reference-20090818/>. SKOS does not provide strong semantics (see RDFS example below), but SKOS concepts and properties can be used to describe looser, more lexically-oriented variations in term usage (as opposed to more formally defined logical assertions, such as *owl:sameAs* or *owl:equivalentClass*),within more expressive knowledge organization frameworks, such as RDFS/OWL ontologies.


**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 and Linked Data, the RDF model relies extensively on dereferenceable URIs in the subject and predicate positions, and dereferenceable 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 concepts are used to enrich the precision and expressivity of the components of a triple, as well as clarify the relationships among these, as opposed to just RDF.


**Q:** An example of a controlled vocabulary with a *rdfs label* or *skos label* would be helpful here in this text about labels.

**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 ECSO8.owl 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.


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

**A:** As mentioned above, RDF is a data model based on *triples*, each of which consists of a *subject*, *predicate*, and *object*. In order to function interoperably on the Web, however, there is the need for these triple components to be constructed of dereferenceable URIs, although the *object* value can also be a *literal*. RDF triples can be "serialized" in several syntaxes, including XML, JSON-LD, Turtle, N-Triples, and others. These syntaxes are isomorphic, such that translations of RDF graphs from one serialization to another are available-- enabling consistent interpretation by machines.

Perhaps the most straigthforward serialization of RDF graphs for human interpretation is N-Triples, where an RDF triple could look like this:

<http://purl.obolibrary.org/obo/CHEBI_16526> <http://purl.obolibrary.org/obo/RO_0000087> <http://purl.obolibrary.org/obo/CHEBI_76413> .

These are three URIs-- representing the Subject, Predicate, and Object of a Triple. The "." indicates the end of the Triple. Dereferencing these URIs (e.g. a Web browser or specialized application) one can see that this Triple represents the statement:

*"Carbon dioxide"*(Subject) *"has role"*(Predicate) *"Greenhouse Gas"*(Object)

While the phrasing is a bit awkward sounding, the meaning is clear by simply depicting the *rdfs:Labels* of those terms from the ChEBI (Chemical Entities of Biological Interest) and RO (Relation) ontologies, that are both robust OBO Foundry ontologies.

As another example:
<http://purl.obolibrary.org/obo/NCIT_C20461> <http://purl.org/dc/elements/1.1/creator> <https://orcid.org/0000-0003-1279-3709> .

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. Alternatively one could use a schema.org predicate as follows:

<http://purl.obolibrary.org/obo/NCIT_C20461> <http://schema.org/creator> <https://orcid.org/0000-0003-1279-3709> .

to similarly assert that

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

A better solution might be to use the more formally 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"*

<http://purl.obolibrary.org/obo/NCIT_C20461> <http://semanticscience.org/resource/SIO_000364> <https://orcid.org/0000-0003-1279-3709> .

...that would translate as (based on content of the rdfs:label):

*World Wide Web*(Subject) *has creator*(Predicate) *Tim Berners Lee*(Object)

or inversely, one could use <http://semanticscience.org/resource/SIO_000365> as the predicate, that has rdfs:Label *"is creator of"*

*Tim Berners Lee*(Subject) *is creator of*(Predicate) *World Wide Web*(Object)

<https://orcid.org/0000-0003-1279-3709> <http://semanticscience.org/resource/SIO_000365> <http://purl.obolibrary.org/obo/NCIT_C20461>.

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.

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

**A:** Yes, tools are being built to assist with the semantic annotation of EML documents, within the DataONE and Arctic Data Center data repository projects, and others.

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