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fix Q's format and wording
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Made Q's bold and changed the wording so they are in the form of questions.
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stevenchong committed Jul 30, 2019
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Expand Up @@ -581,36 +581,36 @@ Following are tutorials and supplemental background reading
Below are answers to questions some readers had, which may be helpful to you. If you have additional questions, please bring them up in your community for feedback.


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

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, 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 Comment) 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?)
**Q: What is the difference between an URI and a URL? Sample URIs look a lot like a URL...**

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: oveeview (“When are ID’s required in the EML”) - context: annotations
**Q: When are ID’s required in the EML (for annotations)?**

A:

Q: What is SKOS?
**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 within more expressive knowledge organization frameworks, such as RDFS/OWL ontologies.

Q: What is RDFS?
**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.

Q: An example of a controlled vocabulary with a rdfs label or skos label would be helpful here in this text about labels.
**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 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?
**Q: An image of an RDF Graph: 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:
Perhaps the most straightforward 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 .

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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?
**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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