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completed another round of proofreading of the RDF doc

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Steve Baskauf 2018-09-30 09:24:05 -05:00
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@ -90,15 +90,15 @@ In this document, the following formatting conventions will be used. Full IRIs w
<http://bioimages.vanderbilt.edu/contact/kirchoff#coblea>
```
Abbreviated UIRIs will be shown as ```inline code``` in the form ```namespace:localName```, e.g., ```rdf:type```. Namespace abbreviations when shown by themselves will also be shown in italics, e.g., ```dwc:``` . Examples will be displayed in Courier type.
Abbreviated UIRIs will be shown as ```inline code``` in the form ```namespace:localName```, e.g., ```rdf:type```. Namespace abbreviations when shown by themselves will also be shown in italics, e.g., ```dwc:``` . Examples will be displayed in code blocks.
XML is a widely understood form of RDF serialization. Therefore, all examples given here will be shown as RDF/XML. In most cases, they will also be shown in Turtle. For more detailed information about RDF serialization, see part 3 of the [Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners3RDFbasics.md) and the references cited there.
XML is a widely understood form of RDF serialization. Therefore, all examples given here will be shown as RDF/XML. In most cases, they will also be shown in Turtle. For more detailed information about RDF serialization, see [part 3 of the Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners3RDFbasics.md) and the references cited there.
#### 1.3.2 Internationalized Resource Identifier (IRI) (non-normative)
Data providers make use of a variety of identifiers to refer to resources they wish to provide. These identifiers may be locally unique within the provider's database, or they may be globally unique. Providers have sought to make their identifiers globally unique through such means as "Darwin Core Triplets" (institutionCode:collectionCode:catalogNumber) and creation of [UUIDs](http://www.iso.org/iso/home/store/catalogue_ics/catalogue_detail_ics.htm?csnumber=62795). However, only identifiers in the form of [IRIs](http://tools.ietf.org/html/rfc3987) can be valid subjects of statements (known as RDF triples) in RDF, so neither “Darwin Core Triples” nor UUIDs can be used in unmodified form for that purpose. IRIs are a superset of a narrower form of identifiers known as Uniform Resource Identifiers (URIs) that can be used in place of [IRIs](http://tools.ietf.org/html/rfc3986). This document will refer exclusively to IRIs with the understanding that URIs may be used in place of IRIs.
The most familiar form of IRI is a Uniform Resource Locator (URL) which not only identifies a resource, but provides information about retrieving an information resource (i.e., a resource that can be transmitted in electronic form) such as text in the form of an HTML web page. However, in general IRIs may identify non-information resources (physical or conceptual entities) that are not transmittable electronically, e.g., ```<http://bioimages.vanderbilt.edu/contact/kirchoff#coblea>```, a person. If a client attempts to retrieve a non-information resource by dereferencing its HTTP IRI, a process called [content negotiation](http://tools.ietf.org/html/rfc2616#section-12) is used to refer the client to the IRI of an information resource representation of the non-information resource. For humans, this is usually a web page, while for semantic clients (machines) the representation is a document in the form of RDF/XML. For more detailed information about IRIs see part 1 of the [Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners1URIs.md) and the references cited there.
The most familiar form of IRI is a Uniform Resource Locator (URL) which not only identifies a resource, but provides information about retrieving an information resource (i.e., a resource that can be transmitted in electronic form) such as text in the form of an HTML web page. However, in general IRIs may identify non-information resources (physical or conceptual entities) that are not transmittable electronically, e.g., ```<http://bioimages.vanderbilt.edu/contact/kirchoff#coblea>```, a person. If a client attempts to retrieve a non-information resource by dereferencing its HTTP IRI, a process called [content negotiation](http://tools.ietf.org/html/rfc2616#section-12) is used to refer the client to the IRI of an information resource representation of the non-information resource. For humans, this is usually a web page, while for semantic clients (machines) the representation is a document in the form of RDF/XML. For more detailed information about IRIs see [part 1 of the Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners1URIs.md) and the references cited there.
##### 1.3.2.1 Persistent Identifiers (normative)
@ -144,7 +144,7 @@ Because of the machine-oriented nature of RDF, a provider must assume that a con
For these reasons, terms should be used as predicates in RDF only after the data provider has carefully examined the documentation and usage guidelines associated with the vocabulary or ontology which defines the term and has determined that use of that term is consistent with the meaning which the provider intends to impart to the triple in which the term is to be used as a predicate.
For more detailed information about the implications of using terms that have range, domain, and subproperty declarations in RDF, see part 4 of the [Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners4Vocabularies.md). For more detailed information about how OWL is used to define complex properties of terms in RDF, see part 7 of the [Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners7OWL.md).
For more detailed information about the implications of using terms that have range, domain, and subproperty declarations in RDF, see [part 4 of the Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners4Vocabularies.md). For more detailed information about how OWL is used to define complex properties of terms in RDF, see [part 7 of the Beginner's Guide to RDF](https://github.com/tdwg/rdf/blob/master/Beginners7OWL.md).
#### 1.4.3 Use of Darwin Core terms in RDF (normative)
@ -178,7 +178,7 @@ Humans commonly use name strings to represent resources that are physical or con
#### 1.5.3 Situations where a string value serves as a keyword to enable searching (non-normative)
Imagine that a person identifies an oak tree as “Quercus alba”. The data associated with that identification may provide the property/value pair ```dwc:scientificName```=”Quercus alba”. This implies that the person asserted that the tree was a representative of a taxon associated with the name _Quercus alba_. The data associated with the identification may also provide the property/value pair ```dwc:order```=”Fagales”. One might think that this would imply that the person who asserted the identification also asserted that the tree was included in the order Fagales. However, it is likely that the person did not make such an assertion and in fact may have never even heard of the order Fagales. Rather, a database manager subscribing to a particular taxonomic hierarchy asserted that all identifications with a ```dwc:scientificName``` value of “Quercus alba” should also have a property/value pair of dwc:order=”Fagales” in order to allow users of the database to search for identifications that were related because they shared the common value for that ```dwc:order``` property.
Imagine that a person identifies an oak tree as “Quercus alba”. The data associated with that identification may provide the property/value pair ```dwc:scientificName```=”Quercus alba”. This implies that the person asserted that the tree was a representative of a taxon associated with the name _Quercus alba_. The data associated with the identification may also provide the property/value pair ```dwc:order```=”Fagales”. One might think that this would imply that the person who asserted the identification also asserted that the tree was included in the order Fagales. However, it is likely that the person did not make such an assertion and in fact may have never even heard of the order Fagales. Rather, a database manager subscribing to a particular taxonomic hierarchy asserted that all identifications with a ```dwc:scientificName``` value of “Quercus alba” should also have a property/value pair of ```dwc:order```=”Fagales” in order to allow users of the database to search for identifications that were related because they shared the common value for that ```dwc:order``` property.
The point is that in order to more accurately describe the real situation, there should be two separate sets of information: one which asserts that the person identified the tree as a representative of a taxon for which the scientific name “Quercus alba” is applied, and one which asserts the relationship between that taxa and higher taxa such as one to which the name “Fagales” is applied.
@ -566,9 +566,9 @@ Turtle
                                   "S. Claramunt, et al. 2009. Polifilia de Campylorhamphus y la Descripción de un Nuevo Género para C. pucherani (Dendrocolaptinae). The Awk 127(2):430-439."@es.
```
In the [RDF 1.1 Semantics](http://www.w3.org/TR/rdf11-mt/#literals-and-datatypes) specification, datatype D-entailment is a direct extension to basic RDF. The [entailment rules in that specification](http://www.w3.org/TR/rdf11-mt/#entailment-rules-informative) establish that literals without explicit datatype attributes or language tags have an implicit datatype ```xsd:string```. That also entails that the ```rdf:type``` of those literals is ```xsd:string```. The practical implication of this is that literals that are exposed without datatype attributes or language tags should be interpreted by clients to be a sequence of characters, and not some other abstract or non-information resource that a human might interpret the sequence of characters to represent. This has practical implications in [Section 2.4.3](./index.htm#2.4.3_Object_resources_that_have_been_previously_represented_by) (where untyped literals are value strings intended to represent non-literal resources) and [Section 2.7](./index.htm#2.7_Darwin_Core_convenience_terms) (where untyped literals provide a convenient means for facilitating string-based searches). Although it is likely that many providers may initially choose to expose literals without datatype attributes, they should move towards replacing them with URIs or datatyped literals that accurately represent the type and properties of the resource that the untyped literals are intended to represent.
In the [RDF 1.1 Semantics](http://www.w3.org/TR/rdf11-mt/#literals-and-datatypes) specification, datatype D-entailment is a direct extension to basic RDF. The [entailment rules in that specification](http://www.w3.org/TR/rdf11-mt/#entailment-rules-informative) establish that literals without explicit datatype attributes or language tags have an implicit datatype ```xsd:string```. That also entails that the ```rdf:type``` of those literals is ```xsd:string```. The practical implication of this is that literals that are exposed without datatype attributes or language tags should be interpreted by clients to be a sequence of characters, and not some other abstract or non-information resource that a human might interpret the sequence of characters to represent. This has practical implications in [Section 2.4.3](#243-object-resources-that-have-been-previously-represented-by-literals-but-which-are-actually-non-literal-resources-non-normative) (where untyped literals are value strings intended to represent non-literal resources) and [Section 2.7](#27-darwin-core-convenience-terms-non-normative) (where untyped literals provide a convenient means for facilitating string-based searches). Although it is likely that many providers may initially choose to expose literals without datatype attributes, they should move towards replacing them with URIs or datatyped literals that accurately represent the type and properties of the resource that the untyped literals are intended to represent.
[Section 3.4](./index.htm#3.4_Terms_defined_by_Darwin_Core_that_are_expected_to_be_used_on) indicates which Darwin Core terms would be appropriately used with values having datatype or language attributes.
[Section 3.4](#34-terms-defined-by-darwin-core-that-are-expected-to-be-used-only-with-literal-values-normative) indicates which Darwin Core terms would be appropriately used with values having datatype or language attributes.
##### 2.4.1.2 Terms intended for use with literal objects (normative)
@ -989,7 +989,7 @@ Turtle
#### 2.7.4 Description of a taxonomic entity (normative)
The consensus embodied in the [TDWG Taxon Concept Transfer Schema (TCS) standard](http://www.tdwg.org/standards/117/) is that identification instances refer to taxon concept instances. Therefore it would be a best practice to describe taxonomic entities in RDF as taxon concepts sensu TCS. However, because the TCS standard is an XML schema, it is not directly translatable to RDF. It is considered to be out of the scope of this document to specify how taxon concepts should be rendered as RDF. Nevertheless, Darwin Core does define many convenience terms listed under the ```dwc:Taxon``` class that can be used as properties of ```dwc:Identification``` instances ([Section 3.5](./index.htm#3.5_Darwin_Core_convenience_terms_that_are_expected_to_be_used_o)).
The consensus embodied in the [TDWG Taxon Concept Transfer Schema (TCS) standard](http://www.tdwg.org/standards/117/) is that identification instances refer to taxon concept instances. Therefore it would be a best practice to describe taxonomic entities in RDF as taxon concepts sensu TCS. However, because the TCS standard is an XML schema, it is not directly translatable to RDF. It is considered to be out of the scope of this document to specify how taxon concepts should be rendered as RDF. Nevertheless, Darwin Core does define many convenience terms listed under the ```dwc:Taxon``` class that can be used as properties of ```dwc:Identification``` instances ([Section 3.5](#35-darwin-core-convenience-terms-that-are-expected-to-be-used-only-with-literal-values-normative)).
It might be argued that these convenience terms would more appropriately be properties of a ```dwc:Taxon``` instance. However, the object properties necessary to relate ```dwc:Taxon``` instances to name entities, references, parent taxa, and child taxa do not exist and the exact relationship between taxonomic entities such as taxon concepts, protonyms, taxon name uses, etc. has not been established using RDF. So the creation of functional ```dwc:Taxon``` instances described using RDF is not possible at the present time. Therefore this document establishes the convention that convenience terms for taxonomic entities should be properties of ```dwc:Identification```. The task of describing taxonomic entities using RDF must be an effort outside of Darwin Core. This guide does establish the object property ```dwciri:toTaxon``` for use in relating a Darwin Core identification instance to a taxonomic entity as defined elsewhere.
@ -1362,7 +1362,7 @@ dwc:lithostratigraphicTerms</br>dwc:group</br>dwc:formation</br>dwc:member</br>d
Darwin Core term | Notes
--- | ---
dwciri:inCollection | Use to link any subject resource that is part of a collection to the collection containing the resource. Recommended best practice is to use IRIs from [Global Registry of Biorepositories](http://grbio.org/). For details, see the list of sources of controlled values in the [Darwin Core informative ancillary web page](https://github.com/tdwg/rdf/blob/master/DwCAncillary.md). See [Section 2.7.3](d#273-ownership-of-a-collection-item-normative) for usage details.
dwciri:inCollection | Use to link any subject resource that is part of a collection to the collection containing the resource. Recommended best practice is to use IRIs from [Global Registry of Biorepositories](http://grbio.org/). For details, see the list of sources of controlled values in the [Darwin Core informative ancillary web page](https://github.com/tdwg/rdf/blob/master/DwCAncillary.md). See [Section 2.7.3](#273-ownership-of-a-collection-item-normative) for usage details.
dwciri:toTaxon | Use to link a ```dwc:Identification``` instance subject to a taxonomic entity such as a taxon, taxon concept, or taxon name use. See [Section 2.7.4](#274-description-of-a-taxonomic-entity-normative) for usage details.
dwciri:inDescribedPlace | Use to link a ```dcterms:Location``` instance subject to the lowest level standardized hierarchically-described resource. It is expected that such resources will be linked to higher levels in the hierarchy by the organization minting the IRI. Recommended best practice is to use IRIs from the [GeoNames geographical database](https://www.geonames.org/). For details, see the list of sources of controlled values in the [Darwin Core informative ancillary web page](https://github.com/tdwg/rdf/blob/master/DwCAncillary.md). See [Section 2.7.5](#275-names-of-geographic-subdivisions-normative) for usage details.
dwciri:earliestGeochronologicalEra<br/>dwciri:latestGeochronologicalEra | Use to link a ```dwc:GeologicalContext``` instance to chronostratigraphic time periods at the lowest possible level in a standardized hierarchy. Use ```dwciri:earliestGeochronologicalEra``` to point to the earliest possible geological time period from which the cataloged item was collected and the object property ```dwciri:latestGeochronologicalEra``` to point to the latest possible geological time period from which the cataloged item was collected. The organization minting the IRI should link those time periods to higher levels in the hierarchy. Recommended best practice is to use IRIs defined by the [International Commission on Stratigraphy](http://www.stratigraphy.org/). For details, see the list of sources of controlled values in the [Darwin Core informative ancillary web page](https://github.com/tdwg/rdf/blob/master/DwCAncillary.md). See [Section 2.7.6](#276-chronostratographic-geological-timescale-descriptors-normative) for usage details.