ont-app/vocabulary

Integration between Clojure keywords and URIs, plus support for RDF-style language-tagged literals.

This library should work under both clojure and clojurescript.

Installation
A brief synopsis
Motivation
Defining keyword Identifiers (KWIs) mapped to URI namespaces
Resource types
Language-tagged strings
Typed Literals
- The tag multimethod
- The untag multimethod
Common Linked Data namespaces
Support for SPARQL queries
- sparql-prefixes-for
- prepend-prefix-declarations
License

Installation

Available at clojars.

For which see the declarations for your favorite build tool.

A brief synopsis

(ns ...
 (:require
   [ont-app.vocabulary.core :as voc]))

> (voc/as-kwi "http://www.w3.org/2000/01/rdf-schema#subClassOf")
:rdfs/subClassOf

> (voc/as-uri-string :rdfs/subClassOf)
"http://www.w3.org/2000/01/rdf-schema#subClassOf"

> (voc/as-qname :rdfs/subClassOf
"rdfs:subClassOf"

> (voc/resource= :rdfs/subClassOf "http://www.w3.org/2000/01/rdf-schema#subClassOf")
true

This works off of metadata assigned to namespaces or vars:

> (voc/put-ns-metadata! 'tmp
   {:vann/preferredNamespacePrefix "tmp"
    :vann/preferredNamespaceUri "file://tmp/"
    })

> (def my-temp-file (clojure.java.io/file "/tmp/my-file.txt"))

> (voc/as-uri-string  my-temp-file)
"file://tmp/my-file.txt"

> (voc/as-kwi my-temp-file)
:tmp/myfile.txt

> (voc/as-qname my-temp-file)
"tmp:myfile.txt"

These methods are dispatched on a resource-type method in the discussed below.

RDF-style language tags and typed literals are also supported ...

(def my-thing {:name #{"my thing@en" "meine Sache@de "mi cosa@es" "我的东西@zh"}
               :height "2.3^^unit:Meter})

Motivation

Clojure provides for the definition of keywords, which function as identifiers within Clojure code, and serve many useful purposes. These keywords can be interned within specific namespaces to avoid collisions. The role played by these keywords is very similar to the role played by URIs within the Linked Open Data (LOD) community, which also has a regime for providing namespaces.

Ont-app/vocabulary provides mappings between Clojure namespaces and URI-based namespaces using declarations within Clojure metadata on those namespaces.

It also lets you attach the same metadata to Clojure vars with the same effect.

There is support for a similar arrangement within Clojurescript, though some things are done a little differently given that Clojurescript does not implement metadata in the same way.

These mappings set the stage for using Keyword Identifiers (KWIs) mappable between Clojure code and the wider world through a correspondence with URIs.

Another construct from RDF that may have application more generally in graph-based data is that of a language-tagged literal, which tags strings of natural language with their associated language. For example we could use such tags to express the differing orthographies of "gaol"@en-GB vs. "jail"@en-US. This library defines a custom reader tag voc/lstr for declaring similar language-tagged strings, e.g. #voc/lstr "gaol@en-GB" and #voc/lstr "jail@en-US".

There is a similar arrangement for typed literals using the #voc/dstr tag, e.g. #voc/dstr "1^^unit:Meter".

Defining Keyword Identifiers (KWIs) mapped to URI namespaces

(ns ...
 (:require
   ...
   [ont-app.vocabulary.core :as voc] 
   ...))

This will load function definitions interned in the vocabulary.core namespace, and also a number of other ns declarations, each dedicated to a commonly occurring namespace in the world of LOD.

Basic namespace metadata

Within standard (JVM-based) clojure, the minimal specification to support ont-app/vocabulary functionality for a given namespace requires metadata specification as follows:

(ns org.example
  {
    :vann/preferredNamespacePrefix "eg"
    :vann/preferredNamespaceUri "http://example.org/"
  }
  (:require 
  [ont-app.vocabulary.core :as voc]
  ...))

This expresses an equivalence between the clojure keyword...

  :eg/example-var

... and the URI ...

 <http://example.org/example-var>

The vann prefix refers to an existing public vocabulary which will be explained in more detail below.

Unfortunately, Clojurescript does not implement namespaces as first-class objects, and so there is no ns object to which we can attach metadata. So ont-app/vocabulary provides this idiom to achieve the same effect in both clj and cljs environments:

(voc/put-ns-meta!
 'org.example
  {
    :vann/preferredNamespacePrefix "eg"
    :vann/preferredNamespaceUri "http://example.org/"
  })

In Clojure, it simply updates the metadata of the named namespace. If the namespace does not already exist, it will be automatically created with create-ns. In Clojurescript, this updates a dedicated map from org.example to 'pseudo-metadata' in a global atom called cljs-ns-metadata.

Adding `vann` metadata to a Clojure Var

On the JVM, You also have the option of assigning the vann metadata described above to a Clojure Var.

(def 
  ^{
      :vann/preferredNamespacePrefix "myVar"
      :vann/preferredNamespaceUri "http://example.org/myVar/"
    }
   my-var nil)

This metadata is attached to the var.

(meta #'my.namespace/my-var)
->
{:vann/preferredNamespacePrefix "myVar",
 :vann/preferredNamespaceUri "http://example.org/myVar/",
 ...
 :name my-var,
 :ns #namespace[my.namespace]}}

All the same behaviors described herein for namespace metadata will apply.

Working with URI strings, KWIs, and qnames

Resources for which the resource-type can be derived can be rendered as URI strings, KWIs, and qnames using the functions described below.

`as-uri-string`

This maps instances of the resource type to a URI string.

URI syntax

There are two dynamic variables defined to recognize and partially parse URI strings under ont-app/vocabulary.

voc/ordinary-iri-str-re by default is defined as "^(http:|https:|file:).*"
voc/*exceptional-iri-str-re* by default is defined as #"^(urn:|arn:).*"
- A dynamic variable. Can be rebound to recognize other patterns as needed

`as-kwi`

Maps instances of the resource type to a KeyWord Identifier (KWI). This will be a qualfied keyword whose namespace is the prefix declared in vann metadata.

`as-qname`

Maps instances of the resource type to a qname string embeddable in many RDF formats. Where possible this will use the prefixes declared in vann metadata, but failing that it will fall back on a URI enclosed in angle brackets.

`resource=`

Returns a truthy value when two different resources map to the same URI, regardless of datatype.

Accessing namespace metadata

`put-ns-meta!` and `get-ns-meta`

Let's take another look at the metadata we used above to declare mappings between clojure namespaces and RDF namespaces:

(voc/put-ns-meta!
 'org.example
  {
    :vann/preferredNamespacePrefix "eg"
    :vann/preferredNamespaceUri "http://example.org/"
  })

Note that the metadata for this module includes some qualified keywords in this format:

:<prefix>/<name>

The relations preferredNamespaceUri and preferredNamespacePrefix are part of the public VANN vocabulary, with well-defined usage and semantics.

The namespace for vann is also declared as ont-app.vocabulary.vann in the ont_app/vocabulary/core.cljc file, with this declaration:

(voc/put-ns-meta!
 'ont-app.vocabulary.vann
 {
   :rdfs/label "VANN"
   :dc/description "A vocabulary for annotating vocabulary descriptions"
   :vann/preferredNamespaceUri "http://purl.org/vocab/vann"
   :vann/preferredNamespacePrefix "vann"
   :foaf/homepage "http://vocab.org/vann/"
 })

Using the put-ns-meta! function ensures that this metadata works on both clojure and clojurescript.

There is an inverse of put-ns-meta! called get-ns-meta:

> (voc/get-ns-metadata 'ont-app.vocabulary.foaf)
{
 :dc/title "Friend of a Friend (FOAF) vocabulary"
 :dc/description "The Friend of a Friend (FOAF) RDF vocabulary,
 described using W3C RDF Schema and the Web Ontology Language."
 :vann/preferredNamespaceUri "http://xmlns.com/foaf/0.1/"
 :vann/preferredNamespacePrefix "foaf"
 :foaf/homepage "http://xmlns.com/foaf/spec/"
 :dcat/downloadURL "http://xmlns.com/foaf/spec/index.rdf"
 :voc/appendix [["http://xmlns.com/foaf/spec/index.rdf"
                 :dcat:mediaType "application/rdf+xml"]]
 })
>

These are much richer descriptions than the minimal example in the previous section, with metadata encoded using several different public vocabularies, described below.

Note that these are all simple key/value declarations except the :voc/appendix declaration which is in the form

:voc/appendix [[<subject> <predicate> <object>]....],

This includes triples which elaborate on constructs mentioned in the key-value pairs in the rest of the metadata, in this case describing the media types of files describing the vocabulary which are available for download at the URLs given. This vector-of-triples format is readable by one of ont-app/vocabulary's siblings, ont-app/igraph.

`prefix-to-ns`

We can get a map of all the prefixes of namespaces declared within the current lexical environment:

> (voc/prefix-to-ns)
{"dc" #namespace[ont-app.vocabulary.dc],
 "owl" #namespace[ont-app.vocabulary.owl],
 "ontolex" #namespace[ont-app.vocabulary.ontolex],
 "foaf" #namespace[ont-app.vocabulary.foaf],
 ...
 }
 >

In Clojurescript, since there's no ns object, the results would look like this:

> (voc/prefix-to-ns)
{"dc" ont-app.vocabulary.dc,
 "owl" ont-app.vocabulary..owl,
 "ontolex" ont-app.vocabulary.ontolex,
 "foaf" ont-app.vocabulary.foaf,
 ...
 }
 >

`ns-to-namespace`

We can get the URI namespace associated with an ns

In Clojure:

> (voc/ns-to-namespace (find-ns 'ont-app.vocabulary.foaf))
"http://xmlns.com/foaf/0.1/"
>

In both Clojure and ClojureScript:

> (voc/ns-to-namespace 'ont-app.vocabulary.foaf)
"http://xmlns.com/foaf/0.1/"
>

`namespace-to-ns`

We can get a map from namespace URIs to their associated clojure namespaces:

> (voc/namespace-to-ns)
{
 "http://www.w3.org/2002/07/owl#"
 #namespace[org.naturallexicon.lod.owl],
 "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#"
 #namespace[org.naturallexicon.lod.nif],
 "http://purl.org/dc/elements/1.1/"
 #namespace[org.naturallexicon.lod.dc],
 "http://www.w3.org/ns/dcat#"
 #namespace[org.naturallexicon.lod.dcat],
 ...
 }
>

With the usual allowance for clojurescript described above.

`ns-to-prefix`

We can get the prefix associated with an ns:

> (voc/ns-to-prefix (voc/cljc-find-ns 'org.naturallexicon.lod.foaf))
"foaf"
>

`clear-caches!`

For performance reasons, these metadata values are all cached. If you're making changes to the metadata and it's not 'taking', you may need to clear the caches:

> (voc/clear-caches!)

Resource types

The as-uri-string, as-kwi, as-qname and resource= methods are each despatched on the resource-type multimethod, which in turn can be associated with named context layers.

The `resource-type` multimethod

Each of the methods described above are dispatched on a method (resource-type <value>) -> [ <context> <datatype>].

The operative context is specified in the @voc/resource-types atom described below.

Resource-type contexts

Different application domains may need to make different distinctions between resource types (for example RDF requires that we recognize blank nodes, and Jena provides special functionality for such nodes). The voc/resource-type-context holds the operative context on which to dispatch resource types.

The default resource-type context is ::voc/resource-type-context.

Here's a toy example:

> (ns com.example.acme.employees
   {:vann/preferredNamespacePrefix "acme-empl"
    :vann/preferredNamespaceUri "http://rdf.example.com/acme/employees"
    }
    (:require
     ...
     [ont-app.vocabulary.core :as voc]
     ...
     ))

> (defrecord Employee [name employee-id])

> (defmethod voc/resource-type [::voc/resource-type-context Employee]
  [_] ::EmployeeId)

> (defmethod voc/as-uri-string ::EmployeeId
    [this]
    (str "http://rdf.example.com/acme/employees/id=" (:employee-id this)))

> (defmethod voc/as-kwi ::EmployeeId
  [this]
  (voc/as-kwi (voc/as-uri-string this)))

> (def smith (->Employee "George Smith" 42))
{:name "George Smith", :employee-id 42}

> (voc/as-uri-string smith)
"http://rdf.example.com/acme/employees/id=42"

> (voc/as-kwi smith)
:acme-empl/id=42

> (voc/as-qname smith)
"acme-empl:id=42"

> (voc/resource= :acme-empl/id=42 "http://rdf.example.com/acme/employees/id=42")
true

Existing resource types

The following existing classes have declared Resource extensions as follows:

Resource	maps to resource type
java.lang.String javascript string	`:voc/UriString` `:voc/Qname` `:voc/NonUriString`
clojure.lang.Keyword cljs.core/Keyword	`:voc/Kwi` `:voc/QualifiedNonKwi` `:voc/UnqualifiedKeyword`
java.io.File	`:voc/LocalFile`

Of the resource class tags defined above, there are "as-X" methods defined for the following:

:voc/UriString
:voc/Qname
:voc/Kwi
:voc/LocalFile

X inferred from Y resource types

Methods dispatched on the following resource class tags are also defined:

:voc/KwiInferredFromUriString
- Derives the KWI based on the as-uri-string method, and vann metadata
:voc/UriStringInferredFromKwi
- Derives the URI string based on the as-kwi method, and vann metadata

So in the the example above we could have done this:

> (defmethod voc/as-uri-string ::EmployeeId
    [this]
    (str "http://rdf.example.com/acme/employees/id=" (:employee-id this)))

> (derive ::EmployeeId :voc/KwiInferredFromUriString)

Registering new resource-type contexts

New layers of logic can be added with register-resource-type-context!:

> (ns my-ns ...)
> (voc/register-resource-type-context! ::resource-type-context ::voc/resource-type-context)

This will enable new methods in my-ns to be dispatched on voc/resource-type [::myns/resource-type-context <some type>], overriding the behavior of voc/resource-type [::voc/resource-type-context <some type>].

Handling ambiguous contexts

Resource type contexts are managed in an atom called @voc/resource-types, one field of which is ::voc/on-ambiguity-fn. By default this will throw an error if there is not a unique lineage of resource-type contexts.

In such cases, you can rebind this key to perform the disambiguation with a function [context1 context2 ...] -> winning-context ...

(swap! voc/resource-types #(-> % assoc ::voc/on-ambiguity-fn
                                        #(-> % myns/order-contexts-by-precedence first)))

Common Linked Data namespaces

Part of the vision of the ont-app project is to provide a medium for expressing what adherents to Domain-driven Design and Behavior-driven Design call a "Ubiquitous Vocabulary". It also shares the vision of the Linked Data community that huge network effects can emerge when vocabularies emerge which are shared amongst a community of users working in the same domain.

There are a large number of public vocabularies dedicated to various application domains, some of which have gained a good deal of traction in the Linked Data community. Ont-app/vocabulary includes declarations of their associated namespaces, packaged within the core module, a module dedicated to wikidata, and another dedicated to linguistics.

Imported with ont-app.vocabulary.core

Requiring the ont-app.vocabulary.core module also loads ns declarations dedicated to some of the most commonly used RDF/Linked Open Data prefixes:

PREFIX	URI	Comments
rdf	https://www.w3.org/2001/sw/wiki/RDF	the basic RDF constructs
rdfs	https://www.w3.org/TR/rdf-schema/	expresses class relations, domain, range, etc.
owl	https://www.w3.org/OWL/	for more elaborate ontologies
vann	https://vocab.org/vann/	for annotating vocabulary descriptons
dc	http://purl.org/dc/elements/1.1/	elements of Dublin Core metadata initiative
dct	http://purl.org/dc/terms/	terms for the Dublin Core metadata initiative
sh	https://www.w3.org/TR/shacl/	for defining well-formedness constraints
dcat	https://www.w3.org/TR/vocab-dcat/	Data Catalog vocabulary
foaf	http://xmlns.com/foaf/spec/	the 'Friend of a Friend' vocabulary
skos	http://www.w3.org/2004/02/skos/core#	for thesaurus-type taxonomies
schema.org	https://schema.org/	mostly commercial topics, with web-page metadata and search-engine indexes in mind
qudt	http://qudt.org/schema/qudt/	Units, Dimensions and Datatypes vocabulary.
unit	http://qudt.org/vocab/unit#	Units module of the QUDT vocabulary.

Imported with ont-app.vocabulary.wikidata

Requiring the ont-app.vocabulary.wikidata module imports declarations for the several namespaces pertinent to the Wikidata database.

It also defines the value for Wikidata's public SPARQL endpoint as this constant:

ont-app.vocabulary.wikidata/sparql-endpoint

Imported with ont-app.vocabulary.linguistics

The ont-app.vocabulary.linguistics module declares namespaces for:

PREFIX	URI	Comments
ontolex	http://www.w3.org/ns/lemon/ontolex#	for encoding lexical data
pmn	http://premon.fbk.eu/ontology/core#	PreMOn - dedicated to describing English verbs
nif	http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#	Natural Language Interchange Format - for annotating corpora

There are also a set of namespaces particular to my Natural Lexicon project, which are still under development.

Language-tagged strings

RDF entails use of language-tagged strings (e.g. "gaol"@en-GB) when providing natural-language content. Typing this directly in Clojure code is a bit awkward, since the inner quotes would need to be escaped.

To enable this language tag, we must require the namespace:

(require ...
  [ont-app.vocabulary.lstr :refer [lang]]
  )

This library defines a reader macro #voc/lstr and accompanying deftype LangStr to facilitate writing language-tagged strings in clojure. The value above for example would be written: #voc/lstr "gaol@en-GB".

The reader encodes an instance of type LangStr (it is autoiconic):

> (def brit-jail #voc/lstr "gaol@en-GB")
brit-jail
> brit-jail
#voc/lstr "gaol@en-GB"
> (type brit-jail)
ont_app.vocabulary.lstr.LangStr
>

Rendered as a string, the language tag is dropped

> (str #voc/lstr "gaol@en-GB")
"gaol"
>

We get the language tag with lang:

> (lang #voc/lstr "gaol@en-GB")
"en-GB"
>

Typed literals

RDF has a regime for representing tagged datatpes analogous to language tags, e.g. 1^^xsd:integer. The ont-app.vocabulary.dstr module provides support for a similar approach in clojure using #voc/dstr...

> (voc/tag 42)
#voc/dstr "42^^xsd:long"
> (type #voc/dstr "42^^xsd:long")
ont_app.vocabulary.dstr.DatatypeStr
> (str #voc/dstr "42^^xsd:long")
"42"
> (dstr/datatype #voc/dstr "42^^xsd:long")
"xsd:long"
> (voc/as-uri-string (dstr/datatype #voc/dstr "42^^xsd:long"))
"http://www.w3.org/2001/XMLSchema#long"
> (voc/untag #voc/dstr "42^^xsd:long")
42
> (voc/tag (short 42))
#voc/dstr "42^^xsd:short"
> (untag #voc/dstr "42^^xsd:short")
42
> (type *1)
java.lang.Short

The `tag` multimethod

This takes one or two arguments.

With a second argument we can explicitly specify the datatype resource. The datatype spec will be translated with voc/as-qname...

> (voc/tag 1 :qudt/Meter)
#voc/dstr "1^^qudt:Meter"

We can omit the second argument if the type of the object is registered in dstr/default-tags ...

> dstr/default-tags
#<Atom@793bab96:
  {java.lang.Long "xsd:long",
   java.lang.Double "xsd:double",
   java.lang.Boolean "xsd:Boolean",
   java.util.Date "xsd:dateTime",
   java.lang.String "xsd:string",
   java.lang.Short "xsd:short",
   java.lang.Byte "xsd:byte",
   java.lang.Float "xsd:float"}>

> (voc/tag #inst "2000")
#voc/dstr "2000-01-01T00:00:00Z^^xsd:dateTime"

Here's a definition of the method for :xsd/dateTime:

(defmethod tag :xsd/dateTime
  [obj & _]
  (dstr/->DatatypeStr (-> obj (.toInstant) str)
                      "xsd:dateTime"))

The `untag` multimethod

This is the inverse of the tag method.

Typically we provide a single DatatypeStr instance, returning a native clojure instance...

> (voc/untag #voc/dstr "2000-01-01T00:00:00Z^^xsd:dateTime")
#inst "2000-01-01T00:00:00.000-00:00"

... with the operative defmethod...

(defmethod untag :xsd/dateTime
  [obj]
  (clojure.instant/read-instant-date (str obj)))

There is an optional second argument to handle cases where there is no untag method for the datatype in question.

With one argument we'll get an error...

> (voc/untag #voc/dstr "2.2^^qudt:Meter")
Execution error (ExceptionInfo) ... No untag method found for 2.2^^qudt:Meter

... so let's convert into feet...

> (defn meters-to-feet [m] (* 3.280839895 m))
> (voc/untag #voc/dstr "2.2^^qudt:Meter" #(-> % str read-string meters-to-feet))
7.217847769000001

Support for SPARQL queries and Turtle/n3

RDF is explicitly constructed from URIs, and there is an intimate relationship between SPARQL queries and RDF namespaces. ont-app/vocabulary provides facilities for extracting SPARQL prefix declarations from queries containing qnames.

`sparql-prefixes-for`

We can infer the PREFIX declarations appropriate to a SPARQL query:

> (voc/sparql-prefixes-for
             "Select * Where{?s foaf:homepage ?homepage}")
("PREFIX foaf: <http://xmlns.com/foaf/0.1/>")
>

`turtle-prefixes-for`

> (voc/turtle-prefixes-for "eg:SomeGuy foaf:homepage eg:SomeWebPage.")
("@prefix eg: <http://rdf.example.com/>."
 "@prefix foaf: <http://xmlns.com/foaf/0.1/>.")

`prepend-prefix-declarations`

Or we can just go ahead and prepend the prefixes...

> (voc/prepend-prefix-declarations
               "Select * Where {?s foaf:homepage ?homepage}")
"PREFIX foaf: <http://xmlns.com/foaf/0.1/>
Select * Where{?s foaf:homepage ?homepage}"
>

SPARQL is the default. Use voc/turtle-prefixes-for for turtle or n3...

> (voc/prepend-prefix-declarations
     voc/turtle-prefixes-for
     "eg:SomeGuy foaf:homepage eg:SomeWebPage.")

"@prefix eg: <http://rdf.example.com/>.\n@prefix foaf: <http://xmlns.com/foaf/0.1/>.\neg:SomeGuy foaf:homepage eg:SomeWebPage."

License

Distributed under the Eclipse Public License either version 1.0 or (at your option) any later version.

Released under Creative Commons Attribution-ShareAlike 4.0 International license. Under the terms of this license, if you display this logo or derivates thereof, you must include an attribution to the original source, with a link to https://github.com/ont-app, or http://ericdscott.com.

ont-app/vocabulary

ont-app/vocabulary

Contents

Installation

A brief synopsis

Motivation

Defining Keyword Identifiers (KWIs) mapped to URI namespaces

Basic namespace metadata

Adding vann metadata to a Clojure Var

Working with URI strings, KWIs, and qnames

as-uri-string

URI syntax

as-kwi

as-qname

resource=

Accessing namespace metadata

put-ns-meta! and get-ns-meta

prefix-to-ns

ns-to-namespace

namespace-to-ns

ns-to-prefix

clear-caches!

Resource types

The resource-type multimethod

Resource-type contexts

Existing resource types

X inferred from Y resource types

Registering new resource-type contexts

Handling ambiguous contexts

Common Linked Data namespaces

Imported with ont-app.vocabulary.core

Imported with ont-app.vocabulary.wikidata

Imported with ont-app.vocabulary.linguistics

Language-tagged strings

Typed literals

The tag multimethod

The untag multimethod

Support for SPARQL queries and Turtle/n3

sparql-prefixes-for

turtle-prefixes-for

prepend-prefix-declarations

License

Adding `vann` metadata to a Clojure Var

`as-uri-string`

`as-kwi`

`as-qname`

`resource=`

`put-ns-meta!` and `get-ns-meta`

`prefix-to-ns`

`ns-to-namespace`

`namespace-to-ns`

`ns-to-prefix`

`clear-caches!`

The `resource-type` multimethod

The `tag` multimethod

The `untag` multimethod

`sparql-prefixes-for`

`turtle-prefixes-for`

`prepend-prefix-declarations`