The Ontologist

Controlled Vocabularies and Semantic Wikis

Kurt Cagle

Information Architect

Avalon Consulting, Ltd.

Copyright © 2012 Kurt Cagle

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The Ontologist

Controlled Vocabularies and Semantic Wikis

Balisage: The Markup Conference 2012
August 7 - 10, 2012

Overview

The Ontologist began its existence as a way of dealing with one of the more vexing problems of modern distributed applications - dealing with controlled vocabularies. This paper and talk will explore the design of the Ontologist at an application and theoretical level, and illustrate how it provides a synergy between XQuery and SPARQL development in order to build everything from list managers to knowledge management systems.

Controlled Vocabularies and Data Feeds

A controlled vocabulary typically appears at first as an enumerated set of terms (with the obvious temptation by schema designers to encode these terms in XSD schemas as enumerated simple types).

However, unlike a "normal" enumeration, controlled vocabulary terms have a number of properties which can make such a temptation a costly trap. In most cases such controlled vocabularies have a number of key characteristics:

  • Distinct labels and codes. The displayed value of the item in question will more than likely not be the same as the underlying code value that references the term in question. For instance, a set of colors might have the color name but use RGB notation for identifying the resources at a system level.

  • Temporality. Items may be added or removed from the underlying set over time, the values of given sets may change, or the preferred ordering of the set may change depending upon context. For instance, if your enumerated set contains the names of stores in a given region, this list may change as stores are added or closed, or as regions are redefined.

  • Subordinate Lists. A list of terms may themselves identify lists of terms. In this respect, there is a relationship (formal or implicit) that connects the parent term (or context) and the child terms. A list of countries, for instance, may contain a list of states, regions or provinces.

  • Uniqueness. The combination of label and code act as a defacto unique key for a given term.

  • Multiple representations. The set of metadata about a term exists independently of the representations used for those terms - a list of controlled vocabulary terms can be displayed as an XML construct of various flavors, JSON, CSV, HTML lists or tables or any other underlying format.

Significantly, these are also characteristics that are found within the notion of both Semantic and REST oriented resources. In effect, the terms of a controlled vocabulary can be thought of as having an associated URI that identifies each term and that also identifies the context. Indeed, in all cases, the context for a list will be a term itself.

One other subtle point that brings the conflation of RESTful services and semantics full circle is the fact that conceptually each term in the given list can consequently be thought of as a reference to a resource, with an associated metadata bundle. That is to say, the URI (a semantic construct) for the term is also either itself or can be associated one-to-one with a unique URL (a RESTful construct) for the term.

Put another way, the context term and its correlated "child" terms are in effect a data feed. The term feed in this case is in fact intended to conflate with the notion of "news feed" - an Atom feed and an RSS feed are in fact both subclasses of data feeds in which the child nodes are "articles" that are returned in a date descending order, are paged, and may actually contain summary content (or even the full content) of the associated article as part of each feed entry.

More formally a data feed can be identified conceptually as the following

  • Feed

    • Feed URI - This identifies the context term's "address" and systemic or global name.

    • Feed Label - This gives the "user centric" label that identifies the feed.

    • Feed Code - This is an identifier or "value" that establishes the internal (or local) state for the context term.

    • Feed Description - This is used to provide a more detailed description of the context term, and could be anything from a few lines of text to the body of a web page.

    • Feed Timestamp - This provides one or more timestamp entities that identify the age of the context term.

    • Context Content - This is effectively the document payload corresponding to the term in question. This will be a representation of the resource indicated by the context item, and may be optional (not all terms necessarily have content payloads, and not all representations need to transmit those payloads if they do).

    • Relationship - This is a (potentially implicit) term identifying the relationship of the context item with its associated entryset. In a folder/file relationship, this will usually be implicit, but in a semantic relationship, this will typically be the predicate of a triple.

    • Entry Set - This is a set of entries that satisfy the relationship between the context term and the associated child items in the ontological space.

      • Entry URI - This identifiest the entry term's address and systemic or global name.

      • Feel Label - This gives the "user-centric" label that identifies the entry.

      • Entry Code - This provides the value for the entry term.

      • Entry Description - This provides a detailed description of the entry term.

      • Entry Timestamp - This provides one or more timestamp entities that identify the age of the entry term.

      • Entry Content - This is a representation of the entry term's corresponding resource.

In theory, such a construct could be recursive, but ultimately it's worth understanding that any context term may in fact have multiple relationships that identify the subordinate entries, and that as some of these relationships are themselves orthogonal the ultimate structure that is conceptually described here is not a recursive descent tree, but is rather a graph that may ultimately end up resolving to multiple "roots".

Note that while the above may be seen as being a description of an atom or RSS feed, it is also, not accidentally, the structure of a typical "search" page, such as the results of a Google search query. In this case, the "context" term is the query expression passed. Typing in "Balisage", for instance, will establish the context for search to be the term "Balisage", while the relationship is implicitly those items that have some contextual relevance to the search. The search results will typically contain as a label the name of the site and the description being a short summary of the site itself as a snippet, with one or more links to different representations of that same resource as hypertext links.

URIs, CURIEs and Triplexes

There is a subtle distinction here - the URI of the resource is effectively the primary URL, but secondary links are still links to different representations of the same conceptual resource. Similarly an "image" search is in fact a feed that establishes its primary representation of resources as image URLs that are then rendered in a table or sequences of hyperlinked images. This only highlights the fact that the feed structure is in fact orthogonal to its representation.

In a typical website, the relationships between pages (which can be thought of as terms) have until fairly recently followed the folder/file model of containment that reflected the underlying file system that stored the relevant web-page resources. This meant that URIs typically tended to follow a containment format as well. However, over the course of the last decade the balance of development has shifted from a file system model to a database model for the storing and generation of web content, which has in turn shifted the URI structures for such resources to a more key oriented one.

This has led to some confusion about the construction of URIs and how they relate to REST. From a purely REST standpoint, a GUID can effectively identify a resource in a data-centric environment. The URL

http://www.myserver.com/term/AFD23C2F559A412C

has one major benefit - it is globally unique. A URL rewriter script could do a lookup on the term and retrieve that particular key with very little parsing overhead. On the other hand, it tells the person requesting the term next to nothing about it, and it is arguable that, in many cases, being able to readily identify such a term by an easily interpretable string outweighs the parsing cost of that string.

After considerable experimentation (which went into the design of the Ontologist), all URIs were designed with the following convention:

http://www.myserver.com/domainName/className/instanceName.faceName

The notation is broken into a domain, a class, and a instance, along with a face that identifies which particular representation to use for displaying the term feed. The class name establishes the category within a given domain, while the instance name establishes a human readible unique name for a given resource. For instance, the color blue would be given as "color/blue". Because classes themselves are also terms, they would be in the "class" category - "class/color".

The domain name arose from a realisation after working with a client who wanted to have classes that might be used by multiple different groups or customers. That is to say, there might be a "class/article" for multiple potential vendors, as well as the possibility of common classes that could be used by all vendors. While it is possible to pass these in parametrically, it was such a useful term for a number of reasons that it was made part of the key description.

Consequently, the Ontologist makes use of a triplex notation of the form

domainName:className:instanceName

which uniquely identified each term in the system, relative to the server host. These were not universal because the application was ported over various servers, from development to staging to deployment, and as a consequence the specific URI could not correspond to a physical server.

It should be pointed out that these triplexes do have a direct correspondance with a qname. For server myserver.com, the corresponding qname for the color blue in the common domain would look like:

{http://myserver.com:8050/common/color/}blue

where everything within the brackets corresponds to the qualifying category term and everything after is the instance term, or conceptually, common:color: represents the qualifying category, and blue again represents the instance term. Similarly, the class of color would be in common:class:, corresponding to

{http://myserver.com:8050/common/class/}color

This notation is odd at first glance (its easy to get confused about the distinction between triplexes and CURIEs), but if you realize that a CURIE such as commonColor:blue corresponds to the triplex common:color:blue, it makes working with these resources in a semantic turtle notation somewhat more intuitive.

Note

It's easy to worry about such "plexes" getting out of control, but in practice none of the applications that have been built on top of the ontologist has ever needed more than three such terms. The combination of domain, class and instance, along with the realization that everything else can be built with these, seems to suffice in limiting the size of such plexes.

Terms and Assertions

Every term in the system is represented internally as an XML document with a structure very similar to that of the feed format, albeit not quite identical. Listing 1 gives an example of such a entry.

<entry xmlns="http://www.avalonconsult.com/xmlns/entry">
    <metadata>
        <id>common:color:Blue</id>
        <url>/common/color/Blue</url>
        <class>common:class:color</class>
        <code>#0000FF</code>
        <domain>app:domain:Common</domain>
        <label key="label">Blue</label>
        <description key="description" xml:space="preserve">Item 'Blue' with code '#0000FF' is in 
        class 'Color'.</description>
        <lastModified>2012-05-02T19:02:51.361676-07:00</lastModified>
    </metadata>
    <assertions>
        <assert subject="common:color:Blue" predicate="app:rel:instanceOf"
            object="common:class:Color"/>
        <assert subject="common:color:Blue" predicate="app:rel:domain" object="app:domain:Common"/>
        <assert subject="common:color:Blue" predicate="app:rel:termOf" object="app:class:Term"/>
        <assert subject="common:color:Blue" predicate="app:rel:workflow"
            object="app:workflow:Active"/>
        <assert subject="common:color:Blue" predicate="app:rel:label" object="#label"/>
        <assert subject="common:color:Blue" predicate="app:rel:description" object="#description"/>
    </assertions>
</entry>
        

This particular term establishes the color blue in the collection common:colors. The metadata block holds the context information. If there was a need for a payload it would be in a content element, though here there isn't any. What's perhaps most important is the assertion elements in the assertions set.

Each assertion is, in effect, an RDF triple, with a subject, predicate and object. In most cases the subject will be the id of the term. The predicate will be a term as well, usually one of a class of relationships that are defined within either the application domain, (part of app:rel:) or in some other domain (such as geo:rel:). The object will be another term resource in the system (the assumption here is that the system is self-contained).

The first predicate is especially worth studying. This defines the instanceOf relationship between the color blue and the class color within the common domain. In effect, this is a directed named vertex pointing to the common:class:Color term. Relative to the color:Blue term, this is an outbound relationship, relative to the class:color term, this is an inbound relationship (that is to say, class:Color does not have any corresponding outbound vector to the color blue). Thus, for the class:Color object, there is a SPARQL query statement of the form

?color app:rel:instanceOf common:class:Color.

that identifies the set of subjects that have an outbound instanceOf assertion to class:Color.

This is a fairly reasonable operation for a triple store. What makes the Ontologist useful is that it provides a set of libraries for doing the same type of operations within an XQuery context in an XML data store such as MarkLogic (though it could do the same in eXist or other fourth generation XML databases).

Note

A question that has been asked by reviewers of this paper is why RDF-XML wasn't employed for this. As it turns out, RDF-XML was explored as a potential vehicle to support this within the Ontologist initially, but it's structure generally does not index well within XML databases - the queries involved are not especially complex but they are involved enough that indexing optimizations becomes a major factor.

Additionally, there is a certain degree of deliberate redundancy in the system because more traditional XQuery searches are also permitted on the Ontologist set, both to order the sequence of returned objects and to create filtered subsets. Given the advantages inherent for optimized searching and indexing, this generally outweighs the cost of maintaining redundant data in multiple forms (and is typical of XQuery applications).

The structure of a class term can provide some additional insight into the application.

<entry xmlns="http://www.rtis.com/xmlns/vocabulary">
    <metadata>
        <qname>common:class:color</qname>
        <url>/common/class/color</url>
        <class>common:class:fda_list</class>
        <code>color</code>
        <domain>app:domain:Common</domain>
        <label key="label">Color</label>
        <description xml:space="preserve" key="description">A vocabulary of colors as defined by 
        the FDA.</description>
        <lastModified>2012-05-02T19:02:51.361676-07:00</lastModified>
    </metadata>
    <assertions>
        <assert subject="common:class:color" predicate="app:rel:subClassOf"
            object="common:class:Class"/>
        <assert subject="common:class:color" predicate="app:rel:domain" object="app:domain:Common"/>
        <assert subject="common:class:color" predicate="app:rel:defaultRel"
            object="app:rel:instanceOf"/>
        <assert subject="common:class:color" predicate="app:rel:label" object="#label"/>
        <assert subject="common:class:color" predicate="app:rel:description" object="#description"/>
        <assert subject="common:class:color" predicate="app:rel:workflow"
            object="app:workflow:Active"/>
    </assertions>
</entry>
        

In this case, the term class:color is treated as a subclass of class:Class, which can be thought of as a folder of classes in the common domain. The term is also an item in the domain app:domain:Common (domain "sweeps" can include a fairly large number of terms. The third assertion, however, is one of the most powerful. The defaultRel predicate is used to determine, when no formal predicate is specified for the Ontologist, what predicate should be used. It is in fact used as in the following SPARQL query:

 $term         app:rel:defaultRel ?relationship.
 ?child-terms  ?relationship      $term.
        

$term here is the term from the XQuery invoking this call (such as common:class:color), ?relationship is the predicate determined by the default relationship and ?child-terms are the ones that satisfy this relations.

A similar relationship can be used to walk "up" the tree of default terms as if it was an inheritance tree (it typically is).

 $child-term   ?relationship      ?parent-term.
 ?parent-term  app:rel:defaultRel ?relationship.
        

Although it should be noted that it is possible that a given term may in fact have more than one such relationship, meaning again that this system, while tending towards hierarchies in its structures, is still very much graphlike in the bigger picture.

Faces, Presentations and Ingestors

One consequence of the use of such XML embodiments of terms is that the entries involved can not only contain assertion pointers, but can also identify and invoke the representations used to both present content and to ingest it. An example can illustrate how this works.

A face, as indicated earlier, is identified by an extension (although it can also be identified parametrically from a query string parameter). The face is also identified as being tied in with an HTTP verb - PUT, POST, GET, or DELETE. Within an entry there is an optional <pipelines> element that can include maps of the form:

<pipelines>
    <error href="/modules/app/class/Error/error.xq"/>
    <method match="GET">
        <face match="html">
            <action href="/path/to/class/get-html.xq">
                <search ref="s1"/>
            </action>
        </face>
        <face match="keys.xml">
            <action href="/path/to/class/get-html.xq">
                <search ref="s1"/>
            </action>
            <action href="/path/to/class/transform-to-keys-xml.xq">
                <search ref="s1"/>
            </action>            
        </face>
        <face match="xml">
            <action href="/path/to/class/get-html.xq">
                <search ref="s1"/>
            </action>
        </face>
        ..
    </method>
</pipelines>
        

With the combination of method and face, it becomes possible to select a particular pipeline of actions for processing, along with the ability to retrieve additional parameters (not shown here). This uses a somewhat complex inheritance model. The Ontologist processor looks first in the term's XML to see if it has a processor. If it does, this is used. If it doesn't (or if the processor passes the modified object up the chain) the class corresponding to that term is queried, then the default rel for that term (in most cases, these are the same thing). This continues until either a match is found or the app:class:Term object (the root object in the system) is reached, which contains defaults for all potential views.

A particularly significant result of this of this is that a generic viewer can be created for terms, but that more specialized viewers can be built for specific classes - for instance, everything in a given domain may have different logos, arrangement of elements and even interpretations of content, and dedicated classes may be able to provide customized viewers or editors for specific types of payloads. This benefit extends to ingesters as well - input formats can be customized for specific class content, so that what gets saved may be processed from other sources. As an example, posting to a json face might take JSON content and convert it into XML before saving the resource, while posting to a zip face would unzip the content, for that particular class, and do some kind of post processing on the individual items in the file.

Summary

By combining such post processing with the creation of relevant assertions (though some editor interface) makes it possible for this system to effectively function as a semantic wiki or knowledge management system, with each term effectively being the same as one entry in the space. It is this piece which I plan on demonstrating at Balisage.

The Ontologist was written on MarkLogic Server 5.0, but it could reasonably work on any document-centric database, including XML databases such as eXist, JSON databases such as CouchDB, and Semantic Triple Stores that combine SPARQL and XQuery. The more important aspect of this is that it has the potential to be used in a wide variety of circumstances, from managing controlled vocabularies to hosting encyclopedic websites to acting as a Linked Data repository with queryable interfaces.

Bibliography

[Roy Fielding 2000] Fielding, Roy ThomasArchitectural Styles and the Design of Network-based Software Architectures, PhD Dissertation Thesis, Chapter 5. Representational State Transfer. University of California, Irvine © 2000. http://www.ics.uci.edu/~fielding/pubs/dissertation/top.htm.

[Semantics for the Working Ontologist 2011] Allemang, Dean and Hendler, JamesSemantics for the Working Ontologists, Effective Modeling in RDFS and OWL Morgan Kaufmann, 2nd Edition © 2011. http://workingontologist.org.