Subject: another SKOS use case
From: Daniel Rubin <[email-masked]>
To: SWD WG <[email-masked]>
Date: Wed, 31 Jan 2007 07:28:42 -0800
List-Id: <public-swd-wg.w3.org>

Hi everyone,
I have one more use case which I just recently received from another community I'm working with.
Sorry this is late.
Daniel

>Call for Use Cases: Simple Knowledge Organization Systems (SKOS)
>
>
>Questions marked with an asterix (*) are more important.
>
>================================================================
>Section 0. Contact and confidentiality
>================================================================
>
>Contact e-mail: [email-masked]
>
>Do you mind your use case being made public on the working group
>website and documents? No
>
>================================================================
>Section 1. Application
>================================================================
>
>In this section we ask you to provide some information about the
>application for which the vocabulary(ies) and or vocabulary mappings
>are being used.
>
>Please note:
>-- If your use case does not involve any specific application, but
>consists rather in the description of a specific vocabulary, skip
>straight to Section 2.
>-- If your application makes use of links between different
>vocabularies, do not forget to fill in Section 3!
>
>  1.1. What is the title of the application?
>  1.2. What is the general purpose of the application?
>       What services does it provide to the end-user?
>
>*1.3. Provide some examples of the functionality of the application.
>Try to illustrate all of the functionalities in which the
>vocabulary(ies) and/or vocabulary mappings are involved.
>
>  1.4. What is the architecture of the application?
>       What are the main components?
>       Are the components and/or the data distributed across a
> network, or across the Web?
>
>  1.5. Briefly describe any special strategy involved in the
> processing of user actions, e.g. query expansion using the
> vocabulary structure.
>
>  1.6. Are the functionalities associated with the controlled
> vocabulary(ies) integrated in any way with functionalities provided
> by other means? (For example, search and browse using a structured
> vocabulary might be integrated with free-text searching and/or some
> sort of social bookmarking or recommender system.)
>
>  1.7. Any additional information, references and/or hyperlinks.
>
>================================================================
>Section 2. Vocabulary(ies)
>================================================================
>
>In this section we ask you to provide some information about the
>vocabulary or vocabularies you would like to be able to represent using SKOS.
>
>Please note:
>-- If you have multiple vocabularies to describe, you may repeat
>this section for each one individually or you may provide a single
>description that encompasses all of your vocabularies.
>-- If your use case describes a generic application of one or more
>vocabularies and/or vocabulary mappings, you may skip this section.
>-- If your vocabulary case contains cross-vocabulary links (between
>the vocabularies you presented or to external vocabularies), please
>fill in section 3!
>
>  2.1. What is the title of the vocabulary? If you're describing
> multiple vocabularies, please provide as many titles as you can.

RadLex
>
>  2.2. Briefly describe the general characteristics of the
> vocabulary, e.g. scope, size...
RadLex provides a structured vocabulary of terms used in the field of radiology.  Currently completed are listings of anatomic terms and "findings", which includes things that can be seen on or inferred from images produced by radiologists.  These two sets include a total of about 7500 terms.  A list of the terms used to describe the creation of such images, including information about the equipment used and the various imaging sequences performed, will be complete by the end of 2007.
>
>  2.3. In which language(s) is the vocabulary provided?
>       In the case of partial translations, how complete are these?
English.
>
>*2.4. Please provide below some extracts from the vocabulary. Use
>the layout or presentation format that you would normally provide
>for the users of the vocabulary. Please ensure that the extracts you
>provide illustrate all of the features of the vocabulary.
>
Below are screenshots from the online browsing version of RadLex, www.radlex.com.
The left side of the screen shows the hierarchy, with the current term in bold.  The right side of the screen shows details of the term, which include:
--Term name
--ID number
--parents, and their relation to the term
--children, and their relation to the term
and optionally, any
--mappings to other vocabularies
--definition
--synonyms
--source (a reference publication which includes this term)
--other comments (such as derivation of the term, special or preferred uses of it, etc.)

Example 1 is a standard entry:

Example 2 includes a definition, a comment, and a synonym:

Example 3 shows a term with several types of relationships to the various children:

>  2.5. Describe the structure of the vocabulary.
>       What are the main building blocks?
>       What types of relationship are used? If you can, provide
> examples by referring to the extracts given in paragraph 2.4.

There are 9 separate hierarchies in the vocabulary:
Treatment; Image acquisition, Processing and Display; Modifier; Finding; Anatomic Location; Uncertainty (to be renamed Certainty); Teaching Attribute; Relationship; and Image Quality(as seen in the screenshots above).  Each term is given a numerical ID with no inherent semantics.  There are currently no relations holding between terms in different hierarchies, though this could be developed in future (e.g. linking of particular Findings to potential Anatomic Locations.)

The relationships used among terms include:

Continuous with  [DEF: Two structures are “continuous with” one another if they are immediately adjacent and physically connected to one another.  This relationship is often used for cavitary and tubular structures, such as the continuity between the left ventricle and the aorta.  This is a reflexive relation.]

Branch of [DEF: a smaller conduit is a “branch of” a larger conduit if it is one of a group of two or more conduits that continue in the direction of flow where only one conduits had existed before.  It is permissible for one of the continuing conduits to maintain the same name of original conduits.  This relation is often used with arteries.]
Branch [DEF: the converse relation to “branch of”]
Tributary of  [DEF: a smaller conduit is a “tributary of” a larger conduit if it is one of a group of two or more vessels that join to form a single conduit in the direction of flow.  This relation is often used with veins. ]
Tributary [DEF: the converse relation to “tributary of”]

Part of  [DEF:  one object is “part of” another object if it comprises less than all of the other object.  This relation is often used with solid body parts and organs.]

Segment of [DEF: one tubular structure is a “segment of” another if it defines a part of that structure divided perpendicular to the axis of the tube.  This relation is often used to define the subparts of tubular structures, such as arteries, veins, and intestines.

·        Part [DEF: the converse relation to “part of”]

Segment [DEF: the converse relation to “segment of”]

Contained in [DEF: One structure is “contained in” another if the first structure is inside the other.  For example the liver is contained in the abdominal cavity.]
Contains [DEF: the converse relation to “contained in”]
Is a; Type of
Member of [DEF: One structure is a “member of” a set of structures.  For example, the “liver” is a member of the “set of viscera of abdomen”]
Member [DEF: the converse relation to “member of”]
Synonym: [the term is a less-preferred synonym of a preferred term]

For instance, in Example 3, “nervous system” has a part called “brain”, and “nervous system” contains “nervous system spaces”.  The view of the hierarchy itself does not reveal the relationships among the terms; this information is found within the term features, shown in this format on the right-hand side.

>  2.6. Is a machine-readable representation of the vocabulary
> already available (e.g. as an XML document)? If so, we would be
grateful if you could provide some example data or point us to a hyperlink.
Yes.  Protégé and XML version of the vocabulary are available at http://www.radlex.org/radlex/docs/downloads.html
>
>  2.7. Are any software applications used to create and/or maintain
> the vocabulary?
>       Are there any features which these software applications
> currently lack which are required by your use case?

The Protege ontology editor is currently used to refine and maintain the vocabulary.  One plug-in was added to enable search in the concept hierarchy, rather than just among the “instances” (this was contributed by Daniel Rubin).
>
>  2.8. If a database application is used to store and/or manage the
> vocabulary, how is the database structured? Illustration by means
> of some table sample is welcome.
Protege is used as the main storage/management application.  Terms are stored as classes.  Synonyms are stored as separate terms.
>
>  2.9. Were any published standards, textbooks or written guidelines
> followed during the design and construction of the vocabulary?
>       Did you decide to diverge from their recommendations in any
> way, and if so, how and why?
We used basic guidelines from Cimino and Chute, such as ensuring that a term only corresponds to one concept. As we are developing the terminology into a more structured form, with more types of relationships, we are allowing different parents, as long as the relationship type is different.  E.g. one ISA parent, one PART-OF parent, etc.  We relied on SNOMED and the American College of Radiology Index as a starting point for terminology development.
>
>  2.10. How are changes to the vocabulary managed?
Potential changes are submitted to the chair of the RadLex Steering Committee of the Radiological Society of North America, who consults with the relevant lexicon development committee.  Accepted changes are periodically incorporated into the vocabulary.  The first release was made public in November 2006.
>
>  2.11. Any additional information, references and/or hyperlinks.
>The vocabulary can be searched and browsed online at www.radlex.org.

>================================================================
>Section 3. Vocabulary Mappings
>================================================================
>
>In this section we ask you to provide some information about the
>mappings or links between vocabularies you would like to be able to
>represent using SKOS.
>
>Please note:
>-- If your use case does not involve vocabulary mappings or links,
>you may skip this section!
>
Ø       3.1. Which vocabularies are you linking/mapping from/to?
Ø       We are developing a mapping to the corresponding terms/codes in SNOMED (Systematized Nomenclature of Medicine) and the ACR (American College of Radiology) Index.
>
>*3.2. Please provide below some extracts from the mappings or links
>between the vocabularies. Use the layout or presentation format that
>you would normally provide for the users of the mappings. Please
>ensure that the examples you provide illustrate all of the different
>types of mapping or link.
These are currently under development.
>
>  3.3. Describe the different types of mapping used, with reference
> to the examples given in paragraph 3.2.
Mappings are stored in slots in the Protégé database.

>  3.4. Any additional information, references and/or hyperlinks.