# Presentation: 313547

## Terminology Curation with the Semantic MediaWiki

- Harold Solbrig
- Informatics Architect
- Apelon, Inc.

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Slide 2

## The Primary Task

- Evaluate the roles, categories and organization of the National Cancer Institute (NCI)’s Cancer Thesaurus with respect to:
- Upper Level Ontological Principles
- ISO TC37 & Related principles
- As with Ontology construction, it was understood by all parties that this was a *process* – not a goal.

## Approach

- Gather appropriate upper level ontologies (BFO, Dolce, Top Bio, UMLS Semantic Net and OBO Relations Ontology) into a single, readily referenced format
- Load NCI Thesaurus into same format
- Multiple parties review, annotate, recommend and categorize
- Publish, analyze and evaluate results

## Solution

- By using the Semantic MediaWiki (SMW), we were able to accomplish all of the goals in a (very) reasonable period of time

## Discussion

- We also discovered that, with some extensions, the SMW could be useful for publishing, annotating and cross-referencing other terminological (and other..) resources.

## Questions?

- ... just kidding.

## Wiki’s

- Community developed
- Collaborative
- “Organic” – to the very core...
- Primary focus (to date) is human consumption
- Traceable, provenance automatically recorded, differences, undo and redo.

## MediaWiki

- _[http://en.wikipedia.org/wiki/Wiki](http://en.wikipedia.org/wiki/Wiki)_
- Base for WikiPedia and many others...
- Key characteristics
- Web based editing
- Page links
- Categories
- Templates

## MediaWiki 	

- Fully documented using (surprise!) mediawiki
- Rich mechanisms for discussion, curation, export, etc.

## Slide 11

## Common constructs

- [[Train Transport]] – hyperlink to page named “Train_Transport”
- ‘‘Italic’’, ‘‘‘Bold’’’
- * Bullet point
- [http://www.w3c.org/ The W3C] – hyperlink
- ... and much more

## Templates

## Templates

## Sample Template

- Parameter

- Extension call

## Semantic MediaWiki

## Semantic MediaWiki

- 3 Key extensions to MediaWiki
- Categories == Class
- PageA ...  [[Category:X]]  pageA rdf:Type category:X
- Category:Y ... [[Category:X]]  category:Y rdfs:subClassOf category:X
- Links == Role
- PageA ... [[PageB]]  PageA ...[[hasPart::PageB]]
- Attributes  == DataProperty
- [[population:=32,154,773]]
- Includes datatypes

## Categories and Relations

## Attributes

## Semantic Rendering

- Type (or superClass)

- Attribute Value

- Relation

- RDF (!)

## Thesaurus Content

## Templates?

- ; Gene_Product_Is_Biomarker_Type
- :  The role is used to designate the type of ...
- Kind: [[:Category:NCI_Kind]]
- ‘‘‘Semantic Type:’’’ [NCI_Semantic_Type::Category:SN_Conceptual_Entity|Conceptual Entity]

- Brittle, not readily changed...

## Templates?

- {{OntylogDescription|ns=NCI|text=“The role is used to designate...”}}
- {{Kind|ns=NCI|target=Kind}}
- {{ResourceRef|name=Semantic_Type|ns=NCI|target=Conceptual_Entity|targetns=SN}}

- Can readily be updated viat template...

## Commentary

- Link to another NCI comment

- Link to external Ontology

- Categorization in external Ontology

## Computed

## How is it Working?

- Very well!

## What can we do to improve it...

## Terminology

- Centrally curated
- Central to the practice of medicine
- Insurance and reporting
- Regulatory
- Research
- Clinical Practice
- Information Sharing
- ICD-9, CPT-4, SNOMED, ...

## Clinical Terminology

- Quality and content is important
- Needs central vetting, integration, qa
- Central model doesn’t scale
- Need input from (many) experts
- Need visible, active feedback loop

## Terminology Workflow 1995

- Controlled
- Terminology

- Curation

- (1)

- Distribution

- Books
- PDF

- Lists and
- Tables

- (2)

- (3)

- (4)

**Notes:**
Until recently, terminology was approached as a monolith, centrally controlled resource that was distributed for use via printed and ad-hoc machine readable formats.

Terminology was curated by a committee or organization composed of subject matter experts.
The distribution processed produced various “write only” outputs such as books and PDF.  If “IT enabled” output was present at all, it was in the for of ad-hoc lists and tables designed specifically for the controlled terminology at hand.
The user community took the outputs of the distribution mechanism, adapted, extended and (hopefully) utililzed the terminological resource for its intended purpose
Feedback, when it was possible at all, tended to be slow and ad-hoc at best.

## Terminology Workflow 1995

- Controlled
- Terminology
- ‘B’

- (1)

- (2)

- (3)

- Curation

- Distribution

- Books
- PDF

- Lists and
- Tables

**Notes:**
Until recently, every terminology had a different workflow, a different distribution mechanism, different formats & models.  Workflow destined for one end user process wasn’t compatible with the second.

## Terminology Workflow 2008

- Controlled
- Terminology

- Curation

- (1)

- Distribution

- (2)

- (3)

- (5)

- Common
- Distribution
- Model

- Online
- Services

- (4)

**Notes:**
Over the past 10+ years, the advent of a common distribution model and common services have enabled a more standardized distribution mechanism

Terminology was curated by a committee or organization composed of subject matter experts.
The distribution process now involves transforming the content into the terms of a common model and/or publishing it via standarized online services
A common model allows multiple terminology to be absorbed and integrated for common consumption
 Standardized API’s allow direct access to terminological content
The feedback mechanism, while improved by having the common model semantics at its disposal, is still limited and, in large, ad-hoc

## Terminology Workflow 2008

- Controlled
- Terminology

- Curation

- (1)

- Distribution

- (2)

- (3)

- (5)

- Common
- Distribution
- Model

- Online
- Services

- (4)

- Controlled
- Terminology
- B

**Notes:**
The common model and services allow multiple terminologies to be merged, published together. 

It also enables the user base to write generalized tools that can utilize mutliple terminologies

## Common Distribution Model

- LexGrid
- (a little bit of...) OWL
- NCI Thesaurus & SNOMED CT
- Still requires LexGrid-like additions
- “Pushing the envelope”
- UMLS RRF
- Although underspecified as a ‘model’

## Online Services

- OMG Terminology Query Services
- Not heavily used
- Perceived (incorrectly) as CORBA specific
- Perceived as too complex
- Object oriented and stateful
- ANSI Common Terminology Services
- Being adopted
- Necessary but not sufficient
- Stateless
- CTS-2
- Co-development beginning w/ HL7 & OMG

## Online Services

- LexBIG
- LexGrid for the Bio Informatics Grid
- Robust query specification
- Meets many end-user (developers) requirments
*Not simple to implement – it actually adds value*
*Not a standard  - but will be used to guide CTS-2*

## Workflow and Feedback

- Controlled
- Terminology

- Curation

- (1)

- Distribution

- (2)

- (3)

- (5)

- Common
- Distribution
- Model

- Online
- Services

- (4)

## The Feedback Component

- Curation

**Notes:**
Requirements
Enable community commentary and input
Provide access to editing and veting process (<Torah commentary>)
Status tracking (submitted, approved, denied, accepted, included in version X)
Community sanctioning (<sanger>)
Adhere to existing semantics (LexGrid, OWL, SKOS(?), etc).

## The Feedback Component

- Curation

- Semantic
- MediaWiki (++)

- Annotations and
- Change Requests

- Community
- Review

- Distribution

- Common
- Distribution
- Model

- Online
- Services

- Version
- Staging

## Issues and Next Steps

- (1) SHARED Semantics
- {{Definition|...}}
- {{Synonym|...}}}
- {{References|...}}
- {{DLSome|...}}
- {{DLAll|...}}
- ...
- 12620 anyone?

## Issues and Next Steps

- (2) Figure out namespaces
- NCI:Activity, AgroVoc:Fish, ...
- NCI_Activity, AgroVoc_Fish
- ???
- (2a) Identifiers (Activity vs. C12345)
- (2b) Versions
- (2c) URI’s (vs. URL’s)
- Internal
- External

## Certification and Sanctioning

- Who can edit?
- Who can validate?
- Who selects updates?
-  ... (see: http://en.citizendium.org/wiki/Main_Page

## Automatic Export

- Selecting sets of updates
- Formatting update recommendations for target curators, etc...

## Synchronization

- Changes implemented in terminology
- Update wiki pages
- Say what changed
- What changes are incorporated by value? By reference?

## Approach and Responsible Parties

- Shared Semantics
- Core set based on LexGrid & OWL
- Post on WIKI and link on SMW site
- Assigned to Apelon, Mayo, NCI, ???
- Extend to OBO, SKOS (?), XMDR...
- Connections to 12620

## Time Frame and Assignments

- URI’s, namespaces, naming
- UK NCR (CancerGrid) – looking at unAPI and servers
- (Hopefully) can provide URI resolver svc.
- Short term – use templates / extensions

## Content

- SNOMED-CT, ICD-9-CM, many, many others are already available via. Apelon DTS Services
- Available soon
- FMA, HL7 Version 3 Terminology, OBO Foundry (GO, PATO, etc) as time permits
- Others as needed (and funded...)

## What we’ve got to date

- Apelon DTS Server Extension
- Includes both defined *and* classified view (!)
- Export in restful XML (currentely Apelon, soon to be LexGrid)
- XMDR Export Format
- Protégé (Native *and* OWL 3.2) prototype
- Done by Mayo
- Both import *and* export
- Still needs templates

## Questions?

- This time for real 
- Note: SMW will be made externally available (w/ simple password) once we get contract specific info cleaned up (NCI will probably publish shortly)... contact:  _[hsolbrig@apelon.com](mailto:hsolbrig@apelon.com)__ for access._