# Presentation: 804314

## Content Conversion Process

**Content Conversion Process**

**Presentation to XMDR Group**
**07/13/2005**
**Harold Solbrig**
**Division of Biomedical Informatics**
**Mayo Clinic**

## Outline

**The conversion task**
**Individual Cases**
**Issues, discussion, etc.**

## The Conversion Task

## The Conversion Task

**Transform an arbitrary thesaurus, terminology, code list, classification scheme, ontology, ... into a common semantic and syntactical form.**

## Target ModelInformation Model (partial)

## Semantic NormalizationBasic Steps

**Identify all of the unique ‘concepts’**
**Primary (concepts/terms/classes/entities)**
**Secondary (classifications, types, etc.)**
**Associations (roles, slots, relationships)**
**Properties (attributes, slots)**
**Anonymous constructs**
**Establish a permanent concept id scheme**

## LexGrid ModelCoded Entry

_**LexGrid Model**_**Coded Entry**

## LexGrid ModelCodedEntry Node

## Semantic NormalizationBasic Steps

**Identify semantically significant properties**
**Concept Code**
**Preferred Designation (language specific)**
**Secondary Designations (synonyms/terms)**
**Definitions**
**Comments/annotations**
**Concept status mappings**

## LexGrid ModelConcept Property

_**LexGrid Model**_**Concept Property**

## LexGrid ModelConcept Property Node

## Semantic NormalizationBasic Steps

**4.****	****Identify explicit and implicit associations**
**Subtype/subclass**
**Broader/narrower**
**Stated associations (causes, hasEtiology)**
**Mappings to other schemes**

## Semantic NormalizationBasic Steps

**5.****	****Classify and catalog associations**
**Transitivity, symmetry, etc.**
**(Note: definitional, not ‘active’)**
**Forward and reverse names**
**Reference to associated concept**

## LexGrid ModelInformation Model (partial)

## LexGrid ModelAssociation Node

## LexGrid ModelAssociation Node

**Source concept**

**Target **
**(concept / Data)**

## LexGrid ModelAssociation Node

## LexGrid ModelAssociation Node

_**LexGrid Model**_**Association Node**

**Body *****(has regional parts)***

**Head**

**Neck**

**Upper limb**

**Right Upper limb**

**Left Upper limb**

**Lower limb**

**Right Lower limb**

**Left Lower limb**

**Trunk**

**                      ****Targets**

**                  ****Source**

## Semantic NormalizationBasic Steps

**Fill in the bits and pieces**
**Assign unique identifier**
**Catalog sources, properties, languages, data types, qualifiers, status, etc**
**Short name, official name, description, copyright, etc**
**7.****	****Versioning/ releases**

## LexGrid ModelCoding Scheme Node

**LexGrid Model****Coding Scheme Node**

## LexGrid ModelCoding Scheme Node

## LexGrid ModelCoding Scheme Node

## LexGrid ModelCoding Scheme Node

## LexGrid ModelCoding Scheme Node

## LexGrid Formats

**.mdl**

**LexGrid Formats**

**XML**
**Schema**

**LexGrid Model**
**Source**

- HyperModel

**XMI**

- EMF

**EMF**
**Java**

**LexGrid Core**

- Castor/Java

**LDAP**
**Schema**

- (manual)

**SQL**
**Schema**

**SQL**
**‘****lite’**
**Schema**

## LexGrid Formats

**.****mdl**

**LexGrid Formats**

**XML**

**XMI**

**Java**
**Objects**

**LDAP**

**SQL**

**SQL**
**‘****lite****’**

## LexGrid Conversions

**XML**

**Java**
**Objects**

**LDAP**

**SQL**

**SQL**
**‘****lite****’**

## LexGrid Conversions

## Syntactic Normalization

**XML (including RDF)**
**XSLT transform   -or-**
**Python/SAX**
**OWL**
**Canonical XSLT transform**
**Protégé CLIPS**
**EMF Plugin for Protégé**

## Lexical Normalization

**UMLS RRF**
**Java transformation tool**
**Excel spreadsheet(s)**
**Ad-hoc at the moment**
**Will attempt to use MS’s XML conversion tools**
**Indented text**
**Java transformation tool**

## Lexical Normalization

**Databases**
**Ad hoc – either Java/SQL or DB->XML->XSLT**
**PDF**
**PDF -> XML**
**Ad hoc XML-> LexGrid**

## LexGrid Modelhttp://informatics.mayo.edu

_**LexGrid Model**_***http://informatics.mayo.edu***

## Individual Cases

## Individual Cases

**NCI Thesaurus**
**GEMET **
**ISO 3166**
**ISO 4217**
**DTIC**
**EPA **
**FMA**
**Adult Mouse Anatomy**

## NCI Thesaurus

**Native form is Ontylog**
**Three identifiers (name, number, code)**
**All/Some/Pos(?)**
**Kinds**
**Properties -> Some are maps, some are others**
**Embedded XML issues**
**Also available as OWL**
**Semantics are questionable**

## NCI Thesaurus

**Multiple source / same text**

## NCI Thesaurus

**<conceptDef>**
**	****<name>Fibrohistiocytic_Neoplasm</name>**
**	****<code>C8402</code>**
**	****<id>8402</id>**
**	****<namespace>NCI</namespace>**
**	****<primitive/>**
**	****<kind>Findings_and_Disorders_Kind</kind>**
**	****<definingConcepts>**
**	****<concept>Mesenchymal_Cell_Neoplasm</concept>**
**	****</definingConcepts>**
**	****<definingRoles>**
**	****</definingRoles>**
**	****	****	****...**

## NCI Thesaurus

**	****	****	****...**
**<properties>**
**<property>**
**<name>Preferred_Name</name>**
**<value>Fibrohistiocytic Neoplasm</value>**
**</property>**
**<property>**
**<name>Semantic_Type</name>**
**<value>Neoplastic Process</value>**
**</property>**
**<property>**
**<name>Synonym</name>**
**<value>Fibrohistiocytic Neoplasm</value>**
**</property>**
**	****	****	****...**

## NCI Thesaurus

**	****	****	****...**
**<name>FULL_SYN</name>**
**<value><![CDATA[<term-name>Fibrohistiocytic Neoplasm</term-name><term-group>PT</term-group><term-source>NCI</term-source>]]></value>**
**</property>**
**<property>**
**<name>FULL_SYN</name>**
**<value><![CDATA[<term-name>Fibrohistiocytic Tumor</term-name><term-group>SY</term-group><term-source>NCI</term-source>]]></value>**
**</property>**
**<property>**
**<name>NCI_META_CUI</name>**
**<value>CL031415</value>**
**</property>**
**</properties>**
**</conceptDef>**

## GEMET

**Native form is XML**
**Augmented by PDF documents**
**Super Groups / Groups / Themes**
**Concept id issues**
**Broader/Narrower**
**Related references**
**PDF includes list of sources**
**Valueable**
**Painful to convert**
**Issues w/ out of datedness**

## GEMET

**<descriptor>**
**	****	****<descriptor-term desc-id="22" desc-type="1" top="0"> access road </descriptor-term>**
**	****	****<original-identifier>**
**	****	****	****<thesaurus-name> UNEP </thesaurus-name>**
**	****	****	****<descriptor-identifier> 16305 </descriptor-identifier>**
**	****	****</original-identifier>**
**	****	****<broader-term desc-ref-id="7272"> road </broader-term>**
**	****	****<theme accronym="BUI" theme-id="5"> building </theme>**
**	****	****<theme accronym="TRA" theme-id="37"> transport </theme>**
**	****	****<group group-id="1062" super-group-id="5499"> ANTHROPOSPHERE (built environment, human settlemen </group>**
**</descriptor>**

## DTIC

**Hierarchical Text**
**Name is identity**
**Identity issues**
**Association: **
**lessSpecificThan/ moreSpecificThan**

## DTIC

**ABANDONMENT                                                                                   **
** ****(1)BAILOUT                                                                                   **
** ****(1)DITCHING                                                                                  **
** ****(1)SUBMARINE ESCAPE                                                                          **
**ABNORMALITIES                                                                                 **
** ****(1)CONGENITAL ABNORMALITIES                                                                  **
**ABSORBERS(EQUIPMENT)                                                                          **
** ****(1)ENERGY ABSORBERS                                                                          **
**    ****(2)SHOCK ABSORBERS                                                                        **
**ACCESS                                                                                        **
** ****(1)COMPUTER ACCESS CONTROL                                                                   **
** ****(1)MULTIPLE ACCESS                                                                           **
**    ****(2)CODE DIVISION MULTIPLE ACCESS                                                          **
**    ****(2)FREQUENCY DIVISION MULTIPLE ACCESS                                                     **
**ACCIDENTS                                                                                     **
** ****(1)AVIATION ACCIDENTS                                                                        **
**    ****(2)CRASH LANDINGS                                                                         **
**       ****(3)DITCHING **

## DTIC

**FOOD                                                                                          **
** ****(1)BEVERAGES                                                                                 **
** ****	****	****...**
** ****(1)CARBOHYDRATES                                                                             **
**    ****(2)GLYCOSIDES                                                                             **
**        ****	****...**
**    ****(2)POLYSACCHARIDES                                                                        **
**       ****(3)ALGINIC ACID                                                                        **
**	****	****	****...**
**       ****(3)STARCHES                                                                            **
**       ****(3)SUGAR ACIDS**
-           (4)URONIC ACIDS
-              (5)ALGINIC ACID

## DTIC

**(****1)ORGANIC ACIDS                                                                             **
**    ****(2)ALIPHATIC ACIDS                                                                        **
**	****	****	****...                                                                     **
**    ****(2)STYPHNIC ACIDS                                                                         **
**    ****(2)SUGAR ACIDS**
-        (3)URONIC ACIDS
-           (4)ALGINIC ACID

## EPA

**Hierarchical Text**
**Position is identity**

## EPA

**636****	****INTERNATIONAL COOPERATION**
**	****62****	****Air Quality**
**	****	****63****	****Air Quality Criteria**
**	****	****64****	****Air Quality Models**
**	****	****65****	****Attainment**
**	****	****66****	****Early Action Compacts**
**	****	****55****	****Emission Factor**
**	****	****56****	****Emission Inventory**
**	****	****67****	****Emissions Measurement**
**	****	****68****	****Emissions Trading**
**	****	****58****	****Measurement**
**	****	****59****	****Models**
**	****	****	****1032****	****Air Models**
**	****	****	****1033****	****Emission Factor Models**
**	****	****	**

## EPA

- INTERNATIONAL COOPERATION
**Air Quality****	**
- 	Atmospheric Deposition
- 	Technical Information
- 				...
- GOVERNMENT
- Tribal Government
**	****Air Quality**

## ISO 3166

**Many resources**
**Fragmented**
**Difficult, manual curation process**
**3 Identifiers per entity**
**Each w/ different semantics**
**Useful history**
**Splits, joins, renames, etc.**
**Errors and other things**
**Difficult to replicate**

## ISO 4217

**(see: ISO 3166)**
**Non-domain entities in both spaces**
**Issues involving management / re-use, etc.**

## FMA

**Native form is Protégé ‘classic’**
**(Arguably) one of the few real “ontologies”**
**Rich classification/rigorous structures**

## FMA

**FMA**

## Adult Mouse Anatomy

**Simple OBO release format**
**Reasonably straight-forward conversion**

## Adult Mouse Anatomy

**[Term]**
**id: MA:0000125**
**name: dorsal pancreatic duct**
**is_a: MA:0000124 ! pancreatic duct**
**[Term]**
**id: MA:0000126**
**name: ventral pancreatic duct**
**is_a: MA:0000124 ! pancreatic duct**
**[Term]**
**id: MA:0000127**
**name: pancreatic islet**
**synonym: "islet of langerhans" []**
**relationship: part_of MA:0001582 ! endocrine pancreas**

## Issues and Discussion

## Issues and Discussion

**Standardized conversion toolkit**
**Reproducible conversion process**
**Keeping up – how to stay current?**
**LexGrid distributed model**
**Verifying transformations**
**Secondary forms**
**NCI->OWL->LexGrid->XMDR**
**NCI->LexGrid->XMDR**

## Issues and Discussion

**Decision process**
**3 codes vs. 3 coding schemes in ISO 3166**
**Identities on DTIC & EPA**
**...**
**Standard URI’s**
**What is the role of LexGrid?**

## Plug

- http://informatics.mayo.edu/protege/conference2005/workshop_1.html