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The UMLS Semantic Network Support for semantic integration and reasoning. Workshop UMLS Semantic Network NLM, NIH, Bethesda, 7-8 Apr 2005 Anita Burgun. Overview. Semantic integration Role of the SN Integration of resources Integration of data Reasoning Reasoning with hierarchies

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The umls semantic network support for semantic integration and reasoning

The UMLS Semantic NetworkSupport for semantic integration and reasoning

Workshop UMLS Semantic Network

NLM, NIH, Bethesda, 7-8 Apr 2005

Anita Burgun


Overview
Overview

  • Semantic integration

    • Role of the SN

    • Integration of resources

    • Integration of data

  • Reasoning

    • Reasoning with hierarchies

    • Reasoning with associative relations

  • Perspectives

  • Illustration

    • Genes, gene products, diseases

    • Findings, signs, diseases


Semantic integration

Semantic integration

1- Role of ontologies


Integration

Mediation system

Ontologies

Integration

DWH

Gene instances

Data Warehouse

Local res.

External resources

Micro-arraydata

Patient

files

…..

GEN

BANK

SWISS

PROT

MED

LINE

GOA


Integrating data in the domain of organ failure and transplantation
Integrating data in the domain of organ failure and transplantation

EfG

transplantation

REIN

End stage renal failure

EfG terminology server

dialysis

Local

Information Systems


The umls semantic network support for semantic integration and reasoning

M transplantation

A

P

P

I

N

G

ONTO-

TERM

T1

T2

mapping

term-term

T3

Metathesaurus

Semantic Network


Semantic integration1

Semantic integration transplantation

2- Resource Integration


Integration1

Mediation system transplantation

Ontologies

Integration

DWH

Gene instances

Data Warehouse

Local res.

External resources

Micro-arraydata

Patient

files

…..

GEN

BANK

SWISS

PROT

MED

LINE

GOA


Introduction

<OrgName> transplantation

<OrgName_name>

<OrgName_name_binomial>

<BinomialOrgName>

<BinomialOrgName_genus>Homo</BinomialOrgName_genus>

<BinomialOrgName_species>sapiens</BinomialOrgName_species>

</BinomialOrgName>

</OrgName_name_binomial>

</OrgName_name>

<OrgName_lineage>Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;

Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo</OrgName_lineage>

<OrgName_gcode>1</OrgName_gcode>

<OrgName_mgcode>2</OrgName_mgcode>

<OrgName_div>PRI</OrgName_div>

</OrgName>

<ORGANISM>Homo sapiens</ORGANISM>

<TAXONOMY>Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;Mammalia;

Eutheria; Primates; Catarrhini; Hominidae; Homo.</TAXONOMY>

Introduction

<OrgName>

<OrgName_name>

<OrgName_name_binomial>

<BinomialOrgName>

<BinomialOrgName_genus>Homo</BinomialOrgName_genus>

<BinomialOrgName_species>sapiens</BinomialOrgName_species>

</BinomialOrgName>

</OrgName_name_binomial>

</OrgName_name>

<OrgName_lineage>Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;

Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo</OrgName_lineage>

<OrgName_gcode>1</OrgName_gcode>

<OrgName_mgcode>2</OrgName_mgcode>

<OrgName_div>PRI</OrgName_div>

</OrgName>

  • Increasing need for physicians and biologists to access information on the Internet

  • Biomedical sources

    • Scattered

    • Multiple heterogeneity

    • Rapid evolution and frequent creation

  • Integration


Objectives
Objectives transplantation

  • Overall: creating a system

    • Global access

    • Homogeneous and up-to-date information

  • Specific: acquiring sources schemas

    • As automatically as possible

    • Dealing with updates, adding new resources

    • Generate different paths to access information


Sources schema
Sources schema transplantation

  • Rarely available or hard to exploit

  • No existing standard

  • Identifying the schema of each source by exploiting its contents

    • Informs on the type of information present in the source

    • Extraction from its Web site


Use of umls
Use of UMLS transplantation

  • Heterogeneity of schemas

  • Need of a common vocabulary: the UMLS

  • Example : finding the site of expression of a gene starting from a gene symbol


Results
Results transplantation

  • 279 distinct terms extracted from 11 sources

    • 232 found in the UMLS corresponding to 495 MTH concepts

      • 318 were correct

      • 177were not

    • 47 not found

  • Of the 318 MTH concepts, 60 concepts are common to at least 2 distinct extracted terms (158 are specific)


Mapping ult to the umls
Mapping ULT to the UMLS transplantation

  • General concepts

    • Citation -> Organism attribute

    • Description -> Research activity

    • Symbol -> Idea or Concept

    • Name -> Intellectual product

    • History -> Finding

    • Matches -> Manufactured object

    • Link -> Chemical Viewed Structurally

    • Association -> Mental Process/ Social Behavior


General concepts
General concepts transplantation

General classes

« Metaterms »

WordNet??

Upper Level

Ontology

General

Ontology

Idea or Concept

Intellectual Product

Attributes

Functional/Spatial/

Temporal Concept

Domain

Ontology


Semantic integration2

Semantic integration transplantation

3- Data Integration


Functional genomics
Functional genomics transplantation

  • Post genomics

  • Gene expression, protein function, biological process, disease

  • van de Vijver MJ et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med. 2002 Dec 19; 347(25): 1999-2009.

  • Objective : provide « medical » annotation of genes (BioMeKe)

  • GeneTraces (Cantor, Lussier)


Gene gene product disease
Gene, gene product, disease transplantation

  • HUGO : manage heterogeneity of data

  • Superoxide dismutase 1, soluble/ amyotrophic lateral sclerosis 1 (adult)

  • C1420306 SOD1 gene (symbol) gene or Genome

  • C0669516 SOD1 gene product (symbol) Amino acid, protein

  • C0002736 ALS (previous symbol) Disease or Syndrome

  • No relation in MTH


Gene gene product disease1
Gene, gene product, disease transplantation

  • HUGO

  • Aconitase 1, soluble

  • C1412126 ACO1 gene (symbol) gene or Genome

  • C0378502 ACO1 protein (symbol)/ IRP 1 protein (alias)

  • Amino acid, protein

  • OR relation between the two concepts in MTH


Gene gene product disease2
Gene, gene product, disease transplantation

  • HUGO synonymous terms

T1

T2

T3

ST2

C2

ST3

ST1

C1

C3


Gene gene product disease3
Gene, gene product, disease transplantation

Gene or Genome

produces

location_of

AA, protein

Disease or Syndrome

affects

causes


Reasoning

Reasoning transplantation


Reasoning1
Reasoning transplantation

SN relations

categorization


Reasoning relations

Reasoning : relations transplantation

1- The hierarchy and the economy principle


The economy principle
The economy principle transplantation

  • R1. Ad hoc precision

    • The intent is to establish a set of semantic types, which will be useful for a variety of tasks without introducing undue complexity. The most specific semantic type in the semantic type hierarchy is assigned to the concept.

  • R2. No hybrid types

    • Instead of creating a lattice structure, with hybrid types inheriting from two supertypes, the SN has a single inheritance tree structure. As a consequence, a Metathesaurus concept inheriting from two STs is assigned to both types.

  • R3. No category “other”

    • Rather than proliferating the number of semantic types to encompass multiple additional subcategories, concepts that cannot be categorized by any sibling Semantic Type are simply assigned their common supertype.


The economy principle and the theory
The economy principle and the theory transplantation

  • Intensions and extensions

    • Taxonomies (isa) are systems in which categories (intensions) are related to one another by means of subordination, or, in class parlance (extensions), systems in which classes are related to one another by means of class inclusion.

  • Categories and classes

    • When a category K has subcategories K1, K2, …. Kn, its extension, the class CK is the union of the classes for each of its subcategories, i.e. CK1, CK2,……CKn.


The umls semantic network support for semantic integration and reasoning

transplantation

Categories

Manufactured Object

physical object made by human beings

Medical Device

Research Device

Clinical Drug

Manufactured object used primarily in the diagnosis, treatment, or prevention of physiologic or anatomic disorders

Manufactured object used primarily in carrying out scientific research or experimentation

Pharmaceutical preparation as produced by the manufacturer

CMD

CRD

CCD

CMD CRD CCD

CMO

45 inch calibre bullet

magnetic tape, matches, corridor

Classes


Reasoning relations1

Reasoning : relations transplantation

2- Associative relations


Diseases and findings
Diseases and Findings transplantation

Event

Entity

Natural phenomenon

or process

Conceptual entity

Finding

Pathologic function

Sign or Symptom

Disease or syndrome


Diseases and findings sn

Associated_with transplantation

Evaluation_of

Manifestation_of

Diseases and Findings: SN

Finding

is_a

Sign or Symptom

Disease or syndrome

Diagnoses


Relations sn
Relations SN transplantation

  • Disease or Syndrome affects Disease or Syndrome

  • Disease or Syndrome associated_with Disease or Syndrome

  • Disease or Syndrome co-occurs_with Disease or Syndrome

  • Disease or Syndrome complicates Disease or Syndrome

  • Disease or Syndrome degree_of Disease or Syndrome

  • Disease or Syndrome manifestation_of Disease or Syndrome

  • Disease or Syndrome occurs_in Disease or Syndrome

  • Disease or Syndrome precedes Disease or Syndrome

  • Disease or Syndrome process_of Disease or Syndrome

  • Disease or Syndrome result_of Disease or Syndrome


Relations in snomed ct vs sn
Relations in SNOMED CT vs SN transplantation

  • Class ASNCT = SNCT concepts assigned to the Semantic Type A

  • Class DISEASESSNCT = SNCT concepts assigned to ‘Diseases or Syndrome’

A

B

C

MTH restricted to SNCT


Relations in snomed ct
Relations in SNOMED CT transplantation

  • MTH restricted to SNOMED CT

  • Relations whose SAB = SNOMED CT

  • 2,220,144 relations

  • 1,392,380 associative relations (including inverse relations)

  • 113 associative relationships (all have inverse except associated_with)

  • 18 relationships have less than 100 instances

    • Has_time_aspect_of : 1

    • Has_property : 77

  • The most frequent :

    • Has_onset : 114,173

    • has_finding_site : 99,156

    • has_method : 70,682


Relations in snomed ct1
Relations in SNOMED CT transplantation

  • Focus on Diseases and Findings

  • Class DISEASESSNCT = SNCT concepts assigned to ‘Disease or Syndrome’

  • Class FINDINGSSNCT = SNCT concepts assigned to {‘Finding’ + ‘Sign or Symptom’}

Finding

Disease or Sd

Sign or symptom

MTH restricted to SNCT


Diseases diseases relations snct

due_to transplantation

definitional_manifestation_of

associated_with

occurs_before

mapped_to

has_finding_site

has_associated_finding

interprets

has_associated_morphology

Diseases-Diseases relations SNCT


Diseases diseases relations snct sn

due_to transplantation

definitional_manifestation_of

associated_with

occurs_before

mapped_to

has_finding_site

has_associated_finding

interprets

has_associated_morphology

result_of

manifestation_of

associated_with

precedes , occurs_in, complicates?

co-occurs_with

degree_of

process_of

affects

Diseases-Diseases relations SNCT/SN

SNCT

SN


Findings diseases relations snct

has_associated_finding / associated_finding_of transplantation

has definitional manifestation/ definitional_manifestation_of

interprets / is_interpreted_by/ has_interpretation

occurs_after / occurs_before

mapped_to /mapped from

has_associated_morphology / associated_morphology_of

due_to / cause_of

focus_of

has_finding_site

isa / inverse is-a

Findings-Diseases relations SNCT


Diseases findings relations snct sn

has_associated_finding / associated_finding_of transplantation

has definitional manifestation/ definitional_manifestation_of

interprets / is_interpreted_by/ has_interpretation

occurs_after / occurs_before

mapped_to /mapped from

has_associated_morphology / associated_morphology_of

due_to / cause_of

focus_of

has_finding_site

isa / inverse is-a

associated_with

manifestation_of

diagnoses

evaluation_of

Diseases-Findings relations SNCT/SN

SNCT

SN


Diseases and findings1

Associated_with transplantation

Evaluation_of

Manifestation_of

Diseases and Findings

Finding

is_a

Is_a

5,592 instances

Sign or Symptom

Disease or syndrome

Diagnoses


Diseases and findings2
Diseases and Findings transplantation

Event

Entity

Natural phenomenon

or process

Conceptual entity

Finding

Pathologic function

Sign or Symptom

Disease or syndrome


Diseases and findings3
Diseases and Findings transplantation

Finding

Disease or syndrome

Sign or Symptom

C1300028

Disorder characterizedby pain

is_a

C0000727

Abdomen, acute


Diseases and findings4
Diseases and Findings transplantation

C0008767

Scar

Finding

has_finding_site

C1300028

Endometriosisin scar of skin

Sign or Symptom

Disease or syndrome


Diseases and findings5
Diseases and Findings transplantation

Event

Entity

Natural phenomenon

or process

Conceptual entity

Finding

Pathologic function

Sign or Symptom

Disease or syndrome


Formal properties
Formal properties transplantation

  • Guarino, Welty

  • Rigidity

    • property that is essential to all the instances.Person (+R). Physician (not R).

  • Identity

    • there is a property that is both necessary and sufficient for identifying an instance. Person (+I)

  • Unity

    • instances are intrinsic wholes. Person (+U).

  • Dependence

    • for all the instances x, necessarily some instance of Z must exist, which is not a part of x, nor a constituent of x (+D). Food (+D)


Formal properties rules
Formal properties transplantationRules

  • Rules

    • (not U) cannot subsume (+U)e.g., Substance cannot subsume Physical Object

    • […]

  • Distinction between roles and sortal types

    • Roles: (Not Rigid) (+Dependent)

    • Sortal types : (+Rigid) (Not Dependent)


Formal properties signs
Formal properties: signs transplantation

  • Signs or Symptoms are Roles

  • Metathesaurus concepts that are assigned only to roles with no sortal Semantic Type represent a numerous set of entities

  • About 90% of the MTH concepts assigned to Findings, and Signs or Symptoms are not assigned to another Semantic Type.


Roles vs relations
Roles vs relations transplantation

  • Findings?

  • Sign or Symptom associated_with Disease or Syndrome

  • Sign or Symptom diagnoses Disease or Syndrome

  • Sign or Symptom evaluation_of Disease or Syndrome

  • Sign or Symptom manifestation_of Disease or Syndrome

  • Finding associated_with Disease or Syndrome

  • Finding evaluation_of Disease or Syndrome

  • Finding manifestation_of Disease or Syndrome


Diseases frames
Diseases: frames transplantation

  • Has_location

  • Has_lesion : necrosis

  • Has_process : infection

    • (has_agent)

  • Has_discriminating_sign_or_finding

    • hematuria

  • Occurs_in


Discussion

Discussion transplantation


Perspectives 1 coverage
Perspectives (1) : coverage transplantation

  • Extend the SN ???

    • Economy principle vs adding general concepts

  • Resource integration ???

    • Needs in BIOmedical

    • Clarify conceptual entities

    • Semantic Types corresponding to general entities


Perspectives 2 compatibility
Perspectives (2) : compatibility transplantation

  • Compatibility with general ontologies

    • Semantic web

  • Alignment with existing domain ontologies

    • FMA (Zhang Medinfo 2004)

    • SNOMED CT (Burgun ongoing work on SN relations)

  • Rules (classification), consistency SN-MTH

    • E.g. sign or symptom is-a disease


  • Perspectives 3 formal aspects
    Perspectives (3): formal aspects transplantation

    • Formal ontology

      • Make relations and concepts more explicit, e.g. roles (ULO), relationships between genes and diseases

      • Cohérence, e.g. is-a relations between findings and diseases (studies and processing)

      • Classification of new concepts, e.g upper MTH concepts (Bodenreider Medinfo 2004)

      • Inference, e.g. use relations between anatomical sites and diseases to suggest new relations between diseases (Burgun submitted AMIA 2005)


    References
    References transplantation

    • Mougin F, Burgun A, Loreal O, Le Beux P. Towards the automatic generation of biomedical sources schema. Medinfo. 2004;2004:783-7.

    • Welty C, Guarino N. Supporting Ontological Analysis of Taxonomic Relationships (2001)  Data Knowledge Engineering, http://www.ladseb.pd.cnr.it/infor/Ontology/Papers

    • Zhang S, Bodenreider O. Comparing Associative Relationships among Equivalent Concepts Across Ontologies. Medinfo. 2004;2004:459-66.