ontologies for data integration: a semantic web perspective training course olivier bodenreider...

Ontologies for Data Integration:A Semantic Web Perspective

Training CourseTraining Course

Olivier BodenreiderOlivier Bodenreider

Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland - USABethesda, Maryland - USA

May 24, 2006

Schloß Dagstuhl

Biomedical OntologyBiomedical Ontology

inin

2 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

OutlineOutline

From terminology integrationto information integrationUnified Medical Language System (UMLS)

UMLS in use:Mapping across terminologies

Beyond UMLS:Towards a Biomedical Knowledge Repository

From terminology integrationto information integration

Unified Medical Language System (UMLS)


What does UMLS stand for?What does UMLS stand for?

UUnifiednified MMedicaledical LLanguageanguage SSystemystem

UMLS®

Unified Medical Language System®

UMLS Metathesaurus®


MotivationMotivation

Started in 1986Started in 1986 National Library of MedicineNational Library of Medicine ““Long-term R&D project”Long-term R&D project”

«[…] the UMLS project is an effort to overcome two significant barriers to effective retrieval of machine-readable information.

• The first is the variety of ways the same concepts are expressed in different machine-readable sources and by different people.

• The second is the distribution of useful information among many disparate databases and systems.»

Overview through an example


Addison’s diseaseAddison’s disease

Addison's disease is a rare Addison's disease is a rare endocrine disorderendocrine disorder

Addison's disease occurs Addison's disease occurs when the when the adrenal glandsadrenal glands do not produce enough of do not produce enough of the hormone the hormone cortisolcortisol

For this reason, the For this reason, the disease is sometimes disease is sometimes called called chronic adrenal chronic adrenal insufficiencyinsufficiency, or , or hypocortisolismhypocortisolism


Adrenal insufficiency Adrenal insufficiency Clinical Clinical variantsvariants

Primary / SecondaryPrimary / Secondary Primary: lesion of the Primary: lesion of the

adrenal glands themselvesadrenal glands themselves Secondary: inadequate Secondary: inadequate

secretion of ACTH by the secretion of ACTH by the pituitary glandpituitary gland

Acute / ChronicAcute / Chronic Isolated / Polyendocrine Isolated / Polyendocrine

deficiency syndromedeficiency syndrome

ACTH


Addison’s disease: Addison’s disease: SymptomsSymptoms

FatigueFatigue WeaknessWeakness Low blood pressureLow blood pressure Pigmentation of the skin (exposed and non-Pigmentation of the skin (exposed and non-

exposed parts of the body)exposed parts of the body) ……


AD in medical vocabulariesAD in medical vocabularies

Synonyms: Synonyms: different termsdifferent terms Addisonian syndromeAddisonian syndrome Bronzed diseaseBronzed disease Addison melanodermaAddison melanoderma Asthenia pigmentosaAsthenia pigmentosa Primary adrenal deficiencyPrimary adrenal deficiency Primary adrenal insufficiencyPrimary adrenal insufficiency Primary adrenocortical insufficiencyPrimary adrenocortical insufficiency Chronic adrenocortical insufficiencyChronic adrenocortical insufficiency

Contexts: Contexts: different hierarchiesdifferent hierarchies

symptoms

clinicalvariants

eponym


Organize termsOrganize terms

Synonymous terms clustered into a conceptSynonymous terms clustered into a concept Preferred termPreferred term Unique identifier (CUI)Unique identifier (CUI)

Addison's disease

Addison Disease MeSH D000224Primary hypoadrenalism MedDRA 10036696Primary adrenocortical insufficiency ICD-10 E27.1Addison's disease (disorder) SNOMED CT 363732003

C0001403

Diseases of the endocrine system

Diseases of the Adrenal Glands

Addison’s Disease

Diseases/DiagnosesSNOMED International

Endocrine Diseases

Adrenal Gland Diseases

Addison’s Disease

DiseasesMeSH

Adrenal Gland Hypofunction

Endocrine disorder

Adrenal disorder

Adrenal cortical disorder

Adrenal cortical hypofunction

Addison’s Disease

AOD

Endocrine disorder

Disorder of adrenal gland

Hypoadrenalism

Adrenal Hypofunction

Corticoadrenal insufficiency

Addison’s Disease

Read Codes

Primary adrenocortical insufficiency

Other disorders ofadrenal gland

Disorders of otherendocrine gland

ICD-10


Organize conceptsOrganize concepts

Inter-concept Inter-concept relationships: hierarchies relationships: hierarchies from the source from the source vocabulariesvocabularies

Redundancy: multiple Redundancy: multiple pathspaths

One One graphgraph instead of instead of multiple multiple treestrees(multiple inheritance)(multiple inheritance)

A

B D E H D E

B

G H

E F H

C

B C

A

E FD

G H

Adrenal Cortex Diseases

Hypoadrenalism



Endocrine Diseases


organize concepts

Addison’s Disease

UMLS

SNOMEDMeSHAODRead Codes


Relate to other conceptsRelate to other concepts

Additional hierarchical relationshipsAdditional hierarchical relationships link to other treeslink to other trees make relationships explicitmake relationships explicit

Non-hierarchical relationshipsNon-hierarchical relationships Co-occurring conceptsCo-occurring concepts Mapping relationshipsMapping relationships

Endocrine Diseases



Hypoadrenalism



Addison’s Disease

Adrenal Cortex Dysfunction

Adrenal Dysfunction

Addison’s disease due to autoimmunity

Secondary hypocortisolism


Disorders of otherendocrine gland

Adrenal Glands

Adrenal Cortex

Endocrine System

Endocrine Glands

Abdominal organ Diseases

relate to other concepts


Categorize conceptsCategorize concepts

High-level categories High-level categories (semantic types)(semantic types)

Assigned by the Assigned by the Metathesaurus editorsMetathesaurus editors

Independently of the Independently of the hierarchies in which these hierarchies in which these concepts are locatedconcepts are located

Disease or Syndrome

Endocrine Diseases


Addison’s Disease

Diseases



How do they do that?How do they do that?

Lexical knowledgeLexical knowledge

Semantic pre-processingSemantic pre-processing

UMLS editorsUMLS editors


Lexical knowledgeLexical knowledge

Adrenal gland diseasesAdrenal disorderDisorder of adrenal glandDiseases of the adrenal glandsC0001621


Semantic pre-processingSemantic pre-processing

Metadata in the source vocabulariesMetadata in the source vocabularies

Tentative categorizationTentative categorization Positive (or negative) evidence for tentative Positive (or negative) evidence for tentative

synonymy relations based on lexical featuressynonymy relations based on lexical features


Additional knowledge: UMLS editorsAdditional knowledge: UMLS editors



Adrenal Cortex Dysfunction

Hypoadrenalism



Addison’s Disease



UMLS: 3 componentsUMLS: 3 components

SPECIALIST LexiconSPECIALIST Lexicon 200,000 lexical items200,000 lexical items Part of speech and variant informationPart of speech and variant information

MetathesaurusMetathesaurus 5M names from over 100 terminologies5M names from over 100 terminologies 1M concepts1M concepts 16M relations16M relations

Semantic NetworkSemantic Network 135 high-level categories135 high-level categories 7000 relations among them7000 relations among them

Lexicalresources

Ontologicalresources

Terminologicalresources

UMLS Metathesaurus


Source VocabulariesSource Vocabularies

139 source vocabularies139 source vocabularies 17 languages17 languages

Broad coverage of biomedicineBroad coverage of biomedicine 5.1M names5.1M names 1.3M concepts1.3M concepts 16M relations16M relations

Common presentationCommon presentation

(2006AB)


Addison’s Disease: Addison’s Disease: ConceptConcept

Addison’s Disease

C0001403

ADRENAL INSUFFICIENCY (ADDISON'S DISEASE) ADRENOCORTICAL INSUFFICIENCY, PRIMARY FAILURE Addison melanoderma Melasma addisonii Primary adrenal deficiency Asthenia pigmentosa Bronzed disease Insufficiency, adrenal primary Primary adrenocortical insufficiency Addison's, disease

MALADIE D'ADDISON - FrenchAddison-Krankheit - GermanMorbo di Addison - ItalianDOENCA DE ADDISON - PortugueseADDISONOVA BOLEZN' - RussianENFERMEDAD DE ADDISON - Spanish

A disease characterized by hypotension, weight loss, anorexia, weakness, and sometimes a bronze-like melanotic hyperpigmentation of the skin. It is due to tuberculosis- or autoimmune-induced disease (hypofunction) of the adrenal glands that results in deficiency of aldosterone and cortisol. In the absence of replacement therapy, it is usually fatal.

SNOMEDMeSHAODRead Codes…

Disease or Syndrome


Metathesaurus Metathesaurus ConceptsConcepts

ConceptConcept (> 1.3M)(> 1.3M) CUICUI Set of synonymousSet of synonymous

concept namesconcept names

TermTerm (> 4.6M)(> 4.6M) LUILUI Set of normalized namesSet of normalized names

StringString (> 5.1M)(> 5.1M) SUISUI Distinct concept nameDistinct concept name

AtomAtom (> 6.2M)(> 6.2M) AUIAUI Concept nameConcept name

in a given sourcein a given source

(2006AB)

A0000001 headache (source 1)A0000002 headache (source 2)

S0000001

A0000003 Headache (source 1)A0000004 Headache (source 2)

S0000002

L0000001

A0000005 Cephalgia (source 1)S0000003

L0000002

C0000001


Cluster of synonymous termsCluster of synonymous terms

ConceptC0001621

[…]TermL0001621

S0011232 Adrenal Gland DiseasesS0011231 Adrenal Gland DiseaseS0000441 Disease of adrenal glandS0481705 Disease of adrenal gland, NOSS0220090 Disease, adrenal glandS0044801 Gland Disease, Adrenal

TermL0041793

S0860744 Disorder of adrenal gland, unspecifiedS0217833 Unspecified disorder of adrenal glands

[…]

TermL0368399

S0586222 Adrenal diseaseS0466921 ADRENAL DISEASE, NOS

[…]

TermL0181041

S0632950 Disorder of adrenal glandS0354509 Adrenal Gland Disorders

[…]

TermL0161347

S0225481 ADRENAL DISORDERS0627685 DISORDER ADRENAL (NOS)

[…]

TermL1279026

S1520972 Nebennierenkrankheiten GER

S0226798 SURRENALE, MALADIESTermL0162317

FRE


Metathesaurus Metathesaurus Evolution over timeEvolution over time

Concepts never die (in principle)Concepts never die (in principle) CUIs are permanent identifiersCUIs are permanent identifiers

What happens when they do die (in reality)?What happens when they do die (in reality)? Concepts can merge or splitConcepts can merge or split Resulting in new concepts and deletionsResulting in new concepts and deletions

Addison's diseaseC0001403

Addison's disease, NOS C0271735

1992 1993 1994 1995 1996 1997 1998 1999 2004…


Metathesaurus Metathesaurus RelationshipsRelationships

Symbolic relations:Symbolic relations: ~9 M pairs of concepts~9 M pairs of concepts Statistical relations :Statistical relations : ~7 M pairs of concepts ~7 M pairs of concepts

(co-occurring concepts)(co-occurring concepts) Mapping relations:Mapping relations: 100,000 pairs of 100,000 pairs of

conceptsconcepts

Categorization: Relationships between concepts Categorization: Relationships between concepts and semantic types from the Semantic Networkand semantic types from the Semantic Network


Symbolic relationsSymbolic relations

RelationRelation Pair of “atom” identifiersPair of “atom” identifiers TypeType Attribute (if any)Attribute (if any) List of sources (for type and attribute)List of sources (for type and attribute)

Semantics of the relationship:Semantics of the relationship:defined by its defined by its typetype [and [and attributeattribute]]

Source transparency: the informationis recorded at the “atom” level


Symbolic relationships Symbolic relationships TypeType

HierarchicalHierarchical Parent / ChildParent / Child Broader / Narrower thanBroader / Narrower than

Derived from hierarchiesDerived from hierarchies Siblings (children of parents)Siblings (children of parents)

AssociativeAssociative OtherOther

Various flavors of near-synonymyVarious flavors of near-synonymy SimilarSimilar Source asserted synonymySource asserted synonymy Possible synonymyPossible synonymy

PAR/CHD

RB/RN

SIB

RO

RL

SY

RQ


Symbolic relationships Symbolic relationships AttributeAttribute

HierarchicalHierarchical isa (is-a-kind-of)isa (is-a-kind-of) part-ofpart-of

AssociativeAssociative location-oflocation-of caused-bycaused-by treatstreats … …

Cross-references (mapping)Cross-references (mapping)

Heart

Concepts

Metathesaurus

22

225

97

4

12

9 31

Esophagus

Left PhrenicNerve

HeartValves

FetalHeart

Medias-tinum

SaccularViscus

AnginaPectoris

CardiotonicAgents

TissueDonors

AnatomicalStructure

Fully FormedAnatomical

Structure

EmbryonicStructure

Body Part, Organ orOrgan Component Pharmacologic

Substance

Disease orSyndrome

PopulationGroup

Semantic Types

SemanticNetwork

UMLS Semantic Network


Semantic NetworkSemantic Network

Semantic types (135)Semantic types (135) tree structuretree structure 2 major hierarchies2 major hierarchies

EntityEntity

– Physical ObjectPhysical Object

– Conceptual EntityConceptual Entity EventEvent

– ActivityActivity

– Phenomenon or ProcessPhenomenon or Process


Semantic NetworkSemantic Network

Semantic network relationships (54)Semantic network relationships (54) hierarchical (isa = is a kind of)hierarchical (isa = is a kind of)

among typesamong types

– AnimalAnimal isaisa OrganismOrganism

– EnzymeEnzyme isaisa Biologically Active SubstanceBiologically Active Substance among relationsamong relations

– treats treats isaisa affects affects

non-hierarchicalnon-hierarchical Sign or SymptomSign or Symptom diagnosesdiagnoses Pathologic FunctionPathologic Function Pharmacologic SubstancePharmacologic Substance treatstreats Pathologic FunctionPathologic Function


““Biologic Function” hierarchy (isa)Biologic Function” hierarchy (isa)

Biologic Function

Pathologic FunctionPhysiologic Function

Disease orSyndrome

Cell orMolecular

Dysfunction

ExperimentalModel ofDisease

OrganismFunction

Organor TissueFunction

CellFunction

MolecularFunction

Mental orBehavioral

Dysfunction

NeoplasticProcess

MentalProcess

GeneticFunction


Associative (non-isa) relationshipsAssociative (non-isa) relationshipsOrganism

process of

EmbryonicStructure

AnatomicalAbnormality

CongenitalAbnormality

AcquiredAbnormality


Structure

AnatomicalStructure

part of

OrganismAttribute

property of

BodySubstance

contains,produces

conceptualpart of

evaluation of

Body Systemconceptual

part of

part of

Body Part, Organ orOrgan Component

part of

Tissue

part of

Cell

part of

CellComponent

Gene orGenome

Body Spaceor Junction

adjacent to

location of

location of

evaluation ofFinding

Laboratory orTest Result

Sign orSymptom

BiologicFunction

PhysiologicFunction

PathologicFunction

Body Locationor Region

conceptualpart of

conceptualpart of

Injury orPoisoning

disrupts

disrupts

co-occurs with


Why a semantic network?Why a semantic network?

Semantic Types serve as high level categories Semantic Types serve as high level categories assigned to Metathesaurus concepts, assigned to Metathesaurus concepts, independently of their position in a hierarchyindependently of their position in a hierarchy

A relationship between 2 Semantic Types (ST) is a A relationship between 2 Semantic Types (ST) is a possible link between 2 concepts that have been possible link between 2 concepts that have been assigned to those STsassigned to those STs The relationship may or may not hold at the concept The relationship may or may not hold at the concept

levellevel Other relationships may apply at the concept levelOther relationships may apply at the concept level


Relationships can inherit semanticsRelationships can inherit semantics

Semantic Network

Metathesaurus

AdrenalCortex

AdrenalCortical

hypofunction

Disease or SyndromeBody Part, Organ,

or Organ Component

Pathologic Functionisa

Biologic Function

isa


Structure

isa

location of

location of


UMLS UMLS SummarySummary

Synonymous terms clustered into conceptsSynonymous terms clustered into concepts Unique identifierUnique identifier

Finer granularityFiner granularity Broader scopeBroader scope Additional hierarchical relationshipsAdditional hierarchical relationships Semantic categorizationSemantic categorization


Integrating subdomainsIntegrating subdomains

Biomedicalliterature


MeSH

Genomeannotations

Genomeannotations

GOModelorganisms

Modelorganisms

NCBITaxonomy

Geneticknowledge bases


OMIM

Clinicalrepositories


SNOMEDOthersubdomains

Othersubdomains

…

AnatomyAnatomy

UWDA

UMLS


Integrating subdomainsIntegrating subdomains



Genomeannotations

Genomeannotations

Modelorganisms

Modelorganisms





Othersubdomains

Othersubdomains

AnatomyAnatomy

Information integrationGenomics as an example


NF2 NF2 GeneGene, , proteinprotein, and , and diseasedisease

Neurofibromatosis 2 is an autosomal dominant disease characterized by tumors called schwannomas involving the acoustic nerve, as well as other features. The disorder is caused by mutations of the NF2 gene resulting in absence or inactivation of the protein product. The protein product of NF2 is commonly called merlin (but also neurofibromin 2 and schwannomin) and functions as a tumor suppressor.


Schwannoma (acoustic neuroma)Schwannoma (acoustic neuroma)

http://www.mayoclinic.com


NF2 geneNF2 gene

http://staff.washington.edu/timk/cyto/human/ http://www.ncbi.nlm.nih.gov/mapview/


MerlinMerlin

SynonymsSynonyms Neurofibromin 2Neurofibromin 2 SchwannominSchwannomin SchwannomerlinSchwannomerlin Neurofibromatosis-2Neurofibromatosis-2

10 isoforms10 isoforms AnnotationsAnnotations

Negative regulation of cell proliferationNegative regulation of cell proliferation CytoskeletonCytoskeleton Plasma membrane Plasma membrane


Neurofibromatosis 2(Type II neurofibromatosis,

Bilateral acoustic neurofibromatosis)C0027832

NF2(Neurofibromin 2 gene)

C0085114 Merlin(Schwannomin,

Neurofibromin 2)C0254123

NEUROFIBROMATOSIS,TYPE II; NF2

#101000

Drosophila melanogaster merlin(Dmerlin) mRNA, complete cds.

U49724OMIM GenbankExternal resources

UMLS Metathesaurus(Concepts and relations)

Amino Acid,Peptide, or Protein

Biologically ActiveSubstance

Neoplastic Process Gene or Genome

UMLS Semantic Network (Semantic Types)

Merlin, Drosophila

Tumor suppressorgenes

Benign neoplasmsof cranial nerves

Neuro-fibromatoses

Tumor suppressorproteins


LimitationsLimitations

Genes not systematically representedGenes not systematically represented Most gene products and diseases areMost gene products and diseases are

Gene/Gene product-Disease relationsGene/Gene product-Disease relations Not systematically representedNot systematically represented Not explicitly represented (e.g., co-occurrence)Not explicitly represented (e.g., co-occurrence)

Cross-references not systematically representedCross-references not systematically represented

Naming conventions (genes)Naming conventions (genes)


ReferencesReferences

UMLSUMLSumlsinfo.nlm.nih.govumlsinfo.nlm.nih.gov

UMLS browsersUMLS browsers (free, but UMLS license required) (free, but UMLS license required) Knowledge Source Server: Knowledge Source Server: umlsks.nlm.nih.govumlsks.nlm.nih.gov Semantic Navigator: Semantic Navigator: http://mor.nlm.nih.gov/perl/semnav.plhttp://mor.nlm.nih.gov/perl/semnav.pl

RRF browserRRF browser(standalone application distributed with the UMLS)(standalone application distributed with the UMLS)



Recent overviewsRecent overviews Bodenreider O. (2004). Bodenreider O. (2004). The Unified Medical Language The Unified Medical Language

System (UMLS): Integrating biomedical terminologySystem (UMLS): Integrating biomedical terminology. . Nucleic Acids ResearchNucleic Acids Research; D267-D270.; D267-D270.

Nelson, S. J., Powell, T. & Humphreys, B. L. (2002 ). Nelson, S. J., Powell, T. & Humphreys, B. L. (2002 ). The Unified Medical Language System (UMLS) The Unified Medical Language System (UMLS) ProjectProject. In: Kent, Allen; Hall, Carolyn M., editors. . In: Kent, Allen; Hall, Carolyn M., editors. Encyclopedia of Library and Information ScienceEncyclopedia of Library and Information Science. New . New York: Marcel Dekker. p.369-378. York: Marcel Dekker. p.369-378.



UMLS as a research projectUMLS as a research project Lindberg, D. A., Humphreys, B. L., & McCray, A. T. Lindberg, D. A., Humphreys, B. L., & McCray, A. T.

(1993). (1993). The Unified Medical Language SystemThe Unified Medical Language System. . Methods Inf Med, 32Methods Inf Med, 32(4), 281-91.(4), 281-91.

Humphreys, B. L., Lindberg, D. A., Schoolman, H. M., Humphreys, B. L., Lindberg, D. A., Schoolman, H. M., & Barnett, G. O. (1998). & Barnett, G. O. (1998). The Unified Medical The Unified Medical Language System: an informatics research Language System: an informatics research collaborationcollaboration. . J Am Med Inform Assoc, 5J Am Med Inform Assoc, 5(1), 1-11.(1), 1-11.



Technical papersTechnical papers McCray, A. T., & Nelson, S. J. (1995). McCray, A. T., & Nelson, S. J. (1995). The The

representation of meaning in the UMLSrepresentation of meaning in the UMLS. . Methods Inf Methods Inf Med, 34Med, 34(1-2), 193-201.(1-2), 193-201.

Bodenreider O. & McCray A. T. (2003). Bodenreider O. & McCray A. T. (2003). Exploring Exploring semantic groups through visual approachessemantic groups through visual approaches. . Journal of Journal of Biomedical InformaticsBiomedical Informatics, 36(6), 414-432. , 36(6), 414-432.

UMLS in UseMapping across Vocabularies


The problemThe problem

For noun phrases extracted from medical texts, For noun phrases extracted from medical texts, map to UMLS conceptsmap to UMLS concepts

Then, select from the MeSH vocabulary the Then, select from the MeSH vocabulary the concepts that are the most closely related to the concepts that are the most closely related to the original conceptsoriginal concepts

Medical text

Noun phrase

UMLS

MeSH descriptor


Map noun phrases to UMLSMap noun phrases to UMLS

NormalizationNormalization normalizenormalize noun phrases noun phrases use the use the normalized string indexnormalized string index

MetaMapMetaMap approximate matchingapproximate matching more aggressive approachmore aggressive approach

use derivational variantsuse derivational variants allow partial matchesallow partial matches


Restrict to MeSHRestrict to MeSH

Based on the principle of semantic localityBased on the principle of semantic locality Use different components of the UMLSUse different components of the UMLS 4 techniques of increasing aggressiveness4 techniques of increasing aggressiveness

Use SynonymyUse Synonymy MRCON + MRCON + MRSOMRSO

Use Associated expressions (ATXs)Use Associated expressions (ATXs) MRATXMRATX

Explore the AncestorsExplore the Ancestors MRREL + MRREL + SNSN

Explore the Other related conceptsExplore the Other related concepts MRREL + MRREL + SNSN


Restrict to MeSH: Restrict to MeSH: SynonymySynonymy

Term mapped to Source conceptTerm mapped to Source concept For this concept, is there a synonym term For this concept, is there a synonym term

that comes from MeSH? that comes from MeSH? (MRSO)(MRSO)


Restrict to MeSH: Restrict to MeSH: Assoc. expressionsAssoc. expressions

If not,If not, Is there an associated expression (ATX) that Is there an associated expression (ATX) that

describes this concept using a combination of describes this concept using a combination of MeSH descriptors? MeSH descriptors? (MRATX)(MRATX)

Endoscopic removal of intraluminal foreign body from oesophagus without incision

AND

Foreign Bodies

MH/SH

Esophagus surgery


Restrict to MeSH: Restrict to MeSH: AncestorsAncestors

If not, let us build the graph of the ancestors of If not, let us build the graph of the ancestors of this conceptthis concept using parents and broader concepts using parents and broader concepts (MRREL)(MRREL)

all the way to the topall the way to the top excluding ancestors whose semantic types are not excluding ancestors whose semantic types are not

compatible with those of the source concept compatible with those of the source concept (MRSTY)(MRSTY)

From the graph, select the concepts that come From the graph, select the concepts that come from MeSH from MeSH (MRCONSO)(MRCONSO)

Remove those that are ancestors of another Remove those that are ancestors of another concept coming from MeSHconcept coming from MeSH


Restrict to MeSH: Restrict to MeSH: Other related conceptsOther related concepts

If not, explore the other related concepts If not, explore the other related concepts (MRREL) (MRREL)

whose semantic types are compatible with those of whose semantic types are compatible with those of the source concept the source concept (MRSTY)(MRSTY)

From those, select the concepts that come from From those, select the concepts that come from MeSH MeSH (MRCONSO)(MRCONSO)


Restrict to MeSH: Restrict to MeSH: ExampleExample

Vein of neck, NOS

There is a MeSH term in the synonyms of SC

SC is described by a combination of MeSH terms (ATX)

The ancestors of SC contain MeSH terms

MeSH terms from non-hierarchically related concepts

Neck+Vein


Restrict to MeSH: Restrict to MeSH: ExampleExample

Vein of neck, NOS

Vein of head and neck, NOS

Neck

Blood Vessels Vascular structure

Veins

Systemic veins

Head

Head and neck, NOS Body part, NOS


Overall resultsOverall results

Synonymy:Synonymy: 24%24% Built-in mapping:Built-in mapping: 1% 1% AncestorsAncestors

From concept:From concept: 49%49% From children:From children: 2% 2% From siblings:From siblings: 1% 1%

Other:Other: 11%11% No mappingNo mapping 12%12%



Bodenreider O, Nelson SJ, Hole WT, Chang HF. Bodenreider O, Nelson SJ, Hole WT, Chang HF. Beyond synonymy: Beyond synonymy: exploiting the UMLS semantics in mapping vocabulariesexploiting the UMLS semantics in mapping vocabularies. Proceedings . Proceedings of AMIA Annual Symposium 1998:815-9.of AMIA Annual Symposium 1998:815-9.http://mor.nlm.nih.gov/pubs/pdf/1998-amia-ob.pdfhttp://mor.nlm.nih.gov/pubs/pdf/1998-amia-ob.pdf

Fung KW, Bodenreider O. Fung KW, Bodenreider O. Utilizing the UMLS for semantic mapping Utilizing the UMLS for semantic mapping between terminologiesbetween terminologies. Proceedings of AMIA Annual Symposium . Proceedings of AMIA Annual Symposium 2005:266-270.2005:266-270.http://mor.nlm.nih.gov/pubs/pdf/2005-amia-kwf.pdfhttp://mor.nlm.nih.gov/pubs/pdf/2005-amia-kwf.pdf

http://mor.nlm.nih.gov/pubs/pdf/1998-amia-ob.pdf

http://mor.nlm.nih.gov/pubs/pdf/2005-amia-kwf.pdf

Advanced Library ServicesTowards a Biomedical Knowledge Repository


DisclaimerDisclaimer

The project presented in this talk is being The project presented in this talk is being proposed as a new research initiative at the Lister proposed as a new research initiative at the Lister Hill National Center for Biomedical Hill National Center for Biomedical CommunicationsCommunications

It has not been approved or reviewed by NLM yetIt has not been approved or reviewed by NLM yet The ideas presented here may not reflect NLM’s The ideas presented here may not reflect NLM’s

viewsviews

In collaboration with Tom Rindflesch, NLMIn collaboration with Tom Rindflesch, NLM


Delivering Health InformationDelivering Health Information

Provide biomedical text to health care Provide biomedical text to health care professionals and consumersprofessionals and consumers

Maintain NLM’s cutting edgeMaintain NLM’s cutting edge Support public health and healthy behaviorSupport public health and healthy behavior Assist clinical practiceAssist clinical practice Enable biomedical research and discoveryEnable biomedical research and discovery

Exploit current Library resources and advanced Exploit current Library resources and advanced technologytechnology


Why additional services?Why additional services?

Biomedical literature is growing at an increasingly Biomedical literature is growing at an increasingly faster pacefaster pace High-throughput approach to literature processingHigh-throughput approach to literature processing

Integration between literature and other resources Integration between literature and other resources is insufficientis insufficient Adequate for navigating purposesAdequate for navigating purposes Insufficient for knowledge processingInsufficient for knowledge processing

Information retrieval is the starting point, not the Information retrieval is the starting point, not the end of the journey for the researcherend of the journey for the researcher


Integration for navigation purposesIntegration for navigation purposes

http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi


What additional services?What additional services?

Multi-document summarizationMulti-document summarization Extract and visualize the facts extracted from 250 Extract and visualize the facts extracted from 250

recent abstracts on the treatment of Parkinson’s diseaserecent abstracts on the treatment of Parkinson’s disease

Question answeringQuestion answering Clinical and biological questionsClinical and biological questions

Knowledge discoveryKnowledge discovery Connect facts from heterogeneous resourcesConnect facts from heterogeneous resources

Refined information retrievalRefined information retrieval Indexing on relations in addition to concepts or Indexing on relations in addition to concepts or

association main heading/subheadingassociation main heading/subheading


Fact-based vs. concept-basedFact-based vs. concept-based

(concept, relationship, concept) triples are the (concept, relationship, concept) triples are the common denominator to the various advanced common denominator to the various advanced servicesservices FactsFacts RelationsRelations Semantic predicationsSemantic predications RDF triplesRDF triples


Biomedical knowledge repositoryBiomedical knowledge repository

Knowledge integrationKnowledge integration Unique repositoryUnique repository Common formatCommon format Seamless environmentSeamless environment Phenotype and genotype information togetherPhenotype and genotype information together

Enabling resource for the various servicesEnabling resource for the various services SummarizationSummarization Question answeringQuestion answering Knowledge discoveryKnowledge discovery Refined information retrievalRefined information retrieval


Sources of knowledgeSources of knowledge

Biomedical literatureBiomedical literature Facts extracted from MEDLINE abstracts and full-text Facts extracted from MEDLINE abstracts and full-text

publicly available articles using text mining techniquespublicly available articles using text mining techniques Other corporaOther corpora

Structured databases / knowledge basesStructured databases / knowledge bases NCBI resourcesNCBI resources Model organism databasesModel organism databases Terminological knowledgeTerminological knowledge ……

Contributed knowledgeContributed knowledge The repository is open to collaborators outside NLMThe repository is open to collaborators outside NLM


Annotated knowledgeAnnotated knowledge

Provenance informationProvenance information Source (e.g., PMID)Source (e.g., PMID) Extraction mechanismExtraction mechanism TimestampTimestamp

Frequency informationFrequency information RedundancyRedundancy

Collaborative annotationCollaborative annotation ““Was this information useful?”Was this information useful?” Context of use/usefulnessContext of use/usefulness


Semantic Web perspectiveSemantic Web perspective

Common format for knowledgeCommon format for knowledge Resource Description Format (RDF)Resource Description Format (RDF)

Common identification schemeCommon identification scheme Unified Resource Identifier (URI)Unified Resource Identifier (URI)

Standard toolsStandard tools RDF browsersRDF browsers RDF “reasoners”RDF “reasoners”

High level of interest for biomedicine in the SW High level of interest for biomedicine in the SW communitycommunity Health Care and Life Sciences Interest GroupHealth Care and Life Sciences Interest Group

BiomedicalKnowledgeRepository

InformationRetrieval

QuestionAnswering

KnowledgeDiscovery

DocumentSummarization

Sourceselection

TextMining

TerminologicalKnowledge

OtherK. Sources

ContributedKnowledge

UMLS

MetaMap

MEDLINE CT.gov

Model organismannotation databases

OMIM

SemRep

01DEC05

Towards aBiomedical Knowledge Repository


Creating the repositoryCreating the repository


MedlineStructuredBiomedical

Data

Enhanced Information Management for Medicine

TextMining

PubMed

ClinicalTrials.gov UMLS Contributed

Knowledge



StructuredBiomedical

Data

PubMed


UMLS ContributedKnowledge


Medline

TextMining

Semantic relations

e.g.,

Rasagiline TREATS Parkinson Disease

ClinicalTrials.gov



Medline

PubMed


TextMining

ClinicalTrials.gov



DataUMLS Contributed

Knowledge


ContributedKnowledgeUMLS


Medline

PubMed


TextMining

ClinicalTrials.gov



Data




Medline

PubMed


TextMining

ClinicalTrials.gov


EntrezGene




Medline

PubMed


TextMining

ClinicalTrials.gov


GeneticsHome

Reference




Medline

PubMed


TextMining

ClinicalTrials.gov


OMIM




Medline

PubMed


TextMining

ClinicalTrials.gov


GeneOntology



DataUMLS


Medline

PubMed


TextMining

ClinicalTrials.gov






DataUMLS

Advanced library servicesAdvanced library services

Medline

PubMedText

Mining

ClinicalTrials.gov






DataUMLS


Medline

PubMedText

Mining

ClinicalTrials.gov


Knowledge Discovery




DataUMLS


Medline

PubMedText

Mining

ClinicalTrials.gov


Question Answering




DataUMLS


Medline

PubMedText

Mining

ClinicalTrials.gov


Summarization andFocused Retrieval

Summarizing Biomedical Text


Summarizing Biomedical TextSummarizing Biomedical Text

SearchSearch MedlineMedline ClinicalTrials.govClinicalTrials.gov

Summarize documentsSummarize documents Most salient semantic relationsMost salient semantic relations

Visualize the summaryVisualize the summary Link the semantic relations toLink the semantic relations to

Original textOriginal text Related structured knowledgeRelated structured knowledge


Text Mining WorkflowText Mining Workflow

Information retrieval

summarization

Text mining

Parkinson disease/therapy

Network of relations

retrieval

294 articles


Text Mining WorkflowText Mining Workflow

Parkinson disease/therapy


MovementDisorders

ParkinsonDisease

pramipexol

DopaminAgonists

Dopamine

Brain

rasagilineLevodopa

Entire subthalamicnucleus

Neuro-degenerative

Diseases

entacapone

Anhedonia

treats

location of

GeneTherapy

Deep brainStimulation

Procedure

Depressivedisorder

Bilateralbreast cancer

Dementia

occurs in

Dyskineticsyndrome

isa treats

Treatment of Parkinson’s diseaseTreatment of Parkinson’s disease SemGen outputSemGen output


MovementDisorders

ParkinsonDisease

pramipexol

DopaminAgonists

Dopamine

Brain

rasagilineLevodopa

Entire subthalamicnucleus

Neuro-degenerative

Diseases

entacapone

Catechol-O-methyl-transferase inhibitor

Anhedonia

Monoamine OxidaseInhibitors

AntiparkinsonAgents

AntidepressiveAgents

treats

isa

location ofpart of

GeneTherapy

Deep brainStimulation

Procedure

Depressivedisorder

Bilateralbreast cancer

Dementia

occurs in

Dyskineticsyndrome

isa treats

associatedwith

SemGen output+ UMLS relations

+ additional UMLS concepts

SemGen output+ UMLS relations

+ additional UMLS concepts

Treatment of Parkinson’s diseaseTreatment of Parkinson’s disease


ConclusionsConclusions

Need to go beyond information retrievalNeed to go beyond information retrieval Need to integrate multiple, heterogeneous Need to integrate multiple, heterogeneous

knowledge sources to support knowledge knowledge sources to support knowledge processing, not only navigationprocessing, not only navigation

Synergistic with the Semantic WebSynergistic with the Semantic Web Emerging standard frameworkEmerging standard framework W3C Health Care and Life Sciences Interest GroupW3C Health Care and Life Sciences Interest Group

http://www.w3.org/2001/sw/hcls/http://www.w3.org/2001/sw/hcls/

http://www.w3.org/2001/sw/hcls/

MedicalOntologyResearch

Olivier BodenreiderOlivier Bodenreider

Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland - USABethesda, Maryland - USA

Contact:Contact:Web:Web:

[email protected]@nlm.nih.govmor.nlm.nih.govmor.nlm.nih.gov

ontologies for data integration: a semantic web perspective training course olivier bodenreider...

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