ontologies for data integration: a semantic web perspective training course olivier bodenreider...
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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
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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
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From terminology integrationto information integration
Unified Medical Language System (UMLS)
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What does UMLS stand for?What does UMLS stand for?
UUnifiednified MMedicaledical LLanguageanguage SSystemystem
UMLS®
Unified Medical Language System®
UMLS Metathesaurus®
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5 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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.»
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Overview through an example
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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
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8 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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9 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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) ……
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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
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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
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Diseases of the endocrine system
Diseases of the Adrenal Glands
Addison’s Disease
Diseases/DiagnosesSNOMED International
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Endocrine Diseases
Adrenal Gland Diseases
Addison’s Disease
DiseasesMeSH
Adrenal Gland Hypofunction
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Endocrine disorder
Adrenal disorder
Adrenal cortical disorder
Adrenal cortical hypofunction
Addison’s Disease
AOD
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Endocrine disorder
Disorder of adrenal gland
Hypoadrenalism
Adrenal Hypofunction
Corticoadrenal insufficiency
Addison’s Disease
Read Codes
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Primary adrenocortical insufficiency
Other disorders ofadrenal gland
Disorders of otherendocrine gland
ICD-10
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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
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Adrenal Cortex Diseases
Hypoadrenalism
Adrenal Gland Hypofunction
Adrenal cortical hypofunction
Endocrine Diseases
Adrenal Gland Diseases
organize concepts
Addison’s Disease
UMLS
SNOMEDMeSHAODRead Codes
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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
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Endocrine Diseases
Adrenal Gland Diseases
Adrenal Cortex Diseases
Hypoadrenalism
Adrenal Gland Hypofunction
Adrenal cortical hypofunction
Addison’s Disease
Adrenal Cortex Dysfunction
Adrenal Dysfunction
Addison’s disease due to autoimmunity
Secondary hypocortisolism
Other disorders ofadrenal gland
Disorders of otherendocrine gland
Adrenal Glands
Adrenal Cortex
Endocrine System
Endocrine Glands
Abdominal organ Diseases
relate to other concepts
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21 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
Adrenal Gland Diseases
Addison’s Disease
Diseases
Adrenal Gland Hypofunction
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How do they do that?How do they do that?
Lexical knowledgeLexical knowledge
Semantic pre-processingSemantic pre-processing
UMLS editorsUMLS editors
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Lexical knowledgeLexical knowledge
Adrenal gland diseasesAdrenal disorderDisorder of adrenal glandDiseases of the adrenal glandsC0001621
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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
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25 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Additional knowledge: UMLS editorsAdditional knowledge: UMLS editors
Adrenal Gland Diseases
Adrenal Cortex Diseases
Adrenal Cortex Dysfunction
Hypoadrenalism
Adrenal Gland Hypofunction
Adrenal cortical hypofunction
Addison’s Disease
Other disorders ofadrenal gland
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26 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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UMLS Metathesaurus
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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)
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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
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30 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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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
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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…
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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
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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
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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
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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)
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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
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UMLS Semantic Network
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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
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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
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““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
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Associative (non-isa) relationshipsAssociative (non-isa) relationshipsOrganism
process of
EmbryonicStructure
AnatomicalAbnormality
CongenitalAbnormality
AcquiredAbnormality
Fully FormedAnatomical
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
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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
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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
Fully FormedAnatomical
Structure
isa
location of
location of
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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
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Integrating subdomainsIntegrating subdomains
Biomedicalliterature
Biomedicalliterature
MeSH
Genomeannotations
Genomeannotations
GOModelorganisms
Modelorganisms
NCBITaxonomy
Geneticknowledge bases
Geneticknowledge bases
OMIM
Clinicalrepositories
Clinicalrepositories
SNOMEDOthersubdomains
Othersubdomains
…
AnatomyAnatomy
UWDA
UMLS
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Integrating subdomainsIntegrating subdomains
Biomedicalliterature
Biomedicalliterature
Genomeannotations
Genomeannotations
Modelorganisms
Modelorganisms
Geneticknowledge bases
Geneticknowledge bases
Clinicalrepositories
Clinicalrepositories
Othersubdomains
Othersubdomains
AnatomyAnatomy
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Information integrationGenomics as an example
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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.
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Schwannoma (acoustic neuroma)Schwannoma (acoustic neuroma)
http://www.mayoclinic.com
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NF2 geneNF2 gene
http://staff.washington.edu/timk/cyto/human/ http://www.ncbi.nlm.nih.gov/mapview/
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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
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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
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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)
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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)
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ReferencesReferences
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.
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ReferencesReferences
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.
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ReferencesReferences
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.
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UMLS in UseMapping across Vocabularies
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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
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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
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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
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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)
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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
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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
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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)
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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
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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
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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%
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ReferencesReferences
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
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Advanced Library ServicesTowards a Biomedical Knowledge Repository
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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
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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
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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
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Integration for navigation purposesIntegration for navigation purposes
http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
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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
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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
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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
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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
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83 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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84 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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BiomedicalKnowledgeRepository
InformationRetrieval
QuestionAnswering
KnowledgeDiscovery
DocumentSummarization
Sourceselection
TextMining
TerminologicalKnowledge
OtherK. Sources
ContributedKnowledge
UMLS
MetaMap
MEDLINE CT.gov
Model organismannotation databases
OMIM
SemRep
01DEC05
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Towards aBiomedical Knowledge Repository
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87 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Creating the repositoryCreating the repository
BiomedicalKnowledgeRepository
MedlineStructuredBiomedical
Data
Enhanced Information Management for Medicine
TextMining
PubMed
ClinicalTrials.gov UMLS Contributed
Knowledge
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88 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Creating the repositoryCreating the repository
StructuredBiomedical
Data
PubMed
Enhanced Information Management for Medicine
UMLS ContributedKnowledge
BiomedicalKnowledgeRepository
Medline
TextMining
Semantic relations
e.g.,
Rasagiline TREATS Parkinson Disease
ClinicalTrials.gov
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89 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Creating the repositoryCreating the repository
Medline
PubMed
Enhanced Information Management for Medicine
TextMining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
StructuredBiomedical
DataUMLS Contributed
Knowledge
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90 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledgeUMLS
Creating the repositoryCreating the repository
Medline
PubMed
Enhanced Information Management for Medicine
TextMining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
StructuredBiomedical
Data
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91 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledgeUMLS
Creating the repositoryCreating the repository
Medline
PubMed
Enhanced Information Management for Medicine
TextMining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
EntrezGene
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92 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledgeUMLS
Creating the repositoryCreating the repository
Medline
PubMed
Enhanced Information Management for Medicine
TextMining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
GeneticsHome
Reference
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93 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledgeUMLS
Creating the repositoryCreating the repository
Medline
PubMed
Enhanced Information Management for Medicine
TextMining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
OMIM
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94 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledgeUMLS
Creating the repositoryCreating the repository
Medline
PubMed
Enhanced Information Management for Medicine
TextMining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
GeneOntology
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95 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
StructuredBiomedical
DataUMLS
Creating the repositoryCreating the repository
Medline
PubMed
Enhanced Information Management for Medicine
TextMining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
ContributedKnowledge
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96 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledge
StructuredBiomedical
DataUMLS
Advanced library servicesAdvanced library services
Medline
PubMedText
Mining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
Enhanced Information Management for Medicine
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97 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledge
StructuredBiomedical
DataUMLS
Advanced library servicesAdvanced library services
Medline
PubMedText
Mining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
Knowledge Discovery
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98 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledge
StructuredBiomedical
DataUMLS
Advanced library servicesAdvanced library services
Medline
PubMedText
Mining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
Question Answering
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99 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContributedKnowledge
StructuredBiomedical
DataUMLS
Advanced library servicesAdvanced library services
Medline
PubMedText
Mining
ClinicalTrials.gov
BiomedicalKnowledgeRepository
Summarization andFocused Retrieval
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Summarizing Biomedical Text
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101 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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102 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Text Mining WorkflowText Mining Workflow
Information retrieval
summarization
Text mining
Parkinson disease/therapy
Network of relations
retrieval
294 articles
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103 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Text Mining WorkflowText Mining Workflow
Parkinson disease/therapy
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104 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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105 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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106 Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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/
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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