All Hands Meeting 2003 BIRN ONTOLOGIES Session Jeffrey Grethe Amarnath Gupta Bertram Ludäscher...
-
Upload
abner-carroll -
Category
Documents
-
view
212 -
download
0
Transcript of All Hands Meeting 2003 BIRN ONTOLOGIES Session Jeffrey Grethe Amarnath Gupta Bertram Ludäscher...
All Hands Meeting 2003
BIRN ONTOLOGIES Session
Jeffrey Grethe
Amarnath Gupta
Bertram Ludäscher
Maryann E. Martone
Overview
First half:• Ontologies (brief; not a “total recall”) (Bertram)• UMLS & “Bonfire” extensions (Jeff)• Disease maps (Maryann, Amarnath)• Ontology-enhanced tools (Maryann)
Second half:• Discussion on policy issues, BIRN ontology curation etc
Kinds of “Ontologies” (simplified cheat sheet)
1. Controlled Vocabularies agreed upon range of values (“enumeration type”) e.g. “standard names” for materials, diseases, …
2. Simple Taxonomies, Classification hierarchies (isa) controlled concept vocabulary
+ subconcept (specialization) relationship e.g. biological taxonomies
3. Graph-like Ontologies isa, has-a, and other relationships
(contained_in, causes, activates, …),
the latter usually w/o formalized semantics (but agreed upon) e.g. semantic nets, RDF, …
4. Full-fledged Ontologies Usually logic-based ontologies; relationships (including isa) are logic consequences of
formal concept definitions (partially) defined semantics
You knew this already: e.g. 5. Conceptual Models DSM-IV(Diagnostic and Statistical Manual of Mental Disorders )
290.11 isa 290.1 isa 290
concept conceptrelationship
conceptconceptconcept
concept concept
isa
concept
Parent Personoffspring.Person
class class
class
relation
part-of
DSM IV Taxonomy
290 Dementia of the Alzheimer's Type, With Late Onset, Uncomplicated
290.1 Dementia Due to Creutzfeldt-Jakob Disease
290.1 Dementia Due to Pick's Disease
290.1 Dementia of the Alzheimer's Type, With Early Onset, Uncomplicated
290.11 Dementia of the Alzheimer's Type, With Early Onset, With Delirium
290.12 Dementia of the Alzheimer's Type, With Early Onset, With Delusions
290.13 Dementia of the Alzheimer's Type, With Early Onset, With Depressed Mood
290.2 Dementia of the Alzheimer's Type, With Late Onset, With Delusions
290.21 Dementia of the Alzheimer's Type, With Late Onset, With Depressed Mood
290.3 Dementia of the Alzheimer's Type, With Late Onset, With Delirium
290.4 Vascular Dementia, Uncomplicated
290.41 Vascular Dementia, With Delirium
290.42 Vascular Dementia, With Delusions
290.43 Vascular Dementia, With Depressed Mood
291 Alcohol Intoxication Delirium
Uses of Ontologies in Data Integration
“Smart” (conceptual-level) data discovery, browsing, querying • looking for “C”, finding “D” (which is C-related)• terminological and semantic “glue” between different “data worlds”
Conceptual / Semantic Modeling of a domain• for terminologies: “domain maps” (in description logic)• for processes: “process maps”, “disease maps” (open issue)
…
Need to provide …• Ontology exchange syntax • Ontology extensions mechanisms ( BONFIRE)• Inter-ontology mapping mechanisms (yours vs. mine)• Data-to-ontology registration mechanisms (data to concepts)
Generic Standards
RDF, RDFS• For graph-based ontologies (=explicit statements)
OWL (Web Ontology Language)
• Three levels: OWL Lite, OWL DL, OWL Full• Some Features:
Ontology O2 uses (refers to) O1 (over the web!)
formalism to exchange, extended, and map between ontologies
concept conceptrelationship
Parent Personoffspring.Person
Generic Tools Ontology authoring: Protégé-2000 ontology tool (Stanford)
• OWL Plug-In (evolving)
Developers’ corner:• Jena-2 Semantic Web Framework (HP), for dealing with OWL ontologies• Logic programming extensions (SWI)
Example: Ontology-enhanced Map Integration (OMI)
1. Upload ontologies O1, O2, … (O2, O3 use O1,…)
2. Upload ontology mapping Om :: Oa Ob
3. Register data sets D1, D2, … to ontology Oa
4. Query data sets through Ob interface!
UMLS &
BONFIRE (Community Ontology Building)
What is UMLS?
UMLS is a long-term research project began on 1986 by the National Library of Medicine (NLM)
UMLS is a collection of knowledge sources designed to facilitate the retrieval and integration of information from multiple machine-readable biomedical information sources
Knowledge Resources
Metathesaurus • The Metathesaurus is organized by concept or meaning, it
provides a uniform, integrated distribution format from about 60 biomedical vocabularies and classifications and links many different names for the same concepts
• The 2000 edition of the Metathesaurus includes more than 730,000 concepts and 1.5 million concept names from over 50 different biomedical vocabularies, some in multiple languages
Knowledge Resources
Semantic Network • Semantic Network contains information about the types or
categories (e.g., "Disease or Syndrome," "Virus") to which all concepts have been assigned and the permissible relationships among these types (e.g., "Virus" causes "Disease or Syndrome")
• The semantic types are the nodes in the Network, and the relationships between them are the links.It has 132 semantic types, 53 links between the semantic types.
Knowledge Resources
Semantic Network • Semantic types: organisms, anatomical structures,
biologic function, chemicals, events, physical objects, and concepts or ideas etc.
• Relations: ‘isa’, `physically related to,' `spatially related to,' `temporally related to,' `functionally related to,' and `conceptually related to’ etc.
Hierarchical relations types:
Associative (non-isa) Relationships
Knowledge Resources
Information Sources Map• The information sources are varied and include
bibliographic databases, diagnostic expert systems, and factual databases
• The Information Sources Map or directory contains both human-readable and machine-"processable" information about the scope, location, vocabulary, syntax rules, and access conditions of biomedical databases of all kinds
Related Sites
Further Information:
http://www.nlm.nih.gov/ http://www.nlm.nih.gov/research/umls/ http://www.nlm.nih.gov/research/umls/UMLSDOC.HTML http://www.nlm.nih.gov/research/umls/umlsmain.html
BONFIRE
BONFIRE will allow BIRN users to accommodate concepts not present in the available pre-defined source ontologies
Whenever possible, users should employ the relationship terms provided within the UMLS or other source ontologies provided by BIRN
Once new terms are defined, when will they will become part of the BIRN Ontology (BONFIRE)?• after appropriate curation?
Ontology Refinement
An Example Data Set
species = rat (UMLS: C003493) region = neostriatum (UMLS: C0162512) cell type = medium spiny cell (No Concept Available) structure = spiny dendrite(No Concept Available) segmented object = dendritic spine (UMLS:
C0872341) segmented object = dendritic shaft (No Concept
Available)
BONFIRE Example
For this data set, no ontology IDs exist for medium spiny cell, spiny dendrite or dendritic shaft.
medium spiny cell (BONFIRE: BID006) medium spiny cell “is a” neuron (UMLS: C0027882) medium spiny cell “has location” neostriatum (UMLS: C0162512) medium spiny cell “is a” neuron AND “has property” dendritic spine (UMLS:
C0872341)
spiny dendrite (BONFIRE: BID007) spiny dendrite “is a” dendrite (UMLS: C0011305) spiny dendrite ‘contains” dendritic spine (UMLS: C0872341)
DISEASE MAPS
Glue Knowledge for Mouse BIRN
Navigating through Multi-resolution information
Linking animal and human imaging data
brain
cerebellum
cerebellar cortex
Purkinje cell
dendritic spine
Entopeduncular nucleus
Globus pallidus, internal segment
Animal Model Disease Process
•Link database concepts to UMLS/Neuronames
•Utilize the neurohomology ontology: M. Bota at USC
•Develop disease and animal model knowledge maps
Knowledge Maps
Parkinson’s Disease
Pathological feature
Alpha synuclein
Abnormal filaments
Substantia nigra
ubiquitin
symptom
tremorakinesia
rigidity
Motor deficit
neurons
Lewy Body C0085200
C0030567
Cell inclusion C0205708
glia
neuronal degeneration
Dopamine neuron
cortex
Basal forebrain
Filamentous inclusion C0230674
C0815003
C024566
C0027746
C0746626
C027746
C0007776
C0175412
C0041538
C0027882
C0027836
Knowledge Map: Animal Model
a-synuclein mousetransgenic animal
Cellular phenotype
Cellular inclusion
Behavioral phenotype
Alpha synuclein C024566
nuclear inclusion C0544907
Alpha synuclein C024566
Cytoplasmic inclusion C0205708
Motor deficit C0746626
ubiquitin C0041538
neurons gliaC0027882 C0027836
C0025936
Knowledge Maps
Parkinson’s Disease
Pathological feature
Alpha synuclein
neurons
Lewy Body Cytoplasmic inclusion
glia
Filamentous inclusion
a-synuclein mouse
Cellular phenotype
Cellular inclusion
nuclear inclusion
ubiquitin
Alpha synuclein
neurons
Cytoplasmic inclusion
ubiquitin
Parkinson’s disease map
disease C0012634
course of illness C0242656
disease phase C0457338
pathology C0677042
disease characteristic C0599878
symptoms C0683368
Pathological process C0030660
sign/symptom C0037088
proneness/risk C0178598
severities C0439793
epidemiology C0699910
disease classification C0683326
prevention, intervention and treatment C0679677
Parkinson’s disease features
Parkinsons disease has a pathological featurepathological feature is a histopathological featureC0243140Lewy Body C0085200 is a histopathological feature
Lewy Body is a cell inclusion C0205708Lewy Body is a filamentous inclusion C0541641filamentous inclusion C0541641 has part of abnormal filamentabnormal filament consists of alpha synuclein C0245466abnormal filament do not consist of beta synucleinabnormal filament do not consist of gamma synucleinLewy Body contains ubiquitin C0041538Lewy Body has property eosinophilia C0014457Lewy Body has component ParkinLewy Body has componetn synphilin-1Lewy Body has component tauPatients with mutation in parkin do not have Lewy Bodies
Parkinsons disease has a pathological featurepathological feature is a histopathological featureC0243140Lewy Body C0085200 is a histopathological feature
Lewy Body is a cell inclusion C0205708Lewy Body is a filamentous inclusion C0541641filamentous inclusion C0541641 has part of abnormal filamentabnormal filament consists of alpha synuclein C0245466abnormal filament do not consist of beta synucleinabnormal filament do not consist of gamma synucleinLewy Body contains ubiquitin C0041538Lewy Body has property eosinophilia C0014457Lewy Body has component ParkinLewy Body has componetn synphilin-1Lewy Body has component tauPatients with mutation in parkin do not have Lewy Bodies
Concept A relationship Concept B
Parkinson’s disease processes
alpha synuclein protofibrils are toxic to DA neurons; filaments are protective
A53T increases protofilamentsA30P increases protofilamentsA30P inhibits filament formation from protofilamentsprotofibrils permeabilize membranessynaptic vesicles have a membraneprotofibrils permeabilize synaptic vesiclespermeabilization of synaptic vesicles results in leaky vesiclesleaky vesicles in DA neuronsincreased DA in cytoplasm causes cell death
alpha synuclein protofibrils are toxic to DA neurons; filaments are protective
A53T increases protofilamentsA30P increases protofilamentsA30P inhibits filament formation from protofilamentsprotofibrils permeabilize membranessynaptic vesicles have a membraneprotofibrils permeabilize synaptic vesiclespermeabilization of synaptic vesicles results in leaky vesiclesleaky vesicles in DA neuronsincreased DA in cytoplasm causes cell death
Concept A relationship Concept B
Object-Oriented Modeling
TOOLS Custom: Know-ME, OMI, … Generic: Protégé-2000, …
Discussion
Getting Organized
…
Join the mailing list:• Mail to [email protected] with subject/body
“subscribe birn-ontologies”