Dynamic Integration of Semantic Metadata in Biomedical Communications
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Transcript of Dynamic Integration of Semantic Metadata in Biomedical Communications
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Tim Clark Harvard Medical School &
Massachusetts General Hospital
Pistoia Alliance Conference April 12, 2011
Copyright 2011 Massachusetts General Hospital. All rights reserved.
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Information sharing and integration requirements for curing complex disorders.
Web 3.0 and semantic metadata. Integrating ontologies, documents, data.
Annotation Ontology & Annotation Framework. Applications
SESL, Hypothesis Mgmt, Nanopublications Open Enterprise Semantic Model
Conclusion
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Yearly mortality (U.S.) = 642,00 people
Yearly costs (U.S.) = $676 B / 4.7% GDP
Prevalence = 5.3 M + 76 M + 14.4 M
= 95.7 M people
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create hypothesis�
design experiment �
run experiment � collect data�
interpret data�
share interpretations�
synthesize knowledge�
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MCI progressors non progressors
PET imaging of PIB (radiolabelled compound binds amyloid beta A4 protein)
MRI imaging of brain structure showing loss of hippocampal volume
Brain. 2010 Nov;133(Pt 11):3336-3348.
= 218 subjects +
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dopaminergic pathway�
α-synuclein, β-amlyoid�
α-synuclein, Tau �
chr 16p11.2 CNV �
chr 16p11.2 CNV �
CRF, glutaminergic system, dopamine, amygdala …�
Alzheimer� Disease�
Parkinson’s �Disease�
Schizophrenia�
Autism�
Bipolar Disorder� Drug �Addiction �
Huntington’s �Disease�
ALS�
Depression �
SIRT2 �
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1. We want to organize all the known facts in neurobiology so we can mash them up.
2. There are no “facts” in neurobiology, except uninteresting ones.
3. All we have, are
assertions supported by evidence, of varying quality.
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1667 2010
Printing Press Web
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We scientists do not attend professional meetings to present our findings ex cathedra, but in order to argue.
John Polanyi, FRS, Nobel Laureate University of Manchester
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Social Web (Web 2.0, read/write)
Shared annotation with controlled terminology systems (Sem Web)
+
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Information sharing within communities or tasks via Social Web (Web 2.0), wikis and forums
Information “permeability” across pharma R&D projects / domains / pipeline stages via shared metadata (semantic annotation)
Web 3.0 improves cross-‐domain Signal to Noise, institutional memory & data “findability”
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Genes
Proteins
Biological Processes
Chemical Compounds
Antibodies
Cells
Brain anatomy
…
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Annotation Ontology (AO) is a domain-‐independent Web ontology. Links document fragments to ontology terms.
Metadata separate from annotated documents. SWAN AF manages document annotation.
Interfaces to textmining svcs & supports curation. Collaborating with
NCBO, UCSD, Elsevier, USC, Manchester, EMBL, Colorado, EBI, etc…
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Text
Shared metadata
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2) Automatic annotation
Dr.
Pao
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icca
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– O
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Dr.
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– O
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, 201
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Semantics on documents (SESL) Vocabulary standards & terminology development
Document & data management Collaboratories & web communities Hypothesis management (SWAN) Nanopublications (OpenPHACTS)
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Model the thinking behind your research Database it, web-ify it, RDF-ize it, share it Link the Models / Hypotheses to
Claims / Interpretations Evidence (publications, experiments, data) Supporting and contradictory claims from others Evidence for these other claims
Web 3.0: share, compare and discuss Manage knowledge while creating it
Can be public, private, or semi-private
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SWAN Ontology: Model of Research Statements
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SWAN Ontology: Provenance of Research Statements
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Dr.
Pao
lo C
icca
rese
– O
ct 8
, 201
0
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Dr.
Pao
lo C
icca
rese
– O
ct 8
, 201
0
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Dr.
Pao
lo C
icca
rese
– O
ct 8
, 201
0
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Cognitive Deficits
(S)
BACE1 (O)
Relate to (p)
provenance context
With thanks to Barend Mons and Paul Groth…
Mons / Groth model of a nanopublication
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swande:Claim <http://tinyurl.com/4h2am3a>
Intramembranous Aβ behaves as chaperones of other membrane proteins
rdf:type
dct:title
G1
<http://example.info/person/1> pav:authoredBy
Vincent Marchesi
foaf:name
foaf:Person
rdf:type
pav: http://purl.org/pav/provenance/2.0/ foaf: http://xmlns.com/foaf/0.1/
G2
With thanks to Paolo Ciccarese
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swande:Claim <http://tinyurl.com/4h2am3a>
Intramembranous Aβ behaves as chaperones of other membrane proteins
rdf:type
dct:title
G1 <http://example.info/person/1> pav:authoredBy
G2 <http://example.info/person/0> pav:curatedBy
G4
Gwen Wong
foaf:name
foaf:Person
rdf:type
With thanks to Paolo Ciccarese
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swande:Claim <http://tinyurl.com/4h2am3a>
Intramembranous Aβ behaves as chaperones of other membrane proteins
rdf:type
dct:title
G1
<http://example.info/person/1> pav:contributedBy
<http://example.info/citation/1>
swanrel:referencesAsSupportiveEvidence
G5
G6 With thanks to Paolo Ciccarese
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G8
<http://example.info/alzswan:statement_f3556dcfc331d9b9af9d5c0cfc570ba6_event_1>
<http://bio2rdf.org/go:0051087>
rdf:type
Event of type GO "chaperone binding"
rdfs:label
<prefix:actor_1>
<prefix:target_1>
<prefix:location_1>
<http://bio2rdf.org/chebi:53002>
<http://bio2rdf.org/mesh:D008565>
<http://bio2rdf.org/go:0005886>
rdf:type
rdf:type
rdf:type
rdfs:label “Beta amyloid”
rdfs:label “Membrane protein”
rdfs:label “Plasma membrane”
With thanks to Nigam Shah & Paolo Ciccarese
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Hyque triples
G8
<http://example.info/person/2> pav:contributedBy
Nigam Shah
foaf:name
foaf:Person
rdf:type G9
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swande:Claim <http://tinyurl.com/4h2am3a>
Intramembranous Aβ behaves as chaperones of other membrane proteins
rdf:type
dct:title
G1
Hyque triples G8
swanrel:derivedFrom
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The target hypothesis will be linked to: Pathway & target relation to disease, Target selection criteria, Validation assays and criteria, Experiment (assay) provenance, Experimental data and computations, Scientist remarks, findings and discussion.
Start as a relatively simple model and extend
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Hypotheses of therapeutic action for compounds and scaffolds, linked to Hypothesis / results for individual assays, Experiment (assay) provenance, Experimental data, Group annotation, Internal databases etc.
Start as a relatively simple model and extend
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Information ecosystem
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Curing complex medical disorders goes hand in hand with next-‐gen biomedical communications
Web 3.0 provides the technology framework Semantic annotation, hypothesis management, nanopubs: tools for next-‐gen biomed comms .
Requires / enables international collaborations of biomedical researchers and informaticians.
Open enterprise model with semantic metadata.
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People Paolo Ciccarese (Harvard) Maryann Martone (UCSD) Anita DeWaard & Tony Scerri (Elsevier) Adam West & Ernst Dow (Eli Lilly & Co) Carole Goble & Sean Bechhofer (U Manchester) Karen Verspoor & Larry Hunter (U Colorado) Gully Burns & Cartik Ramakrishnan (USC) David Newman (U Southampton) Nigam Shah (Stanford / NCBO) Paul Groth & Barend Mons (VU Amsterdam)
Funding: Elsevier, NIH, Eli Lilly, & EMD Serono