Tim Clark of Harvard Medical School & Massachusetts General Hospital and chair of the W3C's scientific discourse task, gave a thorough look at applications for web 3.0, semantic metadata, and an application ontology and annotation framework for use in curing complex disorders.
Dynamic Integration of Semantic Metadata in Biomedical Communications
1. Tim Clark
Harvard Medical School &
Massachusetts General Hospital
Pistoia Alliance Conference
April 12, 2011
Copyright 2011 Massachusetts General Hospital. All rights reserved.
2. 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
3. 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
4. run experiment collect data
design experiment interpret data
synthesize knowledge
create hypothesis share interpretations
5. Brain. 2010 Nov;133(Pt 11):3336-3348.
PET imaging of PIB
(radiolabelled compound
binds amyloid beta A4 protein)
MRI imaging of brain
structure showing loss of
hippocampal volume
MCI progressors + non progressors = 218 subjects
6. SIRT2
Alzheimer Huntington s
Disease Disease
Autism
chr 16p11.2 CNV
-synuclein, -amlyoid
chr 16p11.2 CNV
Parkinson s Schizophrenia
Disease
Depression
-synuclein, Tau
dopaminergic pathway
ALS
CRF, glutaminergic system, Drug
Bipolar Disorder Addiction
dopamine, amygdala …
7. 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.
9. 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
10. Social
Web
(Web
2.0,
read/write)
+
Shared
annotation
with
controlled
terminology
systems
(Sem
Web)
11. 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
20. Semantics
on
documents
(SESL)
Vocabulary
standards
&
terminology
development
Document
&
data
management
Collaboratories
&
web
communities
Hypothesis
management
(SWAN)
Nanopublications
(OpenPHACTS)
21. 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
27. Mons / Groth model of a nanopublication
provenanc
context
e
Cognitive
Relate
to
BACE1
Deficits
(p)
(O)
(S)
With thanks to Barend Mons and Paul Groth…
28. rdf:type
<http://tinyurl.com/4h2am3a>
swande:Claim
dct:title
Intramembranous
Aβ
behaves
as
chaperones
of
other
membrane
proteins
G1
pav:authoredBy <http://example.info/person/1>
G2
foaf:name rdf:type
Vincent
Marchesi
foaf:Person
pav: http://purl.org/pav/provenance/2.0/ With thanks to Paolo Ciccarese
foaf: http://xmlns.com/foaf/0.1/
29. rdf:type
<http://tinyurl.com/4h2am3a>
swande:Claim
dct:title
Intramembranous
Aβ
behaves
as
chaperones
of
other
membrane
G1 proteins
pav:authoredBy <http://example.info/person/1>
G2
pav:curatedBy <http://example.info/person/0>
G4
foaf:name rdf:type
Gwen
Wong
foaf:Person
With thanks to Paolo Ciccarese
30. rdf:type
<http://tinyurl.com/4h2am3a>
swande:Claim
dct:title
Intramembranous
Aβ
behaves
as
chaperones
of
other
membrane
G1 proteins
swanrel:referencesAsSupportiveEvidence
<http://example.info/citation/1>
G5
pav:contributedBy
<http://example.info/person/1>
G6
With thanks to Paolo Ciccarese
31. <http://example.info/alzswan:statement_f3556dcfc331d9b9af9d5c0cfc570ba6_event_1>
rdfs:label Event
of
type
GO
"chaperone
rdf:type binding"
<http://bio2rdf.org/go:0051087>
<prefix:actor_1>
rdf:type <http://bio2rdf.org/chebi:53002>
rdfs:label “Beta amyloid”
<prefix:target_1>
rdf:type <http://bio2rdf.org/mesh:D008565>
rdfs:label “Membrane protein”
<prefix:location_1>
rdf:type <http://bio2rdf.org/go:0005886>
rdfs:label “Plasma membrane”
G8
With thanks to Nigam Shah & Paolo Ciccarese
33. rdf:type
<http://tinyurl.com/4h2am3a>
swande:Claim
dct:title
Intramembranous
Aβ
behaves
as
chaperones
of
other
membrane
G1 proteins
swanrel:derivedFrom
G8
Hyque
triples
34. 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
35. 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
38. 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.
39. 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