18-oct-04 1 semantic web in. km charter 18-oct-04 2 charter outline one page graphic purpose:...
TRANSCRIPT
18-Oct-04
1
Semantic Web in
18-Oct-04KM Charter 2
Charter outline
One page graphic
Purpose: Mission & Vision
Perimeter: Core competencies & activities
Impact
Engagement priority principles
Operating principles with customer
Appendix KM Definition (SWOT)
TBD Organizational Design
18-Oct-04KM Charter 3
Industry productivity vs. investment
Source: PhRMA & FDA 2003
N
ME
s
$0
$5
$10
$15
$20
$25
$30
$35
1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 20020
100
200
300
400
Tot
al R
&D
inve
stm
ent
($ b
illio
ns)
Note:’00-27 ‘01-24, ’02-17 NMEs 23% NME obtain first approval, D. Kessler, H&Q
$ 897 millionincluding post-approval R&D costs
to develop a new prescription drug
= 250% increase in a decade Inflation-adjusted
Including failures
Tufts Center, May 2003: $ 802 million excluding post-approval R&D costs
Rising clinical trial costs -
difficulty in recruiting patients
Expanding development
programs
More chronic &
degenerated diseases
Longer development times
18-Oct-04KM Charter 4
Increase productivity
Improve submissions and approvals
Reduce costs: Clinical and preclinical studies ~80% of total
Segmented patient populations
Complexity of the science and technologies Capturing the innovation and value
Drug-hunting ability
Knowledge creation and transfer Consortium & Alliances
R&D Challenges in Drug Discovery
18-Oct-04KM Charter 5
Facing a Technology Gap in Drug Innovation
Need to utilize Knowledge more
effectively
18-Oct-04KM Charter 6
Knowledge Networks within Pharma that need to be supported
Scientists and Researchers
Regulatory (FDA)
Industrial Operations
Research Alliances
Business Process and Management
Competitive and Market Information
Financial
18-Oct-04KM Charter 7
How Can Scientists Work Together Better?
Chemistry Compound Library Chemists HT Screening Medicinal Chemists Synthetic Chemists Molecular Modelers Rational Designers
Biology Geneticists Pathologists Molecular Biologists Cytologists ADME Toxicologists Clinicians
Informatics Genomicists Functional Genomicists BioStatisticians Bioinformaticists Cheminformaticists Dynamics Modelers DB admins
?Data Integration
18-Oct-04KM Charter 8
Information Interpretation
Sharing data is not sufficient for sharing insights
Simply annotating findings with TEXT does not solve how to locate such insights.
Can researchers find different meaning in the same data?
Merge Legacy data with newly generated
Capture Context!
It is therefore necessary to be able to describe and capture such value-added elements in a formal, searchable way.
! ?“Which side groups?”“The data clearly shows that the
compound series has hERG issues that are exacerbated by its side groups”
18-Oct-04KM Charter 9
A Major Unmet Challenge- Recognizing Information Interpretation
I(x) I(x) I(x) I(x)
How can one guarantee that scientist i interprets data I(x) the same way as j does?
Seeing the data the same way…
ℐℐi i { } { } ~~ ℐℐj j
{ } { }
18-Oct-04KM Charter 10
Social Participation
“[It] refers not just to local events of engagement in certain activities with
certain people, but to a more encompassing process of being active
participants in the practices of social communities and constructing
identities in relation to these communities…. Such participation shapes
not only what we do, but also who we are and how we interpret what we
do.”
- Etienne Wenger, 1999
18-Oct-04KM Charter 11
The Negotiation of Meaning
As described by Friesen:
The meaning of any set of terms, and the significance and utility of any
taxonomy, according to Wenger, can be evaluated only in the context of a
community whose members are involved in similar activities and share
similar values. Wenger calls this process the "negotiation of meaning:"
The production of meanings "that extend, redirect, dismiss, reinterpret,
modify or confirm… the histories of meanings of which they are a part."
(Wenger, 1999; p. 53)
Example: Functional Genomics and Pathologists
18-Oct-04KM Charter 12
Knowledge Networks
Research Process and Knowledge Flow
InterpretationData
AnalysisExpt
DesignDecision Action
18-Oct-04KM Charter 13
Communities and Interoperability Semantic interoperability is tied directly to communities of
practice:
“Within a community or domain, relative homogeneity
reduces interoperability challenges. Heterogeneity
increases as one moves outside of a focal
community/domain, and interoperability is likely [to be] more
costly and difficult to achieve” Moen, 2001
Meanings encoded with a (XML) schema, for use within one community, are defined only implicitly.
Databases can only be used by those who define them; group heterogeneity impedes practical schema definitions
18-Oct-04KM Charter 14
Why a Semantic Web for Life Science Applications?
Improve Scientific Interactions and Exchanges
Data Integration AND Interpretation
Web-compatible strategies for information encoding and sharing
Sharing Best Practices – Knowledge discovery rules
Knowledge Agents –How can they accelerate science?
18-Oct-04KM Charter 15
Framework for Next Generation of the Web Knowledge Exchange within a Semantic Web
OWL (Ontology Web Language) W3C Ontology Specification Goes beyond 1st order Logic (Frames & Descriptive Logic) Extensible by members of any community Structurally based on RDF
RDF (Resource Description Framework) Basic XML Semantic Format that OWL is based upon Allows users to merge and aggregate any set of related data and
relational components Refers to Ontologies specified in OWL
OWL RDF
Defines
Structured
18-Oct-04KM Charter 16
Smarter, Searchable Annotations (Chemistry)
Search feasible for any side chain improving “GI transport”, or semantically related impact
Text found only if compound already selected
Link can be used to find all compounds referencing it– but reason for link is unclear
“The side chain on this compound improves GI transport significantly”
Free-Text
“As evidenced (PKID:392384), the side chain on this
compound improves GI transport significantly”
Free-Text with Link
<side chain “#element=2”>
<improves><GI transport>
RDF Statement
18-Oct-04KM Charter 17
Smarter, Searchable Annotations (Proteins)
Text found only if compound already selected
Link can be used to find all proteins referencing this link– but reason for link is unclear
Search feasible for any protein domain interacting with “Compound Series XV”, or semantically related binding
“The domain on this protein regulates catalytic activity significantly”
Free-Text
“As evidenced (PKID:8832), our compound
series interact with the catalytic site”
Free-Text with Link
<domain “#element=2”>
<interacts><Cmp Series XV >
RDF Statement
18-Oct-04KM Charter 18
Aggregation through Semantics (OWL)
GENE
PROTEIN
mRNA
CASCADE PATHWAY
LOCALIZATION
BIO-PROCESS
DRUGTREATMENT
TARGET MODEL
INTERVENTION POINT
MICROARRAYEXPERIMENT
DISEASEData Sources
18-Oct-04KM Charter 19Courtesy of BeyondGenomics
18-Oct-04KM Charter 20
New Data Paradigm for Research
More than a collection of tables for Set-selection
Data can evolve with additions of attributes and properties as well as through new inferences
Query, Upload
Results
Search
Aggregate
18-Oct-04KM Charter 21
New Sharing Paradigm for Research
Sharing discoveries in a Context
18-Oct-04KM Charter 22
Semantic Communities Vision
DiseaseArea
FGx
Chem
Ontology
Annotated Literature
rDB
Central Referenced
DB
Local Ontology
Local DB’s
Platform Space
Projects
Extended Ontology
18-Oct-04KM Charter 23
Thank You
18-Oct-04KM Charter 24
ScienceJanuary 24, 2003
18-Oct-04KM Charter 25
Information vs. Knowledge
“Information is data that is endowed with relevance or purpose.
Converting data into information thus requires knowledgeknowledge.
And knowledge, by definition, is specialized. (In fact, truly knowledgeable people tend toward
overspecialization, whatever their field, precisely because there is always so much to know.)” –
Peter Drucker, 1988
The conversion of data to information or knowledge is an interpretive process that implies a
sociological context:
“It entails personal involvement in and commitment to specific practices, and participation in a
community of those with similar or complimentary understandings.” - Norm Friesen, 2002
18-Oct-04KM Charter 26
Communities… Encoding is not an isolated activity, defined by mechanical conciseness:
“All of this seems to suggest that the significance of words
and descriptions in metadata may not be so much a matter
of clear and unambiguous definition ... Instead, it is more a
matter of doing, acting, and belonging.”
- Norm Friesen, 2002
18-Oct-04KM Charter 27
…and MeaningPractice both defines and requires meaning:
“This focus on meaningfulness is… not primarily on the technicalities of
‘meaning.’ It is not on meaning as it sits locked up in dictionaries. It is not
just on meaning as a relation between a sign and a reference…. Practice
is about meaning as an experience of everyday life.
- Etienne Wenger, 1999
18-Oct-04KM Charter 28
Explicit vs. Tacit Knowledge Negotiating Meaning helps take what is implicit and make it explicit, tangible, and codifiable.
Context is essential for framing implicit knowledge
No Knowledge is formally either tacit or explicit – when meaning is negotiated so that interpretations and insights can be effectively shared within a context, then what was tacit is now reified.
Communities, if defined appropriately through common semantics, can capture any knowledge that is viewed as relevant and timely, thereby making it functional
18-Oct-04KM Charter 29
Semantic Web for Life Sciences
What SWLS is-What SWLS is-
W3C Discussion Forum for Scientists and Informaticists
Identifying critical needs and defining them as use cases
Help define the relation between information and (codified) knowledge
Effective formation and interaction of research communities
What SWLS isn’t-What SWLS isn’t-
Standards Group
SIG for Vendors
Closed Consortium for Industry
18-Oct-04KM Charter 30
Semantic Web Life Science Activities W3C Workshop Oct 27, 28 Formation of Work Groups
Mailing List: [email protected]
ISMB 2005 (Detroit) – Semantic Web Track
Coordination with BioPAX, GeneOntology, UniProt, NCI, etc
18-Oct-04KM Charter 31
SWLS Resources Semantic Web: http://www.w3.org/2001/sw/
RDF: http://www.w3.org/rdf
SWLS: http://esw.w3.org/topic/
SemanticWebForLifeSciences
DB wrapper: http://www.w3.org
/2004/04/30-RDF-RDB-access/