18-Oct-04 1 Semantic Web in. KM Charter 18-Oct-04 2 Charter outline One page graphic Purpose:...

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


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


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


Facing a Technology Gap in Drug Innovation

Need to utilize Knowledge more

effectively


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


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


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”


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

{ } { }


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


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


Knowledge Networks

Research Process and Knowledge Flow

InterpretationData

AnalysisExpt

DesignDecision Action


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


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?


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


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


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


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


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


New Sharing Paradigm for Research

Sharing discoveries in a Context


Semantic Communities Vision

DiseaseArea

FGx

Chem

Ontology

Annotated Literature

rDB

Central Referenced

DB

Local Ontology

Local DB’s

Platform Space

Projects

Extended Ontology


Thank You


ScienceJanuary 24, 2003


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


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


…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


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


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


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


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/

18-Oct-04 1 Semantic Web in. KM Charter 18-Oct-04 2 Charter outline One page graphic Purpose:...

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