=Paper=
{{Paper
|id=Vol-52/paper-15
|storemode=property
|title=GlaxoSmithKline Position Paper for Workshop on Ontologies in Agent Systems
|pdfUrl=https://ceur-ws.org/Vol-52/oas01-mcentire.pdf
|volume=Vol-52
}}
==GlaxoSmithKline Position Paper for Workshop on Ontologies in Agent Systems==
https://ceur-ws.org/Vol-52/oas01-mcentire.pdf
GlaxoSmithKline Position Paper for Workshop of
Ontologies in Agents Systems
Robin McEntire
GlaxoSmithKline Pharmaceuticals
709 Swedeland Road, PO Box 1539
King of Prussia, PA 19406-0939
610.270.6527
Robin_A_McEntire@gsk.com
ABSTRACT a common syntax, which enables the semantic representations to
This paper describes the position of GlaxoSmithKline with be moved from one site to another without undo, or inaccurate,
respect to the development of ontologies and intelligent, agent- translation of the definitions of the underlying objects. And well-
based systems. defined services allow easy programmatic access to life sciences
objects and to services that manipulate those objects (and produce
other life sciences objects).
Keywords
ontologies, agents, life sciences. 2. Commercial Opportunities
More importantly, over the long run, this combination of well-
1. Motivation defined services and well-understood, easily exchangeable objects
It is clear that the number of data sources available and necessary will create a marketplace in which vendors may compete to
to move forward in the study of the life sciences is quite large and provide services and new data sources. As we have seen in other
diverse and is growing at a remarkable rate. It is also clear that technology areas the greatest driver for the adoption and use of a
there is tremendous growth in the field in computational methods technology is a strong marketplace. GSK, and other pharmas, are
and services for manipulating this data, often manipulating interested in services that provide scientific information that can
multiple, disparate, distributed and heterogeneous sources of data. be easily geared to the specific objectives of its scientific
The proliferation of data formats and schemas for life sciences investigators. So, for example, there is currently work being done
objects and the many methods for accessing or computationally to provide more targeted access to scientific journal articles for
manipulating those objects and services is a serious impediment to the research scientist by many of the electronic journal vendors.
the efficient, effective and scalable use of these data and services. This process could be significantly aided by categories and
The problem will become only more severe as the field continues ontologies that are shared across the industry. The workshop
to grow. However, the recent developments in web technology, organisers have already suggested that one of our goals should be
including web languages, and object-oriented and knowledge- finding applications that provide the greatest internal business
representation technology, are at a level of maturity that they can impact or "the most bang for the buck", which is a laudable goal.
be leveraged to help solve this problem. However, we should also consider the markets that our work
might target and what opportunities there might be for us to
As outlined by the workshop organisers a progressive framework leverage our work into new or existing COTS products. By
for the life sciences has a number of components, which are; focusing on the greatest external business impact this work will
1. the development of common, shareable ontologies for objects yield the greatest impact on our industry as a whole.
within the life sciences domain
2. the development, or, more likely, the adoption of one or a 3. Additional Technologies
few common languages for the exchange of these common In addition, GSK is very interested in intelligent integration of
ontologies, and multiple, heterogeneous data sources. Well-defined services and
3. the definition of services that provide well-characterised, common object definitions will make the job of mediated access
uniform (or, at least, consistent) access to data/information to multiple data sources much easier. It will also make the display
and services and visualization of this information more intelligent and geared
more to the particular interests of each scientist. There are already
Common, shareable ontologies provide the field with an some vendors in the market and others emerging. Our efforts
understandable semantics for discussion and for the programmatic could provide substantial assistance to these vendors. The same
computation of life sciences objects. Exchange languages provide could be said of text mining software and products. We are
seeing a number of vendors emerge in this area. Ontologies and
related services could be a significant aid here as well.
4. Relationships and Synergies
We also encourage the organisers of the workshop to consider
what other organisations might provide in terms of valuable
synergies for our work. For example, the OMG has been in
existence for a considerable time and has been very successful in
defining common services within the life sciences research Encyclopedia of E. coli Genes and Metabolism. Nuc. Acids
domain. Another significant strength of the OMG is that it's Res., Vol 27 No 1, pp 55-58.
membership includes a large number of IT and Life Sciences Karp, P.D., Chaudhri, V, XOL Specification,
organisations, who now have a history of working together on a http://www.ai.sri.com/pkarp/xol/.
number of problems. McEntire, R, et al, An Evaluation of Ontology Exchange
Languages for Bioinformatics, In Proceedings of ISMB
5. References 2000.
Cattell, R.G.G., et al, 2000. The Object Data Standard: Object Management Group, 1997. UML Semantics, Version
ODMG 3.0, Morgan Kaufmann Publishers 1.1, ftp://ftp.omg.org/pub/docs/ad/97-08-04.pdf.
Fikes, R., Kehler, T. 1985. The Role of Frame-Based Riley, M., 1993. Functions of the gene products of
Representation in Reasoning Communications of the Escherichia coli, Microbiological Reviews, 57:862-952.
Association for Computing Machinery, 28(9):904-920. Rumbaugh, J., Jacobson, I., Booch, G., 1998. The Unified
Gruber, T.R. 1993. A translation approach to portable Modeling Language Reference Manual, Addison-Wesley.
ontology specifications. Knowledge Acquisition, 5:199-220.
Karp, P., Riley, M., Paley, S., Pellegrini-Toole, A.,
Krummenacker, M. 1999. EcoCyc: Electronic