W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > June 2011

RE: HCLS task forces

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Thu, 2 Jun 2011 09:07:09 -0700
Message-ID: <170efd1858fdd2c5223f93a0ede836cd@mail.gmail.com>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>
hi all,

> Many of us have expressed interest in personalized medicine in the
> last year. If you define personalized medicine as the application of
> molecular knowledge about a particular patient to tailor therapeutic
> choices for that patient, it is simply the future of medicine. And the
> future isn't very far away.

lee hood's vision at ISB:

Health Care in the 21st Century:
      P4 Medicine™: Predictive, Preventive, Personalized, and
The goal of systems biology is to fundamentally transform the practice of
medicine, and ISB researchers have taken the leadership role in catalyzing
this transformation. We are developing tools and techniques, and pursuing
research that will usher in a new era of predictive, preventive,
personalized and participatory medicine.

Today's medicine is reactive: we wait until someone is sick before
administering treatment. Medicine of the future will be predictive and
preventive, examining the unique biology of an individual to assess their
probability of developing various diseases and then designing appropriate
treatments, even before the onset of a disease. Today's medicine is also
myopic: we use only a few measurements to diagnose disease and are
generally unable to make fine distinctions between individuals or between
subtle variations of the same disease. Medicine of the future will use
more sophisticated measurements, as well as more measurements overall,
thereby yielding accurate health assessments for truly personalized

Improved personal measurements and personalized treatments are the keys to
improving health care. Diseases arise from either genetic abnormalities,
detrimental environmental factors, (poor diet, infectious organisms, or
toxins), or a combination of these. We know certain genetic patterns can
make a person unusually susceptible to factors in their environment. We
also know certain defective genes will increase the probability of an
individual having certain health problems. For example, a woman with a
single copy of the mutant breast cancer 1 gene (BRCA-1) has a 70 percent
chance of developing breast cancer by the time she´s 60 years old.
Unfortunately, today there is no practical way for each of us to determine
our genetic makeup and, more important, to understand the likely health
consequences. However, in the future individuals will be able to easily
obtain such information, and then work closely with their health
practitioner to develop a predictive, preventive and personalized
health-care program.

Prediction. The technologies and tools of systems biology will provide
medical practitioners with two exciting sources of health-related
diagnostic data: By examining an individual´s complete genetic makeup, a
physician will be able to generate comprehensive predictions about the
patient´s health prospects. And by examining protein markers which
naturally occur in an individual´s blood, a physician will be able to
accurately determine a person's health status, including both the current
effects of any abnormal genes and the current reactions to any
environmental toxins or infectious pathogens.

Prevention. The new approach to medicine, based on each individual's
genetic makeup, will help us determine the probability of an individual
contracting certain diseases, as well as reveal how an individual may
respond to various treatments, thereby providing guidance for developing
customized therapeutic drugs. Thus another use of the technologies and
tools of systems biology will be to develop preventive treatments for
individuals, based on their potential health problems, as indicated by
their genetic makeup and current blood- protein markers.

The goal of this new approach to medicine will be to use the most
fundamental health-related information — an individual's genetic makeup
plus current health status (as identified by blood protein markers) — to
prescribe appropriate preventive drugs. For example, given your genetic
makeup, you may have a 40% chance of developing breast cancer by age 50,
but if you start taking a certain drug at age 35, that chance could drop
to 5% at age 50.

In fact, scientists at ISB are currently involved in several research
programs involving blood diagnosis of complex diseases, including type I
diabetes, breast cancer, and prostate cancer. Cancer is the second leading
cause of death in the United States, with prostate cancer accounting for
one third of all cancer cases among men, and breast cancer accounting for
approximately half of all cancer cases among women. ISB scientists are
currently researching protein markers which occur in blood to better
identify the onset, metastatic potential, and probable course of these
cancers in individuals, with the eventual goal of developing more
effective treatments.

The common theme running through all of this research and its application
to medicine -- the predictive and preventive potential of systems biology
-- is personalization. On average, each human differs from another by less
than one percent of their genetic makeup. But these genetic differences
give rise to our physical differences, including our potential
predisposition to various diseases. So the ability to examine each
individual's unique genetic makeup and thereby customize our approaches to
medical treatment is at the heart of this new era of predictive,
preventive, personalized medicine.

As a result of this personalization, medicine will become participatory.
Patients will actively participate in personal choices about illness and
well–being. Participatory medicine will require the development of
powerful new approaches for securely handling enormous amounts of personal
information and for educating both patients and their physicians.


> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
> lifesci-request@w3.org] On Behalf Of M. Scott Marshall
> Sent: Thursday, June 02, 2011 5:03 AM
> To: HCLS
> Subject: HCLS task forces
> Today is a holiday in much of Europe so I won't be able to make it to
> the HCLS telcon. I will try to supply my input to the anticipated
> discussion.
> I will attempt to *briefly* summarize what the currently active task
> forces are doing:
> Scientific Discourse - planning a demonstration of linking literature
> to experiments
> BioRDF - working on a W3C note for expression RDF
> Linked Open Drug Data (LODD) - working on a W3C note for emerging best
> practices in life sciences RDF / linked data
> Translational Medicine - pharmacogenomics modeling, biomarkers
> Terminology - using an RDF representation of clinical reports from
> radiology and pathology to alert clinicians to discrepancies
> It is nice to know that several products of HCLS activities and
> Semantic Web have been applied across the board. Specific industrial
> examples include Iker's Semantic Web company (see
> http://lists.w3.org/Archives/Public/public-semweb-
> lifesci/2011May/0028.html),
> TripleMap http://triplemap.com/, Collabrx http://collabrx.com/, IO
> Informatics
> http://www.w3.org/2001/sw/sweo/public/UseCases/IOInformatics/.
> All of these examples enable personalized medicine. I don't think that
> there will be a 'killer app' that 'launches' the Semantic Web. Just as
> happened with XML, the day will come when the same critical mass is
> reached - when people realize that most of them are using RDF to
> exchange data as the obvious technology choice. As RDF versions of
> each important data type become available along with plugins for the
> most popular applications, it will become easier to employ linked data
> for dynamically customized interfaces and visualizations.
> I would characterize our approach to forming task forces as bottom-up
> aggregation of interests expressed by teleconference participants.
> Generally, the people who have worked together in a given task force
> have stuck together and started new activities because imposing a
> reshuffle of the deck and the ensuing re-synchronization would have
> disrupted ongoing work in some task forces.
> A few observations:
> * Motivation for participants seems to have been publication - other
> than altruism and the thrill of creating the next phase of scientific
> research.
> * In general, an emphasis on building applications and demonstrations
> helps to ground discussions that can quickly become too abstract to
> lead to concrete actions.
> * A bottleneck remains getting access to actual data to validate our
> methods and tools
> Many of us have expressed interest in personalized medicine in the
> last year. If you define personalized medicine as the application of
> molecular knowledge about a particular patient to tailor therapeutic
> choices for that patient, it is simply the future of medicine. And the
> future isn't very far away.
> Cheers,
> Scott
> --
> M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
> http://staff.science.uva.nl/~marshall
Received on Thursday, 2 June 2011 16:07:36 UTC

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