convergence of chemistry and biology
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From Science Information to Science Informatics: Parallels and Paradoxes in Chemistry and Molecular Biology Gary Wiggins [email protected]. Convergence of Chemistry and Biology. Biochemistry/MolecularBiology. Physical Science Negative public perception - PowerPoint PPT PresentationTRANSCRIPT
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From Science Information to Science Informatics:
Parallels and Paradoxes in Chemistry and Molecular
Biology
Gary [email protected]
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Convergence of Chemistry and Biology Biochemistry/MolecularBiology
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Chemistry vs. Biology Physical Science Negative public
perception Women a distinct
minority in the profession
High-cost information products (not much free)
Life Science Positive public
perception Lots of women in
the professions Lots of free (or
low-cost) information sources
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Physical Sciences Sciences that explore the nature
and properties of energy and nonliving matter
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Physical Sciences Disciplines Chemistry Physics Materials science Climatology Oceanography Environmental
sciences
Astronomy Geology Engineering Mathematics Computer Science
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Chemistry science that deals with the
properties, composition, and structure of substances (defined as elements and compounds), the transformations that they undergo, and the energy that is released or absorbed during these processes.
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Public Perception of Chemistry Recognition of higher standard of
living through chemical advances Career for people in white lab coats
who make smelly concoctions Polluters of the environment Who has seen a TV program about
chemistry in the last month?
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Public Perception of Chemistry
…the North American and Western European public by and large still do not believe that the chemical industry is anything but a necessary evil.
--Mark S. Reisch, C&EN, September 4, 2000
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Life Sciences Study of living organisms from their
molecular and biochemical subsystems to the ecosystems created by the interactions of multiple species
Continuity and interdependence make it difficult to define the boundaries of the life sciences
http://www.lifesciences.umich.edu/overview/commission/scope.html
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Life Sciences Disciplines Biology Pharmacology Anatomy Physiology Microbiology Genetics Molecular Biology
Medicine Dentistry Nursing Pharmacy Epidemiology Public Health
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Molecular Biology Concerned with studying the
chemical structures and processes of biological phenomena at the molecular level
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Public Perception of Life Sciences Strongly tied to efforts to protect
the environment, cure disease, etc.
Career for caring, dedicated individuals
Lots of engaging and entertaining nature programs on TV
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Public (Free) Databases in Life Sciences GenBank and many other
biomolecular sequence and structure databases
PubMed (NCBI and NLM) PubMed Central
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NCBI’s Coffee Break
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BioOne: A SPARC Initiative
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BioMed Central Publishes journals in all areas of biology
and medicine Free access to peer-reviewed research
articles through The British Library through PubMed Central
Subscription-based access to reviews, commentaries and other information serviceshttp://www.biomedcentral.com/
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E-BioSci EMBO (European Molecular Biology
Organization) initiative Services to access and retrieve
digital information in the life sciences
Nature Publishing Group will participate
http://www.e-biosci.org
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E-BioSci Objectives Foster optimal pooling and use of
European biological archives and data collections
Stimulate the development of common protocols and methodologies Searching and retrieval in:
bibiographic databases sequence databases
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E-BioSci Objectives Provide a framework for further research
into more effective strategies for linking of bibliographic with molecular, genomic, and (3D-)image databases
Act as host for the web-publication of digital articles
Operate in harmony with other international efforts, including PubMed and PubMed Central in the USA
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Physical Sciences Information Infrastructure (PSII) Workshop: May 20-21, 2000
http://www.osti.gov/physicalsciences/ Included 2 SLA representatives as
participants Representatives from AAAS (publisher
of Science) and Nature Magazine Lots of government & academic types No one from the BIG DEAL publishers
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PSII Workshop Conclusions Endorsement of a national
infrastructure“When comparing The National Library of
Medicine’s amazing success as a benchmark, it is clear that much can be done in the physical sciences to positively impact research and practice in the physical sciences.”
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PSII Workshop Recommendations Common knowledge base Point of convergence for all
information Openly available source of
information to serve all users in an electronic environment
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Public Library of Science (PLoS) Non-profit organization of
scientists committed to making the world's scientific and medical literature freely accessible to scientists and to the public around the world, for the benefit of scientific progress, education and the public good.http://www.publiclibraryofscience.org/
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PLoS Objectives Free access to scientific journal
articles six months after publication
Centralized archives of life sciences literature in a repository such as PubMed Central
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PLoS Successes Open letter signed by 28,166 scientists
from 172 countries as of 10/8/01 HOWEVER, only 3,000 in the US as of
late August 2001 New journal production companies
springing up: Blue Sky: www.BlueSkyScholars.com bepress: www.bepress.com ejournalPress.com: www.ejpress.com
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PLoS: Impact Few publishers have agreed to put their
journals on PubMed Central for free, BUT: Science now offers free access to research
articles one year out Royal Society of Chemistry has free access two
years out Highwire Press has ~ 325,000 free articles NASA Astrophysics Data System has over
300,000 free articles PLoS will launch their own publishing
effort: page charges @ $300/article
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PubMed Central and PubScience PubMed Central began in February
2000 54 journals available as of 10/10/01, 43
of which are BioMed Central journals http://www.pubmedcentral.nih.gov
PubSCIENCE began in 1999, with a focus on the physical sciences Over 40 participating publishers http://pubsci.osti.gov/
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PubSCIENCE: Who cares? …while keeping medical research
out of the hands of physicians and patients might be considered a moral outrage, the research needs of those involved with physics and the natural sciences are going to elicit a mere shrug from the average person.
--Robin Peek, Information Today, September 2001, p. 42
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PLoS Failures ARL Board of Directors refused to
issue a public statement of support last July
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PLoS: ACS Reaction …no editor or author has indicated
an unwillingness to participate in the ACS journal publishing program because of PLOS.
--Robert D. Bovenschulte, Director, ACS Publications Division
(C&EN, September 3, 2001, p. 44)
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Statement of the ACS, July 31, 2001 The American Chemical Society
(ACS), the world’s largest scientific society, believes that government should scrutinize its role as a provider of S&T information in order to avoid harming the scientific enterprise, jeopardizing the stewardship of S&T information, and competing unnecessarily with businesses and nonprofit groups.
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Future Directions More emphasis on standards for
information production and retrieval systems: author empowerment
Research on user behavior and use of computer systems
New paradigms for science publishing Increased emphasis on informatics
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IU School of Informatics http://informatics.indiana.edu http://www.informatics.iupui.edu/ http://www.newmedia.iupui.edu/
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Chemical Informatics Chemical informatics provides the
tools to acquire, organize, and evaluate data, yielding new insights for further chemical research.
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Major Areas of Interest in Chemical Informatics Productivity applications Informatics techniques Simulation (Molecular Modeling)
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Bioinformatics Bioinformatics is a pure and an
applied science dealing with the collection, management, analysis and dissemination of biological data and knowledge, especially with respect to genetics and molecular biology.
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Major Areas of Interest in Bioinformatics Study of the genome code Understanding role of the genome
in regulating biological functions Intense concentration on proteins,
their structure and function Proteomics
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School of Informatics BS Degree: 122 hours Informatics core courses: 30 hours Other informatics courses: 9 hours
Some may be from a department/school outside the School of Informatics
Cognate area courses: 15-18 hours
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Representative Core Courses Information infrastructure Information representation Mathematical foundations Social informatics Organizational informatics
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Master of Science in Informatics Programs Human Computer Interaction Health Informatics Bioinformatics Chemical Informatics
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Graduate Courses
Introduction to Informatics Information Management Chemical Information Technology Molecular Modeling & Computational
Chemistry
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Informatics: Opening the Door to New Careers!
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Who owns: www.chemistry.org? Ans: American Chemical Society www.biology.org? Ans:Howard Hughes Medical
Institute
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OSTI ProductsDOE Information Bridge (gray
literature) http://www.osti.gov/bridge
PubSCIENCE (journal literature) http://www.osti.gov/pubscience
PrePRINT Network (preprint literature) http://www.osti.gov/preprint
Federal R&D Project Summaries http://www.osti.gov/fedrnd
GrayLit Network http://www.osti.gov/graylit
EnergyFiles (virtual library collections) http://www.osti.gov/energyfiles
Research and Development Project Summaries http://www.osti.gov/rnd
DOE R&D Accomplishments http://www.osti.gov/accomplishments
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Bibliography Reisch, Mark S. “Responsible Care.” C&EN September 4, 2000, 78(36),
21-26.http://pubs.acs.org/cen/coverstory/7836/7836bus1.html
Challenges and Opportunities in Understanding the Complexity of Living Systems: Scope of the Life Sciences
http://www.lifesciences.umich.edu/overview/commission/scope.html Future e-access to the primary literature (Nature Forum)
http://www.nature.com/nature/debates/e-access/