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Convergence of Chemistry and Biology

From Science Information to Science Informatics: Parallels and Paradoxes in Chemistry and Molecular Biology Gary Wiggins wiggins@indiana.edu. Convergence of Chemistry and Biology. Biochemistry/MolecularBiology. Physical Science Negative public perception

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Convergence of Chemistry and Biology

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  1. From Science Information to Science Informatics: Parallels and Paradoxes in Chemistry and Molecular BiologyGary Wigginswiggins@indiana.edu

  2. Convergence of Chemistry and Biology • Biochemistry/MolecularBiology

  3. 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 Chemistry vs. Biology

  4. Physical Sciences • Sciences that explore the nature and properties of energy and nonliving matter

  5. Chemistry Physics Materials science Climatology Oceanography Environmental sciences Astronomy Geology Engineering Mathematics Computer Science Physical Sciences Disciplines

  6. 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.

  7. 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?

  8. 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

  9. 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

  10. Biology Pharmacology Anatomy Physiology Microbiology Genetics Molecular Biology Medicine Dentistry Nursing Pharmacy Epidemiology Public Health Life Sciences Disciplines

  11. Molecular Biology • Concerned with studying the chemical structures and processes of biological phenomena at the molecular level

  12. 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

  13. Public (Free) Databases in Life Sciences • GenBank and many other biomolecular sequence and structure databases • PubMed (NCBI and NLM) • PubMed Central

  14. NCBI’s Coffee Break

  15. BioOne: A SPARC Initiative

  16. 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 services http://www.biomedcentral.com/

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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.”

  22. 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

  23. 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/

  24. 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

  25. 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

  26. 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

  27. 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/

  28. 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

  29. PLoS Failures • ARL Board of Directors refused to issue a public statement of support last July

  30. 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)

  31. 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.

  32. 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

  33. IU School of Informatics • http://informatics.indiana.edu • http://www.informatics.iupui.edu/ • http://www.newmedia.iupui.edu/

  34. Chemical Informatics • Chemical informatics provides the tools to acquire, organize, and evaluate data, yielding new insights for further chemical research.

  35. Major Areas of Interest in Chemical Informatics • Productivity applications • Informatics techniques • Simulation (Molecular Modeling)

  36. 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.

  37. 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

  38. 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

  39. Representative Core Courses • Information infrastructure • Information representation • Mathematical foundations • Social informatics • Organizational informatics

  40. Master of Science in Informatics Programs • Human Computer Interaction • Health Informatics • Bioinformatics • Chemical Informatics

  41. Graduate Courses • Introduction to Informatics • Information Management • Chemical Information Technology • Molecular Modeling & Computational Chemistry

  42. Informatics: Opening the Door to New Careers!

  43. Who owns: • www.chemistry.org? • Ans: American Chemical Society • www.biology.org? • Ans:Howard Hughes Medical Institute

  44. DOE 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 OSTI Products

  45. 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/

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