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Meeting the Challenge of "The New Biology" for College Libraries and Librarians in the Post-genomic era CNIF—27






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Meeting the Challenge of "The New Biology" for College Libraries and Librarians in the Post-genomic era CNIF—27. Frederick Stoss American Chemical Society National Meeting This One is Just Right! Information Resources for Small Colleges Division of Chemical Information March 26, 2007.
Meeting the Challenge of "The New Biology" for College Libraries and Librarians in the Post-genomic era CNIF—27

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Slide 1

Meeting the Challenge of "The New Biology" for College Libraries and Librarians in the Post-genomic eraCNIF—27

Frederick Stoss

American Chemical Society National Meeting

This One is Just Right! Information Resources for Small CollegesDivision of Chemical Information

March 26, 2007

Slide 2

Abstract

Sequencing the Human Genome was one of the greatest scientific achievements in history. The results unleashed a wave of research in molecular and structural biology giving rise to "The New Biology" of genomics, proteomics, bioinformatics, systems biology. Research universities have larger budgets than colleges to support libraries addressing these new endeavors. Four-year liberal arts colleges often serve as academic incubators for incoming cohorts of students into Masters and Doctoral programs at larger universities and must adequately prepare these undergraduates. This presentation provides insights for college librarians to access the new generation of genomic databases, describes development of essential monograph and journal particularly among the life, physical, and computational sciences. collections, addresses reference services and librarian expertise in these subjects, and describes roles college librarians can play in innovative librarian-faculty collaborations. The later aspect of this presentation will outline various strategies for library and librarian outreach to college faculties and students, particularly among the life, physical, and computational sciences.

Slide 3

Digging Deeper into “The New Biology”

Slide 4

Chemistry + Biology = The “New Biology”

Slide 5

It Starts with DNA — The Molecule of Life

Slide 6

“Friedrich Miesclher: The Man Who Discovered DNA”

by George Wolf in Chemical Heritage 21(2):10-11,37-41, 2003

1869

Nuclein

leukocyte nuclei from (pus)

Looking for chemical composition of tissues

High phosphate

Sperm of Salmo salar

Almost entirely nuclein

A Brief History — Friedrich Mieschler

Slide 7

Albrecht Kossel 1910 Medicine

  • Physiological chemist

  • Studied proteins and nucleins

  • Discovered a protein-like composition of nucleins

  • Also a non-protein component: nucleic acids

    • Adenine

    • Cytosine

    • Guanine

    • Thymine

    • Uracil

  • 1st Nobel Prize (nucleic acids)

Slide 8

James Watson & Francis Crick 1962

  • Erwin Chargaff

    • Equal number of A—T bases

    • Equal number of C—G bases

  • Linus Pauling

    • Helical shape of protein

    • Hydrogen bond

  • X-Ray crystallography

    • Franklin’s Photo 51

  • Form of A, C, G, T bases

  • Avery, MacLeod, & McCarty

    • DNA linked to heredity

  • Nobel with Maurice Wilkins

Slide 9

Evolution of the “New Biology”

Biology & Life Sciences Chemistry

Biochemistry & Medicine Medicinal/Pharmacy

GeneticsCombinatorial Chemistry

Cell Biology & Physiology Instrumentation

Molecular & Structural Biology/Genetics

Engineering

Genomics, Pharmacogenomics, Toxicogenomics, etc.Biotechnology Laboratory Automation

Informational Molecular Biology, Chemical Biology, Robitics

Computational Biology, Systems Biology

Mathematics & StatisticsComputer Science

Hardware Configuration

Software Development

Programming

BioinformaticsInformation Science

Applications

Simulations and Modeling

Visualization

Uses: Education, Business & Management, Policies & Regulations, R&D Data Archives

Slide 10

Growth of Information: Nucleic AcidsChemical Abstracts, 1907-2005

Slide 11

Growth of Genomic Data & Access NCBI

Slide 12

Human Genome Project

Slide 13

Managing the Data & Informationwww.ncbi.nlm.nih.gov

  • National Center for Biotechnology Information (NCBI)

    • Established in 1988

    • public databases,

    • conducts research in computational biology

    • develops software tools for analyzing genome data

    • disseminates biomedical information

Slide 14

NCBI at a (VERY QUICK) Glance

1 gcgggcgggc gggcaggagg ccgggaggag ggaggcggcg gcggcggcgg cggcggcggc

61 gagagcccag agccagagcc cggccggggc cgagcggagc gcggcggcgg cggcggcggc

121 ggcggctggg ccgggagagg ctggcgcgcc gggcggctcc gcgaatcctc cggcatccgc

181 cccggcgggc cgcccccgcc cgcggcagcc ccccgagcag tggcccggca tcggcgcctt

241 cccggcgggc aagagtgagc catggagcta cgtgtgggga acaagtaccg cctgggacgg

301 aagatcggga gcgggtcctt cggagatatc tacctgggtg ccaacatcgc ctctggtgag

361 gaagtcgcca tcaagctgga gtgtgtgaag acaaagcacc cccagctgca catcgagagc

421 aagttctaca agatgatgca gggtggcgtg gggatcccgt ccatcaagtg gtgcggagct

481 gagggcgact acaacgtgat ggtcatggag ctgctggggc ctagcctcga ggacctgttc

541 aacttctgtt cccgcaaatt cagcctcaag acggtgctgc tcttggccga ccagatgatc

601 agccgcatcg agtatatcca ctccaagaac ttcatccacc gggacgtcaa gcccgacaac

661 ttcctcatgg ggctggggaa gaagggcaac ctggtctaca tcatcgactt cggcctggcc

721 aagaagtacc gggacgcccg cacccaccag cacattccct accgggaaaa caagaacctg

781 accggcacgg cccgctacgc ttccatcaac acgcacctgg gcattgagca aagccgtcga

841 gatgacctgg agagcctggg ctacgtgctc atgtacttca acctgggctc cctgccctgg

901 caggggctca aagcagccac caagcgccag aagtatgaac ggatcagcga gaagaagatg

Slide 15

Challenge #1 Collections — Books, Popular

Slide 16

Well Known Book Series

Slide 18

Books — Reference You Can Afford?Or Can’t Afford To Be Without?

Slide 19

Journals — Making the Right Calls

Slide 20

Science Education Journals

Slide 21

Bibliometrics — Data from SciFinder Scholar

  • Chemical Abstracts Citations

    • Genome/ics 237,067

    • Bioinformatics 21,646

    • Proteome/ics 20,806

    • Total 399,181

    • Journals are the PacMan!!

      • They are important!

Slide 22

English Articles Published 2002-2007

  • Nucleic Acids Research 1,251

  • Bioinformatics 1,022

  • Proc. Nat. Acad. Sci. 910

  • BMC Bioinformatics 800

  • J. Virology 727

  • J. Proteomics Research 682

  • Genome Research 660

  • J. Biological Chemistry 580

  • J. Bacteriology 530

  • BMC Genomics 508

  • 48,230 articles published

  • 2,800+ journals

Slide 23

Database Inventory—University at Buffalo

Slide 24

Bibliographic Databases — Final Four

Slide 25

SciFinder Scholar — It’s Not Just Chemistry

Slide 26

Databases on a Tighter Budget

  • Bachleor’s Program

    • 1-5 seats

      • $15,550-$22,550

    • 3 schools sharing 2 users

      • $7,030/school

    • 6 schools sharing 3 users

      • $4,440/school

    • Universal—Pooled Schools

      • $2,990/school

  • Master’s Program

    • 1-5 seats

      • $23,325-$56,625

    • 2 schools sharing 2 users

      • $15,825/school

    • 3 schools sharing 2 users

      • $10,550/school

    • Universal—Pooled Schools

      • $6,995/school

  • Do Libraries have to assume costs of this?

    • Consider Department Buy-ins

      • Chemistry

      • Biology

      • Biochemistry

      • Nursing

      • Environmental Science

Slide 27

Non-Scientific Alternatives

  • Academic Search Premier

Slide 28

Challenge #2 Reference ServicesLibrarian Web Compilations

Slide 29

FREE Reference Resources

BioPharmaceutical Glossaries

Cambridge Health Institute

  • Molecular Biology Desk Reference

    • National Institutes of Health

WWW Virtual Library: Biotechnology

WWW Virtual Library: Genetics

Slide 30

Staying Current

  • The Scientist

    • www.the-scientist.com/

  • Chemical & Engineering News

    • pubs.acs.org/cen/index.html

  • Science

    • www.sciencemag.org/content/vol291/issue5507/ index.shtml

  • About.Biotech

    • biotech.about.com/

  • Nature

    • www.nature.com/genomics/

  • Bio-IT World

    • www.bio-itworld.com/index.html

  • Nucleic Acid Research

    • 1st January issue—Database Reviews

      (became “Database Issue” 2004)

      • Reviews and updates of database developments

      • 40-50 articles per issue (1996 to present)

    • 1st July issue—Web/Internet Reviews (became “Web Servers Issue” 2004)

      • Reviews Web servers and services

      • 40-50 articles per issue (2003 to present)

        nar.oupjournals.org/contents-by-date.0.shtml

Slide 31

Staying Current

  • About Biotech

    • biotech.about.com/

  • Bio-IT World

    • www.bio-itworld.com/index.html

  • Chemical & Engineering News

    • pubs.acs.org/cen/index.html

  • Nature

    • www.nature.com/genomics/

  • Science

    • www.sciencemag.org/content/vol291/issue5507/ index.shtml

  • The Scientist

    • www.the-scientist.com/

Slide 32

Challenge #2 Librarian Training

Slide 33

NCBI Science Primer—Basics of Biology

Slide 34

Molecular biology basics

Overview of flagship databases

nucleotide sequences

protein sequences

three-dimensional structures

complete genomes and maps

20 hours CEU from MLA

5/30-6/1 at MIT, Cambridge, MA

11/7-9 at NCBI/NIH, Bethesda, MD

NCBI: 3-day Workshop for Librarians

Slide 35

NCBI: 5-day Advanced NAWBIS Training

  • Bioinformatics support personnel

    • Subject Specialist Librarians

    • Bioinformatics educators & trainers

  • Prerequisites

    • Knowledge of molecular biology or genetics

    • basic experience with NCBI resources such as Entrez, BLAST, Cn3D, and Map Viewer

  • 8/6-10 at NCBI/NIH, Bethesda, MD

Slide 36

HGP Education Resources

Slide 37

Challenge #3 Librarian-Faculty Collaboration

  • Resource Awareness and Data Retrieval

    • direct users to the appropriate resource(s) for their needs

      • Current awareness and communication

    • promote awareness of molecular biology resources

      • Librarian instruction with faculty co-teaching

    • assist with the use of text-term search systems such as Entrez and LocusLink

      • Librarian instruction with faculty co-teaching

    • direct users to NCBI site map and other database/software directories for additional resources

      • Reference & Referral

Slide 38

Integrate information literacy skills into classroom instruction

Foster critical thinking skills

Team teaching

Literature → data searching skills

Librarian/Faculty Collaborations

Slide 39

With Increased Proficiencies You Can:

  • Assist users (students) with BLAST sequence similarity searches:

    • enter query sequence in FASTA format

    • select appropriate BLAST program (blast, blastp, blastx, etc.)

    • explain the basic features of the BLAST output

    • direct them to appropriate BLAST help documents and tutorials for additional information

  • purchase and maintain subscriptions/license agreements for commercial sequence databases and software packages

  • arrange for courses to be taught by representatives of the companies, or teach courses yourself

  • provide ongoing user support for the commercial packages

  • Slide 40

    Library-hosted NCBI Workshops for Faculty

    Slide 41

    Readings on Outreach from NCBIwww.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/OutreachCommunication/outreachreferences.html

    • Geer R, Rein DC. FOCUS ISSUE INTRODUCTION: Building the role of medical libraries in bioinformaticsJ Med Libr Assoc. 2006 July; 94(3): 284–285. [Full text from PubMed Central]Introduces multiple papers by NAWBIS instructors and participants from the July 2006 issue, 94(3) of the Journal of the Medical Library Association available full text in PubMed Central

    • Tennant MR. Bioinformatics Librarian: Meeting the information needs of genetics and bioinformatics researchers.Ref Serv Rev. 2005;33(1):12-19.

    • MacMullen WJ, Vaughan KTL, Moore ME. Planning Bioinformatics Education and Information Services in an Academic Health Sciences Library. College & Research Libraries. 2004 Jul;65(4):320-33.

    • Helms AJ, Bradford KD, Warren NJ, Schwartz DG. Bioinformatics opportunities for health sciences librarians and information professionals.J Med Libr Assoc. 2004 Oct;92(4):489-93. [Full text from PubMed Central]

    • Lyon J, Giuse NB, Williams A, Koonce T, Walden R. A model for training the new bioinformationist.J Med Libr Assoc. 2004 Apr;92(2):188-95. [Full text from PubMed Central]

    • Wheeler D, Rapp B. User Services: Helping You Find Your Way.NCBI Handbook. Available online: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.ch23

    • Lyon J. Beyond the Literature: Bioinformatics Training for Medical Librarians.Med Ref Serv Q. 2003 Spring;22(1):67-74. [PubMed Abstract]

    • Alpi K. Bioinformatics Training by Librarians and for Librarians: Developing the Skills Needed to Support Molecular Biology and Clinical Genetics Information Instruction.Issues in Science & Technology Librarianship. Spring 2003, 37. [Full text online].

    • Tennant MR, Miyamoto MM. The role of the medical library in undergraduate education: a case study in genetics.J Med Libr Assoc. 2002;19(2):181-93. [Full text from PubMed Central]

    • Delwiche FA. Introduction to resources in molecular genetics. Med Ref Serv Q. 2001 Summer;20(2):33-50. [PubMed Abstract]

    • Alpi KM, Hendler GY, Ohles J. Making Sense of Molecular Medicine: New York Librarians' Involvement with Bioinformatics. NAHSL/NY-NJ Annual Meeting, 2001 October 15 [Poster available online]

    • Yarfitz S, Ketchell DS. A library-based bioinformatics services program.Bull Med Libr Assoc 2000 Jan; 88(1): 36-48. [Full text from PubMed Central]

    Slide 42

    Bioinformatics Degree Programs U.S.ils.unc.edu/informatics_programs/doc/Bioinformatics_2006.html

    Slide 43

    Molecular Biology SIG MLA

    • Home Page: medicine.wustl.edu/~molbio/

    • Current SIG Convener:Susan KendallMichigan State University LibrariesEast Lansing, MIskendall@mail.lib.msu.edu

    • SIG Member List (Directory)

    • Listserv:   molbio@molbiosig.mlanet.org(instructions for subscribing and unsubscribing to the list are given on the SIG listserv web page)

    Slide 44

    Websites in Presentation

    • Human Genome Project

    • http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

    • National Center for Biotechnology Information (NCBI)

    • www.ncbi.nlm.nih.gov

    • Pharmaceutical Glossaries (Cambridge Health Institute)

    • http://www.genomicglossaries.com/

    • Genetics Home Reference

    • http://ghr.nlm.nih.gov/

    • Molecular Biology Desk Reference

    • http://molbio.info.nih.gov/molbio/desk.html

    • WWW Virtual Library for Biotechnology

    • http://www.cato.com/biotech/

    • WWW Virtual Library for Genetics

    • http://www.ornl.gov/sci/techresources/Human_Genome/genetics.shtml

    • Bioinformatics & Genomics (Database Inventory for the University at Buffalo)

    • http://libweb1.lib.buffalo.edu/infotree/resourcesbysubject.asp?subject=Bioinformatics+%26+Genomics

    • Genomics Research (Web Guide for the University at Buffalo)

    • http://ublib.buffalo.edu/libraries/asl/guides/bio/genome/human_genome.html

    • Proteomics (Web Guide for the University at Buffalo)

    • http://ublib.buffalo.edu/libraries/asl/guides/proteomics.html

    • NCBI Education

    • http://www.ncbi.nlm.nih.gov/Education/

    • NCBI Science Primer

    • http://www.ncbi.nlm.nih.gov/About/primer/

    • Human Genome Project Education Page

    • http://www.ornl.gov/sci/techresources/Human_Genome/education/education.shtml

    • NCBI Workshops & Tutorials: Mini-Courses

    • http://www.ncbi.nlm.nih.gov/Class/minicourses/

    • NCBI Workshops & Tutorials: Field Guide to NCBI Resources

    • http://www.ncbi.nlm.nih.gov/Class/FieldGuide/

    • Bioinformatics Degree-granting Programs in the U.S., 2006 (UNC)

    • http://ils.unc.edu/informatics_programs/doc/Bioinformatics_2006.html

    Slide 45

    Future: Your Challenge!

    • The words of Winston Churchill, spoken in 1942 after 3 years of war, capture well the HGP era:

      "Now this is not the end. It is not even the beginning of the end. But it is, perhaps, the end of the beginning."


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