Transcript Biological Information for Chemists, Pt. 2

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
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.
Digging Deeper into “The New
Biology”
Chemistry + Biology = The “New Biology”
It Starts with DNA — The Molecule of Life
A Brief History — Friedrich Mieschler
• “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
Albrecht Kossel
• Physiological chemist
• Studied proteins and nucleins
• Discovered a protein-like
composition of nucleins
• Also a non-protein
component: nucleic acids
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Adenine
Cytosine
Guanine
Thymine
Uracil
• 1st Nobel Prize (nucleic acids)
1910 Medicine
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
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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
Evolution of the “New Biology”
Biology & Life Sciences
Biochemistry & Medicine
Genetics
Cell Biology & Physiology
Chemistry
Medicinal/Pharmacy
Combinatorial Chemistry
Instrumentation
Molecular & Structural Biology/Genetics
Engineering
Genomics, Pharmacogenomics, Toxicogenomics, etc.
Informational Molecular Biology, Chemical Biology,
Computational Biology, Systems Biology
Bioinformatics
Uses: Education, Business & Management, Policies & Regulations, R&D
Biotechnology
Laboratory Automation
Robitics
Mathematics & Statistics
Computer Science
Hardware Configuration
Software Development
Programming
Information Science
Applications
Simulations and Modeling
Visualization
Data Archives
Growth of Information: Nucleic Acids
Chemical Abstracts, 1907-2005
Molecular/Structural Biology/Genetics,
Chemical Abstracts 1907-2005
Citations/yr
20000
15000
10000
5000
0
1
10
19
28 37
46
55
years
64 73
82
91 100
Growth of Genomic Data & Access
NCBI
Human Genome Project
Managing the Data & Information
www.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
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
Challenge #1 Collections — Books, Popular
Well Known Book Series
Books — Reference You Can Afford?
Or Can’t Afford To Be Without?
Journals — Making the Right Calls
Science Education Journals
Bibliometrics — Data from SciFinder Scholar
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Chemical Abstracts Citations
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Genome/ics
237,067
Bioinformatics
21,646
Proteome/ics
20,806
Total
399,181
Journals are the PacMan!!
• They are important!
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English Articles Published 2002-2007
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Nucleic Acids Research
Bioinformatics
Proc. Nat. Acad. Sci.
BMC Bioinformatics
J. Virology
J. Proteomics Research
Genome Research
J. Biological Chemistry
J. Bacteriology
BMC Genomics
• 48,230 articles published
• 2,800+ journals
1,251
1,022
910
800
727
682
660
580
530
508
Database Inventory—University at Buffalo
Bibliographic Databases — Final Four
SciFinder Scholar — It’s Not Just
Chemistry
Databases on a Tighter Budget
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Bachleor’s Program
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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
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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
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Do Libraries have to assume
costs of this?
• Consider Department Buy-ins
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Chemistry
Biology
Biochemistry
Nursing
Environmental Science
Non-Scientific Alternatives
• Academic Search Premier
Challenge #2 Reference Services
Librarian Web Compilations
FREE Reference Resources
BioPharmaceutical Glossaries
Cambridge Health Institute
WWW Virtual Library: Biotechnology
WWW Virtual Library: Genetics
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Molecular Biology Desk
Reference
• National Institutes of Health
Staying Current
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The Scientist
• www.the-scientist.com/
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Chemical & Engineering News
• pubs.acs.org/cen/index.html
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Science
• www.sciencemag.org/content/
vol291/issue5507/ index.shtml
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About.Biotech
• biotech.about.com/
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Nature
• www.nature.com/genomics/
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Bio-IT World
• www.bioitworld.com/index.html
• Nucleic Acid Research
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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
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/
Challenge #2 Librarian Training
NCBI Science Primer—Basics of Biology
NCBI: 3-day Workshop for Librarians
• Molecular biology basics
• Overview of flagship
databases
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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: 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
HGP Education Resources
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
Librarian/Faculty Collaborations
Integrate information literacy
skills into classroom
instruction
Foster critical thinking skills
Team teaching
Literature → data searching
skills
With Increased Proficiencies You Can:
• Assist users (students) with BLAST sequence similarity searches:
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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
Library-hosted NCBI Workshops for
Faculty
Readings on Outreach from NCBI
www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/OutreachCommunication/outreachreferences.html
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Geer R, Rein DC. FOCUS ISSUE INTRODUCTION: Building the role of medical libraries in bioinformatics J
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): 3648. [Full text from PubMed Central]
Bioinformatics Degree Programs U.S.
ils.unc.edu/informatics_programs/doc/Bioinformatics_2006.html
Molecular Biology SIG MLA
• Home Page: medicine.wustl.edu/~molbio/
• Current SIG Convener:
Susan Kendall
Michigan State University Libraries
East Lansing, MI
[email protected]
• SIG Member List (Directory)
• Listserv: [email protected]
(instructions for subscribing and unsubscribing to the
list are given on the SIG listserv web page)
Websites in Presentation
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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
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."