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Biopharmaceutical Taxonomy bibliography

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Mary Chitty mchitty@healthtech.com
Last revised June 9, 2002

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*particularly recommended

Cautious optimism
"The Pharmaceutical Industry and the Revolution in Molecular Biology: Exploring the Interactions between Scientific, Institutional and Organizational Change, Iain M. Cockburn, Rebecca Henderson, Scott Stern, 1999. Available as a PDF at  http://www.cid.harvard.edu/cidbiotech/events/henderson.htm

* "The Diffusion of Science Driven Drug Discovery: Organizational Change in Pharmaceutical Research" by Rebecca Henderson, MIT Sloan School of Management and NBER; Luigi Orsenigo, Universita' Commerciale Luigi Bocconi; Gary P. Pisano, Harvard Business School, 1999. Available as a PDF at http://www.cid.harvard.edu/cidbiotech/events/henderson.htm

What is really going on here? http://www.genomicglossaries.com/presentation/SLAwhatisgoingonhere.asp

 

What are taxonomies?
Liz Edols, Taxonomies: beyond thesauri and classification, Online Currents, No. 97, Sept. 2001. http://www.freepint.com/issues/041001.htm?FreePint_Session=c3e1f1a5e8aa3a961de4ebce19395ba5

Deborah L. McGuinness, "Ontologies Come of Age". To appear in Dieter Fensel, Jim Hendler, Henry Lieberman, Wolfgang Wahlster, eds. The Semantic Web: Why, What, and How, MIT Press, 2001. http://www.ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-mit-press-(with-citation).htm

Christina Wodtke, Unraveling the mysteries of metadata and taxonomies, April 9, 2002. http://www.boxesandarrows.com/archives/002570.php

 

How taxonomies can help
* Katharine C. Adams, How Taxonomies Ease Knowledge Retrieval and Facilitate Associative Learning, Mohomine, April 2001 http://www-3.ibm.com/ibm/easy/eou_ext.nsf/EasyPrint/1817

How taxonomies became chic and why it matters, Factiva, 2001  http://www.factiva.com/infopro/newsletters/vol22001art2.asp?node=news-letter_link14

Taxonomies role in content management, Thomas Pack, EContent, Mar. 2002  http://www.econtentmag.com/r5/2002/r5pack3_02.html

 

How to get started with taxonomies
About Thesauri, Jessica Milstead, 2000  http://www.bayside-indexing.com/Milstead/about.htm 

How do you build a thesaurus? Peter Morville, Web Review, Oct. 30, 1998 http://www.ddj.com/184412945  

Thesaurus construction, Tim Craven, Univ. of Western Ontario, Canada, 1997- 2002.  http://instruct.uwo.ca/gplis/677/thesaur/main01.htm

* Building Taxonomies, Susan Conway and Char Sligar, Unlocking Knowledge Assets, Chapter 6, Microsoft Press, 2002. http://www.microsoft.com/mspress/books/sampchap/5516.asp#SampleChapter

Practical Taxonomies: Hard-won wisdom for creating a workable knowledge classification system, Sarah L. Roberts-Witt, 1999. http://www.phys.uni.torun.pl/~duch/ref/s-search/taxonomy/featureb1.htm

* Ontology 101: A guide to creating your first ontology, Natalye Fridman Noy and Deborah McGuinness, Knowledge Systems Laboratory, Stanford University, Mar. 2001.  http://ksl.stanford.edu/people/dlm/papers/ontology-tutorial-noy...l

Advanced taxonomists only! Robert Stevens' slides, Univ. of Manchester, UK at Synopsis of the Bio- Ontologies Workshop at the EBI for MGED, Dec. 5, 2001] http://www.cbil.upenn.edu/Ontology/EBI_Bioontologies_Workshop.html Ontology life cycle, provisional methodology for building. No standard yet. 

Don't reinvent the wheel: Look here first
Life sciences
 Josef Ingenerf, Medical Terminology Medizinische Universität zu Lübeck, 2001 http://www.medinf.mu-luebeck.de/~ingenerf/terminology/Index.html

Michael Krauthammer, Brief review of clinical vocabularies, MGED Microarray Gene Expression Data Society, Ontology Working Group, 2002 http://www.cbil.upenn.edu/Ontology/MKreview.html

Dennis Wollersheim, Implementation of dynamic taxonomies for clinical guidelines retrieval, La Trobe Univ., Australia, c. 2001 http://homepage.cs.latrobe.edu.au/lewisba/SPIRT/dw2001c.pdf.

More general 
XML Cover Pages: Resource Description and Classification, Robin Cover, 2002. http://www.oasis-open.org/cover/classification.html Covers standard industry taxonomies and ontologies, library cataloging, news industry and metadata initiatives

Thesauri and controlled vocabularies, National Library of Canada, 2002 http://www.nlc-bnc.ca/8/4/r4-280-e.html

Carol Ellerbeck, Business Information Taxonomist, Baker Library, Harvard Business School, Recommendations from her Jan. 22, 2002 email on the xml-dev listserv, Active State Programmer Network  http://lists.xml.org/archives/xml-dev/200201/msg01530.html  

Controlled vocabularies, Queensland Univ. of Technology, Australia, 2002 http://sky.fit.qut.edu.au/~middletm//cont_voc.html 

Controlled vocabularies, thesauri and classification systems available in the WWW. DC Subject, Traugott Koch, Lunds Universitets Bibliotek, Sweden, 2001. http://www.lub.lu.se/metadata/subject-help.html

 

 Dynamic taxonomies for faster drug discovery & development?

Alfred R. Steinhardt, F. Hoffmann-LaRoche, Ltd. "New Information Management Technologies to improve the drug development process, 2001. http://www.infonortics.com/chemical/ch01/presentations-01/steinhardt.pdf

* Knowledge Management Dos and Don'ts, Charlie Matthews, VisualInterConnections, 2002]  http://www.visualinterconnections.com/CEM/dos.htm

Nicola Guarino "Formal Ontology and Information Systems, 1998 http://www.ladseb.pd.cnr.it/infor/Ontology/Papers/FOIS98.pdf.

Jeff Heflin, James Hendler "Dynamic Ontologies on the Web" American Association for Artificial Intelligence, 2000 http://www.cs.umd.edu/projects/plus/SHOE/pubs/aaai2000.pdf

Jim Hendler "Introduction to ontologies on the semantic web", 2001 http://www.cs.umd.edu/users/hendler/ontologies.html

Gio Wiederhold and Jan Jannink "Composing Diverse Ontologies:, 1999  http://www-db.stanford.edu/SKC/publications/ifip99.html

Maged N. Kamel Boulos, Towards a Semantic Medical Web: HealthCyberMap’s Dublin Core Ontology in Protégé 2000  http://protege.stanford.edu/ontologies/dublincore/hcm_dc_in_protege_newcastle.pdf

Gene Ontology TM consortium http://www.geneontology.org/ The goal of the Gene OntologyTM Consortium is to produce a dynamic controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing.

 

Humans vs. computers - classification
Jean Graef, "Managing taxonomies strategically" Montague Institute, 2001 http://www.montague.com/review/taxonomy3.html

Taxonomies put content in context, Russell Letson, Transform Magazine, Dec. 2001 http://www.transformmag.com/db_area/archs/2001/12/tfm0112f1.shtml?enterprisesolutions

Peter Morville "Little Blue Folders", Argus Center, 2000
http://argus-acia.com/strange_connections/strange003.html

Lynda Moulton, LWM Technologies Readings of interest in 2001 http://www.lwmtechnology.com/publish/bib_2001.htm

" William Woods, Sun Microsystems
Conceptual indexing/Retrieval technology, Sun Labs http://research.sun.com/knowledge/technology.html
Finding information on the web: A knowledge representation approach http://www.ai.mit.edu/projects/iiip/conferences/www95/woods.html

 

Community building
Amy Jo Kim, Community Building on the Web: Secret Strategies for Successful Online Communities, 2000

Etienne Wenger et. al. Communities of practice http://www.ewenger.com/tech/index.htm

Gladwell, Malcolm, The Tipping Point: How little things can make a big difference, 2000, links to Amazon reviews.  Read about "connectors" and mavens

Lincoln Stein "Creating a bioinformatics nation" Nature 417:119- 120, 9 May 2002

 

 

Change Bibliography 
Dubinskas, Frank. "Janus Organizations: Scientists and Managers in Genetic Engineering Firms" Pages170-232 in Frank Dubinskas (ed.), Making Time Ethnographies of High Technology Organizations, Philadelphia: Temple University Press, 1988 Also in Technology Review. http://www.techreview.com/ May/ June 1985: 24-30, 74 Why scientists and managers have trouble getting along. Any good updates?

 

Acknowledgements

Cambridge Healthtech Institute
Mary Addonizio                           Liz Doubleday
Malorye Branca                           Peet Glowacki
Debbie Brooks                             Shauna Kelly
Beth Castrodale                           Phillips Kuhl
Phil Conti                                     Edel O'Regan
Mike Croft                                     Angie Parsons
David Cunningham                       Andrea Surov
                                                     Chris White

GlaxoSmithKline                     Warren Casey

LWM Technology                    Lynda Moulton
Services

Library & Information            Rosanne Labree
Services

New England Storytelling     Marjorie Turner
                                              Dr. Florence Ames

Oklahoma University                 Ricardo Saban
Health Sciences Center

Treadwell Library                      Julie Whelan
Massachusetts General Hospital

Tufts Center for the                  Peg Hewitt
Study of Drug Development

VisualInterconnections           Charlie Matthews

Where's my stuff: change, opportunities & threats, best practices, lessons learned, ongoing challenges, integrating, remember
Genomics I metaphors
Genomics II post-genomic
What is really going on?  change, disruptive technologies, best practices, lessons learned, ongoing challenges, lead users,  really want reinventing, reinventing ,  technology strategy

 

 

mchitty@healthtech.com  http://www.genomicglossaries.com  Cambridge Healthtech Institute http://www.healthtech.com

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