1. John MacMullen SILS Bioinformatics Journal Club Fall 2002
Swanson & Smalheiser’s Arrowsmith and the Fragmentation of Biomedical Knowledge
John MacMullen
SILS Bioinformatics Journal Club
Fall 2002

2. How do literatures become fragmented?
By discipline… Advances in Biophysics; Astrophysics; Journal of Mathematical Physics
By sub-discipline… Aquatic Toxicology; Proteomics; Molecular Immunology
By professional specialty… Annals of Oncology; Biological Research for Nursing
By theory / practice… Experimental Gerontology; Veterinary Dermatology
By language… Zeitschrift für Pflanzenernährung und Bodenkunde
By topic (e.g., disease)… Cancer; Molecular Carcinogenesis; Multiple Sclerosis; Pain
By physical subject… Journal of Fish Diseases; Yeast
By structure… Blood; Cell; Lipids; Nucleic Acids Research
By function… Apoptosis; Journal of Molecular Catalysis; Traffic - The International Journal of Intracellular Transport
By technique… Electrophoresis; International Journal of Mass Spectrometry; Ultramicroscopy
German title is “Journal of Plant Nutrition and Soil Science“
Other reasons literatures become fragmented include:
The sheer number of journals
The high cost of journals
non-trivial access / searching / synthesis methods
SILS Bioinformatics Journal Club

3. How do literatures become integrated?
By reviews… Annual Review of Genomics and Human Genetics
By special issues… Nucleic Acids Research annual database issue; JASIS&T bioinformatics issue
By sub-discipline… Bioinformatics; Computers & Chemistry
By citations… …within and across domains
By search tools… Indexes, databases, search engines, etc.
By discovery support systems…?
SILS Bioinformatics Journal Club

4. SILS Bioinformatics Journal Club
Integration Timeline
H.G. Wells recognizes significance of fragmentation of knowledge across disciplines; conceives “World Encyclopedia”
mid-1960s Herbert Bohnert & Manfred Kochen explore “World Encyclopedia” concept in light of growth of computers; Eugene Garfield develops Science Citation Index and ISI to enable “information discovery & information recovery”
mid-1970s Manfred Kochen revisits “World Encyclopedia” concept in book Integrative Mechanisms in Literature Growth
1980s – 1990s Don Swanson & Neil Smalheiser explore “complementary but mutually disjoint, non- interactive literatures” and find “undiscovered public knowledge” via Arrowsmith
1990s – present Claire Beghtol, Roy Davies, Susan Dumais, Sherilynn Fuller et al, Michael Gordon, Mark Spasser, Marc Weeber, et al. pursue Swanson’s ideas
SILS Bioinformatics Journal Club

5. SILS Bioinformatics Journal Club
Swanson’s premises
Specialization causes knowledge to be fragmented into non-interactive (mutually disjoint) literatures
Some non-interactive literatures are complementary
Two non-relevant things may become relevant when joined
Implicit vs explicit linkages
Undiscovered public knowledge
Toward ‘hypothesis-generation-’ / ‘discovery support systems’
These ideas had a profound effect on Swanson’s research.
In his speech when he received the ASIS award of merit, Swanson said of the Renaud’s / fish oil experience, “in 1985 I was struck by lightning and have never recovered”.
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6. SILS Bioinformatics Journal Club
Arrowsmith
Multi-step, multi-tool process
Procedure 1: Citation acquisition
Search MEDLINE for topical cites (‘C’ list)
Apply stopword list and extract unique terms (‘B’ list)
Search MEDLINE for ‘B’ term cites; prune list
Perform MEDLINE searches for each ‘B’ term
Classify results into likely categories
Derive the intersection of each ‘B’ set with the restriction set, and the union of intersection sets (‘U’)
Search the resulting terms of ‘U’ set in MEDLINE
‘U’ list becomes potential ‘A’ terms, with each ‘A’ term attached to the ‘B’ term that generated it
Rank ‘A’ term results against ‘B’ co-occurence
Procedure 2: Relationship Mining
Search for pre-existing A→C &/or A→B→C relationships
Search for novel A→C relationships
Output: Display of ‘A’ & ‘C’ cites by their common ‘B’ terms
Goal: a plausible testable hypothesis
Human relevance judgments in each step influence future steps
SILS Bioinformatics Journal Club