Biology Reference
In-Depth Information
10. I use the past tense here because, although cgi.pm was the standard for
a long time, it has now been largely eclipsed by other methods, including those
using JSP (Java Server Pages) and PHP (PHP Hypertext Processor).
11. Stewart, “An Interview with Lincoln Stein.”
12. Quoted in O'Reilly et al., “The Importance of Perl.”
13. Stein, “How Perl Saved the Human Genome Project.”
14. Berners-Lee, “The Web.”
15. Berners-Lee, “Transcript of Talk.”
16. Berners-Lee, “Digital Future.”
17. World Wide Web Consortium, “RDF Primer.”
18. World Wide Web Consortium, “OWL.”
19. Smith et al., “OWL.”
20. OWL evolved in part from a language known as DAML-OIL (DARPA
Agent Markup Language—Ontology Inference Layer) that was funded by
ARPA and managed by Bolt, Beranek, and Newman.
21. For lists of biomedical ontologies, see the website of the National Cen-
ter for Biomedical Ontology (http://www.bioontology.org/ncbo/faces/pages/
ontology_list.xhtml) and the website of the Open Biomedical Ontologies
(http://obofoundry.org/).
22. Feigenbaum et al., “The Semantic Web.”
23. Berners-Lee convinced his research group at MIT that biology, because
of the richness of its data, was the best test case for the Semantic Web. Another
example of an attempt to use Semantic Web technology for biology is the
Interoperable Informatics Infrastructure Consortium (I3C). I3C aimed to
create tools for data exchange and data management by developing common
protocols and software. One of its fi rst creations was the Life Sciences Identi-
fi er (LSID), which provided a standard way to refer to and access biological
information from many different kinds of sources on the web.
24. Neumann, “Semantic Web.”
25. Neumann, “Semantic Web.”
26. Small-world networks are those in which the average distance between
any two nodes is much less than that for a random network of the same size.
Scale-free networks are those for which the distribution of the number of edges
over vertices follows a power law. This means that the networks have hubs—
some few very important nodes to which many other nodes are connected—
but many nodes with one or very few edges.
27. Barabási, and Oltvai, “Network Biology,” 106.
28. Han et al., “Effect of Sampling.”
29. Kelleher, “Google, Sergey, and 23andMe.”
30. Goetz, “23andMe.”
31. Cisco and Intel (Dossia) also have plans to roll out medical records
systems. See Lohr, “Microsoft Rolls Out Personal Health Records.” BBN has
a Semantic Web system for health care; Accelrys offers life science-specifi c
modeling, simulation, and text mining applications.
32. For example, the collaborative fi ltering sites del.icio.us and Flickr.
33. Wells, “Web 3.0 and SEO.”
34. Zand, “Web 3.0.”
