Bridging chemistry islands to the web data silo

1. Bridging chemistry islands to
the web data silo
Mining Drug Space
http://miningdrugs.blogspot.com
Jörg Kurt Wegner, PhD
2009-03-22
(c) 2009, JKW, miningdrugs.blogspot.com

2. One upon a time there was a lonely
compound on a data island ...
(c) 2009, JKW, miningdrugs.blogspot.com

3. ... with an identity crisis...
The compound felt lonely, isolated, and unimportant
nobody had given it a name.
nobody had builded a bridge to it.
nobody had showed it the world outside.
The compound named itself
O=C(NCC3OC(=O)N(c2ccc(N1C(=O)COCC1)cc2)C3)c4sc(Cl)cc4
an old traditional name taken
from his SMILES tribe
(c) 2009, JKW, miningdrugs.blogspot.com

4. ... underappreciated by a lost
expedition ...
An ancient explorer
found the compound and told the king on the
CAS continent about the island, the tribe, and the
compound. The king was too important to listen.
Since the compound had a complicated name
the explorer called it just CAS x666, locked the
knowledge up*, and Innova7ion, a small
emerging tribe, never heard about it.
*Beside, the compound was still unhappy, and hoping for
being able to find friends and a purpose in the world.
(c) 2009, JKW, miningdrugs.blogspot.com

5. ... and the evolution was going on
ignoring the compound ...
Many other continents and islands
evolved and were growing, but inbreeding made
their compounds weak.
Only the Innova7ion tribe
was using boats to visit other closeby islands and
sometimes evolution created completely new
chemical entities. Some, which shared even
similar interests to
O=C(NCC3OC(=O)N(c2ccc(N1C(=O)COCC1)cc2)C3)c4sc(Cl)cc4, but
nobody told any of both sides, they did not know.
(c) 2009, JKW, miningdrugs.blogspot.com

6. ... then more bridges were created ...
The Innova7ion tribe
lost much of their folk, because their boats were
not safe. Compound sharing was risky and
dangerous at that time, still they kept doing it.
Still, they believed in making the world better,
they started building bridges, a safer and more
efficient way to communicate to islands. Since
many islands used many different compound
names, the IUPAC decided to help in providing a
publicly accepted naming to every compound.
(c) 2009, JKW, miningdrugs.blogspot.com

7. ... and through bridges the compound
KGFYHTZWPPHNLQ found its purpose ...
(c) 2009, JKW, miningdrugs.blogspot.com

8. ... now the compound is happy, it is
helping people and having friends ...
(c) 2009, JKW, miningdrugs.blogspot.com

9. ... hoping to see the in the future the
whole planet and even universe ...
... for helping even more people.
(c) 2009, JKW, miningdrugs.blogspot.com

10. References
http://miningdrugs.blogspot.com/2006/10/bounded-rational-drug-design.html
http://depth-first.com/articles/2007/02/19/google-for-molecules-with-inchimatic
http://depth-first.com/articles/2007/03/05/why-the-web-isnt-ready-for-chemistry
http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
http://en.wikipedia.org/wiki/International_Chemical_Identifier
http://www.chemspider.com/blog/the-inchi-resolver-goes-live-in-time-for-the-acs-meeting.html
http://inchis.chemspider.com
http://www.nature.com/press_releases/nchem.html
http://miningdrugs.blogspot.com/2009/03/reflect-annotate-protein-and-small.html
http://www.chemmantis.com/
http://blogs.nature.com/thescepticalchymist/2008/05/jj_day_98_service_with_a_simpl.html
http://chem-bla-ics.blogspot.com/2009/03/nature-chemistry-improves-publishing.html
http://chem-bla-ics.blogspot.com/2008/05/re-what-should-nature-chemistry-paper.html
http://www.elseviergrandchallenge.com
http://miningdrugs.blogspot.com/2009/03/drug-design-paradigms-get-involved-in.html
http://en.wikipedia.org/wiki/File:Terrestrial_planet_size_comparisons.jpg
(c) 2009, JKW, miningdrugs.blogspot.com