[Orechem] FW: As Open Sources of Chemical Information Become More Common, What Role Can a Publisher Play?

Tue Jan 26 03:20:12 EST 2010

Of interest...
-jld

-----Original Message-----
From: Outsell Insights [mailto:insights at mailer.outsellinc.com] 
Sent: Tuesday, January 26, 2010 12:03 AM
To: Lee Dirks
Subject: As Open Sources of Chemical Information Become More Common, What Role Can a Publisher Play?

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Outsell Insights for   January 26, 2010
Analysis of events, data, and trends
affecting the information industry
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As Open Sources of Chemical Information Become More Common, What Role Can a
Publisher Play?

by David Bousfield, Vice President & Lead Analyst - United Kingdom

* ChEMBLdb, an open access online database of information about the
properties and activities of over half a million drugs and drug-like small
molecules and their targets, was launched by the European Bioinformatics
Institute (EBI) earlier this month. There are now dozens of
publicly-accessible databases containing chemical information, so what is
the future role of the publisher in this area?

Important Details:  Data such as these lie at the heart of translating
information from the human genome into successful new drugs in the clinic,
so it is perhaps unsurprising that there are so many different sources.  As
well as ChEBI/ChEMBL [1] (a dictionary of small chemical entities and
catalogue of  interactions between pharmacologically active molecules and
their receptors), significant players include:

* ChemIDPlus [2] (a database of over 380,000 chemicals, synonyms,
structures, regulatory list information, and links to other databases
supported by the National Library of Medicine's Specialized Information
Services);

* Drugbank [3] (a resource that combines detailed chemical, pharmacological
and pharmaceutical data with comprehensive drug target, i.e. sequence,
structure, and pathway information);

* LipidMAPs [4] (a portal for lipid biologists hosted by Nature Publishing
Group);

* PubChem [5] (NIH's database contains details of 37 million chemical
compounds, 71 million substances and bioactivity results from 1644
high-throughput screening programs);

* ZINC [6] (commercially-available compounds used by pharmabiotech
companies for virtual screening).

Implications: These database resources fall into two categories.  Those
that aim for comprehensiveness, but often at the expense of 'findability'
and data quality, and those that are designed to deliver a specific
functionality at a particular point in a given chemistry workflow. 
Publishers should look to the latter for commercial inspiration.  Here we
take a look at chemical procurement as an example.

The Royal Society of Chemistry's (RSC) ChemSpider [7] (see Insights 23 June
2009, InChI InChI Spider - Royal Society of Chemistry Acquires ChemSpider)
is being developed as a publicly accessible chemistry search engine that
aggregates and indexes as many possible open access and proprietary
chemical structures and  associated information sources into a single
searchable repository.  RSC recently announced a joint project with Symyx'
DiscoveryGate enabling customers to browse chemical structure information
on ChemSpider while simultaneously searching synthetic reactions,
bioavailability information and up-to-date compound availability
information from over 860 suppliers stored on DiscoveryGate.  RSC benefits
from custom fees and Symyx' products gain increased functionality.

EMolecule, a small company based on the West Coast has taken this
data/workflow integration one step further.  The company tried to take a
Google-like approach to open access chemistry databases in 2006 but ran
into trouble with its name - Chmoogle [8].  Realising that Amazon perhaps
represented a better role model than Google, they paired up with ChemSW
[9],  provider of chemical and biochemical inventory management systems to
create an integrated procurement solution which allows chemists to search
the eMolecules database for details of more than 5.5 million unique
commercially-available chemical structures from the most important chemical
suppliers.  Users can now perform one-stop shopping and stocking for
batches of hundreds of compounds at a time (an essential stage in the drug
discovery workflow), and because details of vendor reliability, pricing
information, product availability and shipping times are all actively
curated, purchasers can be confident that their orders will be fulfilled on
time.  SciQuest [10] and also Sigma-Aldrich [11] (with its acquisition of
ChemNavigator [12]) have taken similar approaches by combining open access
data with focused curation to provide a valuable service.

As certain types of content become commoditized, sometimes by sheer volume
alone, publishers must learn how to create products that integrate content
from many different sources and which can be curated with a specific
end-user workflow in mind.  They should also be on the lookout for
acquisition opportunities.  In 2007, Thomson Reuters bought Biomolecular
Interaction Network Database (BIND) which had been developed largely at the
expense of the Canadian taxpayer.  Late last year, Nature reported [13]
that the world's most valued plant database, the Arabidopsis Information
Resource (TAIR), faces extinction because its funding is being phased out
by the US National Science Foundation (NSF), and no alternative source is
on the horizon. The NSF suggested that TAIR develop its own self-supporting
funding model, based on user subscriptions and other sources of income. EBI
bought ChEMBLdb from its biotech developers Galapagos NV with a GBP 4.7
million Strategic Award from the Wellcome Trust.  The price reflects the
cost of assembling and maintaining a database of this size.  Without a
business model, such resources can become millstones around the neck of
government budgets in the not-too-distant future.

Links contained in this article:
[1] http://www.ebi.ac.uk/chebi/init.do
[2] http://sis.nlm.nih.gov/chemical.html
[3] http://www.drugbank.ca/
[4] http://www.lipidmaps.org/
[5] http://pubchem.ncbi.nlm.nih.gov/about.html
[6] http://zinc.docking.org/
[7] http://www.chemspider.org
[8] http://www.outsellinc.com/our_industry/headlines/31605
[9] http://www.chemsw.com/
[10] http://www.sciquest.com/
[11] http://www.sigmaaldrich.com/sigma-aldrich/home.html
[12] http://www.chemnavigator.com/
[13] http://www.nature.com/news/2009/091118/full/462258b.html

Links to Outsell profiles of companies mentioned:
Nature Publishing Group:
   https://clients.outsellinc.com/vendormarket/co.php?c=4708
Royal Society of Chemistry (RSC):
   https://clients.outsellinc.com/vendormarket/co.php?c=4861
Symyx Technologies, Inc.:
   https://clients.outsellinc.com/vendormarket/co.php?c=7848
Thomson Reuters:
   https://clients.outsellinc.com/vendormarket/co.php?c=2396
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