Chemistry and Web 2.0

Martin A. WalkerDept. of Chemistry, SUNY Potsdam

Member of the Wikipedia Chemistry Project

Overview

• Chemistry information in 2010– The “lay of the land”– Chemistry Web 1.0– Chemistry Web 2.0

• Wikipedia• ChemSpider• Project Prospect• Educational resources

– Open Access and Open Notebook Science• Concerns• The future?• Discussion

CHEMISTRY: THE LAY OF THE LAND

The lay of the land

• Chemistry has long had superb information resources– Beilstein, Chemical Abstracts, etc

Picture by JOE M500from Flickr, CC licence

The lay of the land

• Chemistry has long had superb information resources– Beilstein, Chemical Abstracts, etc

• Traditional ties with the chemical and pharmaceutical industries have fostered a “for-profit” environment e.g., for publication– A chemistry book is typically

$200, and many journals cost >$1 per page

Picture by JOE M500from Flickr, CC licence

The lay of the land

• Chemistry has long had superb information resources– Beilstein, Chemical Abstracts, etc

• Traditional ties with the chemical and pharmaceutical industries have fostered a “for-profit” environment e.g., for publication– A chemistry book is typically

$200, and many journals cost >$1 per page

• As a result, chemistry has been slower to adapt to “Web 2.0”

Picture by JOE M500from Flickr, CC license

CHEMISTRY ON THE WEB (VERSION 1.0)

Web 1.0

The Web has already transformed chemical information

Picture by azure elixir, on Flickr. CC license.

Chemistry Web 1.0

We can read articles without leaving our desks

Chemistry Web 1.0

We can search, find and read patents:

Chemistry Web 1.0

• Google Scholar can also help us find recent articles by Lavoisier…

One of the oldest sites is still one of the best

Organic Chemistry Portal

Web 1.0

The information

is the same, just packaged differently

CHEMISTRY ON THE WEB(VERSION 2.0)

Chemistry Web 2.0

What’s chemistry got to do

with “social

networks?”

Am I going to find improved methods for Suzuki couplings by

contacting my “friends” on MySpace?

Picture by Mighty Mighty Big Mac, Flickr , CC License

Chemistry Web 2.0

• Scientists already depend on their own social networks to learn, share ideas

• The Web offers us the chance to share the sum of human knowledge – including the deep knowledge of specialists such as scientists.

• Mashups can allow seamless sharing of data between sites

Picture courtesy ofJim Hendrickson, Brandeis

Some Chemistry Web 2.0 initiatives

• Wikipedia chemistry and other wikis• ChemSpider• NMRShiftDB• RSC Project Prospect• Blue Obelisk, Jmol and the open source

movement• Educational initiatives

Wikipedia Chemicals Project

• ~60 members (~20 active)• Collaborated on writing

quality articles and standards for:– developing data boxes for

articles– chemical naming, structure

drawing– article assessment

• Data validation• New collaboration with CAS

Wim Van Dorst, a Dutch member of WP:Chem since March 2005.

Wikipedia Chemicals Project

Traffic can be very high….

Even for specialized topics

And people too!

References for sodium sulfate

Content validation

• In 2008 a data validation drive was initiated for basic chemical identifiers

• Led to a collaboration with CAS, to ensure Wikipedia CAS registry nos. are correct

• Now around 3500 substances have been validated against CAS Common Chemistry, as having correct name, structure & CAS RN

• Validated content indicated with a check mark

CommonChemistry

• Launched in April 2009• Came about as a result of a

collaboration between CAS & Wikipedia

• Offered as a free service for CAS RNs for members of the public.

Pfizerpedia

Thanks to Antony Williams

Wikis for IUPAC

• One IUPAC workgroup recently used a wiki to reach consensus on Mass Spectrometry terms.

ChemSpider

• Started by Antony Williams, March 2007. Acquired by the Royal Society of Chemistry in May 2009.

• Now the world’s largest open chemical database (over 20 million substances).

• Open access, all content is free.• Brings together data from many

different sources, with links out to those sources. Search for structural information, physical properties, etc..

• Data uploads and curation by volunteers.

ChemSpider

ChemSpider

ChemSpider

ChemSpider

• The goal of ChemSpider is to build a “community of chemists”

• Not trying to be “Facebook for chemists”, instead it offers useful chemical information, FREE.

• Chemists can share their own data

New this week – ChemSpider

Synthetic Pages!

NMRShiftDB

Blue Obelisk group

• An informal international group of chemists committed to open science and open source software for chemistry, e.g. Jmol for visualizing molecules in 3D

Picture courtesy of Wikipedia/NicoV, GFDL license

Project Prospect

Blogs

Nature Island in Second Life

“I think that being able to walk around a molecule can add valuable new insight to thinking about and doing chemistry.” Jean-Claude Bradley, April 5, 2007.

Ionicviper.org

WikiEducator

OPEN ACCESS

Open Access

• Web 2.0 methods depend on sharing data, to produce a network of information. The data need to be freely available and accessible.

• For information to be found (e.g., by Google), it needs to be open.

• “3Bs” (Budapest, Bethesda, Berlin) – agreements that define OA.

• Groups that keep data behind a subscription firewall may lose market share.

Open Access

Open Access

Open Science

Open Notebook Science

SOME CONCERNS

Is it reliable?

• Traditional peer review vs community controls– Current review system is flawed– Community controls are highly

variable– Look for validation– Confirmation may be just a click

away!– On Wikipedia, high traffic =>

more reliable

Peer review: How will publications be evaluated in the Web 2.0

world?

Traditional• Critical review by

subject experts within months

• Reviews may be cursory, or worse – “Did you even read the paper???!”

• Review process is not very transparent

• Hard to update• Valued in tenure &

promotion

Web 2.0• Review often by non-

experts, and the main point may be overlooked or misunderstood

• Review may be fast – or may not occur at all?!

• Potential for “many eyeballs”

• Transparent, updateable• Not considered at all in

tenure and promotionBoth approaches can lead to very bad – and very good - reviews

Judge the quality of the output, not the perceived quality of the

process

THE FUTURE?

The Future?

• “Grey” questions can be answered• Data shared openly – a web of all

information• Chemistry “social networks”?• Free, fully open sites will thrive; closed

sites may end up “closed” forever….?• Open sites that can get ordinary

chemists to share their data will really thrive!

• Simple semantic searches• Lab results open & uploaded in real

time?

The future?

What

if?

•You could upload your lab results directly onto the Web, for people to read immediately?

What

if?

•You could perform “meta-searches,” such as, “Find me all of the silver-containing compounds that have a melting point below 200 oC and are soluble in benzene.”

What

if?

•The Web was truly “Semantic” – so web objects (structures, reactions, etc.) could be completely understood by search engines?

WHAT DO YOU THINK?How does this apply to my field?

Is open access a dead end? Who will pay for everything?

How will the tenure process work under the new paradigm?

I don’t want my rivals to steal my data and get the credit!

What about peer review?