Chemistryand web2 ma walker 2 5 10Presentation Transcript
Chemistry and Web 2.0 Martin A. Walker Dept. 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 M500 from 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 M500 from 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 M500 from 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
Chemistry on the web(Version 2.0)
Chemistry Web 2.0 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 of Jim 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
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 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!
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
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.
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 Notebook Science
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 promotion Both 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? “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 reallythrive! Simple semantic searches Lab results open & uploaded in real time?
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?