Category Archives: data

Open Data in Science

I have been invited to write an article for Elsevier’s Serials Review and mentioned it in an earlier post (Open Data: Datument submitted to Elsevier’s Serials Review). I had hoped to post the manuscript immediately afterward but (a) our DSpace … Continue reading

Posted in data, publishing | Tagged , , , | 13 Comments

Does the semantic web work for chemical reactions

A very exciting post from Jean-Claude Bradley asking whether we can formalize the semantics of chemical reactions and synthetic procedures. Excerpts, and then comment… Modularizing Results and Analysis in Chemistry Chemical research has traditionally been organized in either experiment-centric or … Continue reading

Posted in chemistry, data, open notebook science | Tagged , , | 8 Comments

Chemical information on the web – typical problem

Here’s a typical problem with chemical (and other) data on the web and elsewhere. I illustrate it with an entry from Wikipedia, knowing that they’ll probably correct it and similar as soon as it’s pointed out. You don’t have to … Continue reading

Posted in data, fun | Tagged | 1 Comment

What does USD 29 billion buy? and what's its value?

Like many others I’d like to thank the The Alliance for Taxpayer Access … … a coalition of patient, academic, research, and publishing organizations that supports open public access to the results of federally funded research. The Alliance was formed … Continue reading

Posted in data, open issues | Tagged , , | Leave a comment

Update on Open crystallography

There’s now a growing movement to publishing crystallography directly into the Open. Several threads include: The Crystallography Open Database which pioneered the idea of collecting crystallographic data and making them Openly available. Nick Day’s CrystalEye – aggregation of published Open … Continue reading

Posted in data, open issues, programming for scientists | Tagged , , | Leave a comment

Open Access Data, Open Data Commons PDDL and CCZero

This is great news. We now have a widely agreed protocol for Open Data, channeled through Science Commons but with great input for several sources including Talis, and the Open Knowledge Foundation. Here is the OKFN report (I also got … Continue reading

Posted in data, open issues | Tagged | Leave a comment


Last spring I visited Illinois (UIUC) and presented the SPECTRa tools. Scott Wilson who runs the crystallographic facility and many of the LIS community were keen to see how it could be used for capturing their crystallography. Yesterday I met … Continue reading

Posted in data, open issues | Tagged | Leave a comment

Scraping HTML

As we have mentioned earlier, we are looking at how experimental data can be extracted from web sources. There is a rough scale of feasibility: RDF/XML > (legacy)CIF/JCAMP/SDF > HTML > PDF I have been looking at several sites which … Continue reading

Posted in data, repositories, semanticWeb | 2 Comments

Survey of open chemistry in Chemistry World

Richard Noorden has written a balanced and informative view of Open Chemistry ( Surfing Web2O, Chemistry World, December 2007. )  He has read much of the chemistry blogosphere and talked with many of us on the phone. The article highlights … Continue reading

Posted in data, open issues, open notebook science | 2 Comments

Chemspider and Pubchem – open data

I was very pleased to see: ChemSpider Blog » Blog Archive » The Entire ChemSpider Database is On Its Way to PubChem! which describes how the Chemspider database is being offered to Pubchem as “open data”. Chemspiderman has made a … Continue reading

Posted in data, open issues | 2 Comments