Author Archives: pm286

The birth of a movement

Posted on August 3, 2007 by pm286

From Peter Suber’s blog. An account of the roots of the Open Access declarations: Intro to OA for the FOSS community Bruce Byfield, Academia’s Open Access movement mirrors FOSS community, Linux.com, August 2, 2007. Excerpt: Free and open source software … Continue reading →

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Molecules in Wikipedia and RDF

Posted on August 3, 2007 by pm286

I’ve just arrived in Mountain View for the Nature Google O’Reilly Foo Camp. Expect either silence (i.e. swamped) or gushings. I doubt I’ll have much time to blog. To keep readers happy here’s Egon making things happen in the world … Continue reading →

Posted in chemistry | 1 Comment

legacy molecules: 2-fooyl-ethanol?

Posted on August 1, 2007 by pm286

More thoughts on recovering legacy molecules – this time from names. In journals and elsewhere we frequently come across lists like: 2-chloro-ethanol ClCH2CH2OH 2-fluoro-ethanol FCH2CH2OH 2-phenyl-ethanol C6H5CH2CH2OH These all have a generic representation with “R” groups: RCH2CH2OH Is there a … Continue reading →

Posted in chemistry | 6 Comments

OSRA and others; how to retrieve legacy molecular structures

Posted on July 31, 2007 by pm286

Egon Willighagen blogged this. There is now a real opportunity for the Open Source chemistry community to create high-quality tools for the extraction of molecular information from legacy documents. Besides full-text articles other good areas to look are probably theses … Continue reading →

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Request for Open publication of crystallographic data in Elsevier's Tetrahedron

Posted on July 31, 2007 by pm286

=========== Open letter to editors of Tetrahedron ========== Professor L. Ghosez , Professor Lin Guo-Qiang , Professor T. Lectka , Professor S.F. Martin , Professor W.B. Motherwell , Professor R.J.K. Taylor , Professor K. Tomioka Subj: Request for Open publication … Continue reading →

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cyberscience: Changing the business model for access to data

Posted on July 31, 2007 by pm286

I have been reviewing the availability of Open Data for cyberscience – concentrating recently on crystallography and chemical spectra as examples. I’ll propose a new business model here, still very ill-formed and I welcome comments. It applies particularly to disciplines … Continue reading →

Posted in cyberscience, open issues | 1 Comment

Request for clarification of copyright and re-use on CIFs from Elsevier/CCDC

Posted on July 30, 2007 by pm286

==== copy of letter to CCDC requesting clarification on copyright ==== To:data_request@ccdc.cam.ac.uk Greetings (Sorry to use a generic address but I am not sure who is the person to contact about permissions). We have a systematic program of carrying out … Continue reading →

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Republican vision of Open Source Research

Posted on July 29, 2007 by pm286

from Peter Suber’s blog: Tommy Thompson wants open source research Tommy Thompson, Republican presidential candidate and former Secretary of the Department of Health and Human Services, has announced his science platform: double the budget of the NIH (to $58 billion/year), … Continue reading →

Posted in data, open issues | 3 Comments

cyberscience: extracting crystallography from Elsevier's Tetrahedron via CCDC

Posted on July 29, 2007 by pm286

Regular readers will know of our Crystaleye repository where Nick Day’s robots have – quite legally – extracted ca 100,000 crystal structures from the Open AND closed literature. However it is not yet comprehensive as some publishers do not expose … Continue reading →

Posted in data, open issues | 1 Comment

Closed access damages peer-review

Posted on July 28, 2007 by pm286

I talked today with a scientist (R) whom I meet frequently and who works in a leading bioscientific research establishment (not a University, but with Nobel laureate and FRS on the staff). In addition to their day job, R acts … Continue reading →

Posted in open issues | 3 Comments