Author Archives: pm286

Adding semantic markup with InChI

Posted on October 15, 2007 by pm286

If we could require all authors to provide machine-readable chemical structures in their chemistry articles the quality of chemistry would increase dramatically and immediately. We could create Open databases immediately, that were machine-searchable (just like crystalEye). No-one doubts that, but … Continue reading →

Posted in chemistry, open issues | Leave a comment

What does "Open Access" mean

Posted on October 15, 2007 by pm286

Stevan Harnad is one of the founders of the OA movement and has tirelessly promoted the idea of Green and Gold OA. I applaud and support Stevan’s achievements. However I find and argue that Green Access does not give the … Continue reading →

Posted in data, open issues | 5 Comments

Oh Dear … Patent on Name2Structure conversion

Posted on October 15, 2007 by pm286

Chemspider has reported a new patent which claims the conversion of chemical names to structures. (BTW I am genuinely grateful for this post, as for several of the others). He writes: Name to Structure Conversion – and What One Little … Continue reading →

Posted in open issues | 2 Comments

Indexing Open Access and Free Access articles

Posted on October 15, 2007 by pm286

I reported that Chemspider had been asked to take down indexes of scientific articles (based presumably on chemical names) and stated that I did not think this was reasonable. (My language was probably rather more heated – I shall choose … Continue reading →

Posted in open issues | Leave a comment

Open-Data-driven science and a brokering system for ONS

Posted on October 14, 2007 by pm286

Cameron Neylon and Jean-Claude Bradley have blogged about a directory of Open Notebook Science (ONS) where projects including this approach can register. Growing a community – Open Notebook Science directories 21:19 14/10/2007, Cameron Neylon, As has been flagged up by … Continue reading →

Posted in blueobelisk, data, open issues, open notebook science | 6 Comments

ODOSOS and an article on OA

Posted on October 14, 2007 by pm286

Egon reminds us of the importance of the intensity of purpose that we need in the Blue Obelisk. (ODOSOS is our mantra: Open Data, Open Source, Open Standards). I won’t add very much new to that but I’ll also add … Continue reading →

Posted in blueobelisk, open issues | 1 Comment

Fun graph

Posted on October 14, 2007 by pm286

I love Rich Apodaca’s idea of “name that graph” (example). I am not competing, but just occasionally a bit of fun: Shouldn’t be hard

Posted in fun, puzzles | 8 Comments

ACS: Why it matters

Posted on October 14, 2007 by pm286

I have posted as an outsider why I am concerned about the current state of governance at ACS, particularly with regard to truth and integrity in the scholarly process. You may ask “why is this Brit slagging off a society … Continue reading →

Posted in open issues | 1 Comment

OPSIN/OSCAR: you + us = we; please help

Posted on October 14, 2007 by pm286

I’m exploring how you and we may be able to work to improve OSCAR and OPSIN. Even if you aren’t interested in chemical names, you may find the general principles useful. One of the drawbacks of full Open Source and … Continue reading →

Posted in chemistry, open issues, oscar, programming for scientists, XML | Leave a comment

The thing about Wikipedia is that it only works in practice. In theory, it can never work.

Posted on October 14, 2007 by pm286

A correspondent asked my opinion about Freebase: This blog entry may be of interest, about Freebase a collaborative database project which may or may not be open.  Are you familiar with it? http://brianna.modernthings.org/article/20/freebase-wikipedia-and-the-right-to-fork Also see http://www.nytimes.com/2007/03/09/technology/09data.html?ex=1331096400&en=a87d4f61e6052888&ei=5090&partner=rssuserland&emc=rss I must admit to … Continue reading →

Posted in data, open issues | 4 Comments