The Blue Obelisk Movement
One of my Ph.D. advisors, Mark Ratner, loves to say that science is about the people doing it and is best done in the company of good people. Of course this is partly because Mark is an extremely friendly, warm person.
Right now, I’m at the American Chemical Society meeting in San Diego and have met up with a number of old friends and some new friends. In particular, last night a number of open source / open science developers met for dinner and some beers. Peter Murray-Rust called us the “Blue Obelisk Movement” in honor of the place we met this evening. (Although it turned out that there are two blue obelisks in San Diego — fortunately they’re at separate corners of the same plaza.)
The meeting was a lot of fun, and we did talk on a little bit of work as well. One of the sessions here at the ACS meeting focuses on open access and the future of chemical publishing. Peter and Henry Rzepa gave an excellent “tag-team” back-to-back talks discussing some of the work they’ve done on establishing unique chemical identifiers (INChI) and pushing towards two key points:
- Can we access data in scientific publications and databases?
- Can we reuse data once we access it?
Of course all of this centers on intellectual property laws, including patent literature, copyrights and the like. Chemistry is not the only discipline working on these problems — Henry gave an excellent analogy with music.
If I take my iPod and plug it in, I can “rip mix and burn” a CD to my iPod — it’s within my legal rights. Moreover, all the metadata like the artist and song name are embedded into the music files. That’s recognized on any computer platform and almost any music player.
Why can’t we do the same for chemistry? If I hand someone a presentation or publication, shouldn’t include all sorts of information on the molecules in it?
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Mentioned Elsewhere
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Trackback by World Wide Molecular Matrix — 3 years, 3 months ago.
Open Access and the Chemical Semantic Web
Peter Murray-Rust and Henry Rzepa
University of Cambridge and Imperial CollegeACS, 2005-03-14, San Diego
The Semantic Web is becoming a reality
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Pingback by The Blue Obelisk Movement » geoff hutchison: blog — 2 years, 12 months ago.
[...] I talked about the first informal meeting in March but things are becoming a little more organized this summer. [...]
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Pingback by Blue Obelisk at the ACS Fall Meeting ‘06 » geoff hutchison: blog — 7 months, 2 weeks ago.
[...] Starting at last year’s American Chemical Society national meeting in spring 2005 in San Diego, CA, the Blue Obelisk movement of open chemistry was started. [...]
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Peter Murray-Rust — 3 years, 3 months ago.
Thanks geoff
Only discovered this today - by Googling for “Blue Obelisk”. Indeed I didn’t know this existed.
Have just mentioned the Blue Obelisk on the taverna list. Taverna is a workflow tool and althohough originally developed for bioinformatics is completely general. We see it as an important tool for uniting the sort of approach that the Blue Obelisk represents. it’s a unfying technology as it is paltform and OS dependent and allows people to integrate their applications without worrying about languages.
openbabel has a prominent place in our applications. It’s an excellent example of a tool - precisely defined function, inputs and outputs. This is how chemoinformatics should be built.
P.
Geoff — 3 years, 3 months ago.
Peter,
Great to see your comments. The blog is fairly new, so I’m still feeling my way about what I want to include here — think of it an experiment of sorts.
I’m generally amazed by the amount of traffic it receives — my molecule pictures are quite popular, thanks to Google.
I’ll definitely investigate Taverna more closely. Personally, I have several workflows designed for the UNIX environment which make my life easier when dealing with 100s to 1000s of computational results. But it’s nice to see the beginnings of more general approaches.
And you’re flattering me about “precisely defined” function of Open Babel. We’re getting there, but any large codebase will have countless bugs. Prof. Donald Knuth, a famous CS professor, says “I can always take a program and cut out at least one line of code and fix at least one bug.” I think the exciting part about “Blue Obelisk” is that there are multiple open, reliable chemistry codebases for integrating all sorts of different chemical problems. Each has a niche in terms of project goals and use, but there’s a large amount of sharing of code, ideas, and support.