Comments on: Public apology to CCDC http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/ Addressing the challenges of computational drug discovery Wed, 19 Jun 2013 13:20:46 +0000 http://wordpress.org/?v=2.0.11 by: will http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1503 Sun, 22 Jun 2008 22:09:26 +0000 http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1503 The tools being developed by SimBioSys, once fully developed, will put the curation of complex chemical data possible for many scientists not just a few. Imagine the possibilities of combining Chemical OCR software with a Google-type indexer (another technology recently now usable by those with few resources). Even worse (or better in my opinion), these technologies threaten to expose the errors in traditional databases which have prided themselves on high quaility but have not been sufficiently independently scrutinised for mistakes due to their closed nature, and software is heartless in reporting these once the doors are open. The tools being developed by SimBioSys, once fully developed, will put the curation of complex chemical data possible for many scientists not just a few.

Imagine the possibilities of combining Chemical OCR software with a Google-type indexer (another technology recently now usable by those with few resources).

Even worse (or better in my opinion), these technologies threaten to expose the errors in traditional databases which have prided themselves on high quaility but have not been sufficiently independently scrutinised for mistakes due to their closed nature, and software is heartless in reporting these once the doors are open.

]]> by: Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Update and emphasis on publishing and Crystallography http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1502 Sat, 21 Jun 2008 18:29:44 +0000 http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1502 [...] SimBioSys, and others have blogged about the availability of data from the CCDC (post). This raises some extremely serious points about the closing of data meant to be public. [...] […] SimBioSys, and others have blogged about the availability of data from the CCDC (post). This raises some extremely serious points about the closing of data meant to be public. […]

]]> by: Jim Downing http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1499 Fri, 20 Jun 2008 12:03:13 +0000 http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1499 ChemSpider is a great aggregator and data overlay of chemistry information, and it's great that they've indexed CrystalEye. CrystalEye has it's own (rudimentary as yet) community based curation process (http://wwmm.ch.cam.ac.uk/blogs/downing/?p=171); we want the CrystalEye data to be as error free as possible. You've drawn my attention to the fact that we haven't yet got a mechanism for exchanging curation information between the two. Hopefully we'll be able to work on this over the summer. I'd also draw your attention to eCrystals: http://ecrystals.chem.soton.ac.uk/. We're part of the eCrystals3 project, aiming to establish a federation of open crystallographic data. eCrystals federation project: http://www.jisc.ac.uk/whatwedo/programmes/programme_rep_pres/repositories_sue/ecrystals.aspx ChemSpider is a great aggregator and data overlay of chemistry information, and it’s great that they’ve indexed CrystalEye. CrystalEye has it’s own (rudimentary as yet) community based curation process (http://wwmm.ch.cam.ac.uk/blogs/downing/?p=171); we want the CrystalEye data to be as error free as possible. You’ve drawn my attention to the fact that we haven’t yet got a mechanism for exchanging curation information between the two. Hopefully we’ll be able to work on this over the summer.

I’d also draw your attention to eCrystals: http://ecrystals.chem.soton.ac.uk/. We’re part of the eCrystals3 project, aiming to establish a federation of open crystallographic data.

eCrystals federation project: http://www.jisc.ac.uk/whatwedo/programmes/programme_rep_pres/repositories_sue/ecrystals.aspx

]]> by: zsolt http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1495 Thu, 19 Jun 2008 14:33:05 +0000 http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1495 I am glad to see that CrystalEye is not the only competition offering open, free access to crystallographic data, but such data is now also available on ChemSpider: http://www.chemspider.com/blog/crystaleye-structure-collection-deposited-on-chemspider.html ChemSpider has a community based curation process, so anybody who spots problems, errors can contribute to the correction, improvement of the data. Thi s is a very powerful process, similar to the Open Source development model of Linux, Apache, Mozilla and OpenOffice. I hope ChemSpider will prove to be just as successful and the data quality will surpass the closed, restricted, proprietary alternative. We will definitely consider it as a source of data for future efforts to improve our scoring and prediction models, and we will contribute to the curation with any errors we may find. ZZ I am glad to see that CrystalEye is not the only competition offering open, free access to crystallographic data, but such data is now also available on ChemSpider:
http://www.chemspider.com/blog/crystaleye-structure-collection-deposited-on-chemspider.html

ChemSpider has a community based curation process, so anybody who spots problems, errors can contribute to the correction, improvement of the data. Thi s is a very powerful process, similar to the Open Source development model of Linux, Apache, Mozilla and OpenOffice. I hope ChemSpider will prove to be just as successful and the data quality will surpass the closed, restricted, proprietary alternative. We will definitely consider it as a source of data for future efforts to improve our scoring and prediction models, and we will contribute to the curation with any errors we may find.

ZZ

]]> by: ChemSpider Blog » Blog Archive » When a Scientific Blog Posting, Data Licensing and Open Data Access Come Together http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1494 Thu, 19 Jun 2008 12:37:20 +0000 http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1494 [...] Those of you who have been watching the discussion between myself and ACS over the past few months will know I have been trying to get confirmation that “supplementary data” are Open Data and that we could scrape the CIFs if we chose to…it’s a MANY month conversation at this point. The Unilever School at Cambridge, via Nick Day’s work, has generated CrystalEye and, after many conversations, we were provided the data source and have it on ChemSpider now. We are awaiting constructive feedback from Nick and Peter Murray-Rust regarding our implementation of their data on our site. THis is especially important when there are licnesing issues as appear to have been enforced on SimBioSys, evidenced by this Public Apology to CCDC. Read the post for details. [...] […] Those of you who have been watching the discussion between myself and ACS over the past few months will know I have been trying to get confirmation that “supplementary data” are Open Data and that we could scrape the CIFs if we chose to…it’s a MANY month conversation at this point. The Unilever School at Cambridge, via Nick Day’s work, has generated CrystalEye and, after many conversations, we were provided the data source and have it on ChemSpider now. We are awaiting constructive feedback from Nick and Peter Murray-Rust regarding our implementation of their data on our site. THis is especially important when there are licnesing issues as appear to have been enforced on SimBioSys, evidenced by this Public Apology to CCDC. Read the post for details. […]

]]> by: Vladimir http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1492 Thu, 19 Jun 2008 06:54:06 +0000 http://www.simbiosys.com/blog/2008/06/18/public-apology-to-ccdc/#comment-1492 It's terrible to hear! Shame on CSD! Once I hear the story from my chief that many molecules from the CSD were determined by supervision of one of the great Russian scientist from the http://www.crys.ras.ru/. So my next question was - what is the legal status of the data? Because all of the data was derived from the literature published by the corresponding author. Chief said: That is the property of the CSD. I was greatly amazed. The close question arise according to the QSAR datasets eg Syracuse Research, PHYSPROP database - if you by it you can't use it for QSAR research (you can't sell derived QSAR models). It might be the example of greedy data owners :) It’s terrible to hear! Shame on CSD!

Once I hear the story from my chief that many molecules from the CSD were determined by supervision of one of the great Russian scientist from the http://www.crys.ras.ru/. So my next question was - what is the legal status of the data? Because all of the data was derived from the literature published by the corresponding author. Chief said: That is the property of the CSD. I was greatly amazed.

The close question arise according to the QSAR datasets eg

Syracuse Research, PHYSPROP database - if you by it you can’t use it for QSAR research (you can’t sell derived QSAR models). It might be the example of greedy data owners :)

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