Thanks Chris, I attended the Pistoia meeting at BIO-IT I would certainly accept Pistoia resolutions as "standards" in the BO sense.
This is a good example of the flexible and undocumented process of the BO. If there is a group that has the trust of the BO community (which is also not defined) then its outputs can be regarded as "Open standards". I think we should not strive too hard for precision. We are happy that a group of people can produce a program that has the confidence of the community. I see that being possible with "standards". It's the BO community's "best endeavour" to create a useful, public, rellatively stable specification. Here's my take of BO standards - I'm typinf during an eResearch lecture so it's just a start... * The BOS must be usable and used. There is no point in building complex standards which no-one uses. (I was invited to help an OMG-CORBA spec for small molecules using CML - it was a lot of work and no-one supported it (1.5 pharma companies). I like the IETF motto "rough consensus and running code". IETF suggest there should be 2 codes that run. * It must have the trust of the community. That does not necessarily mean a completely democratic process. CML is a benevolent dictatorship with input from the community. Most takes place in Cambridge / Imperial but we had major community involvement (Christoph, StefanK, RobertL, etc.) for CMLSpect. These were the people intimately involved and it was a lot of work. Similarly CMLReact involved the EBI. CMLCryst involves the Int. Union of Crystallography over several years and is heavily predicated on CIF. CMLComp involves UK eMinerals community and the European COSTD37 WG5 action. If anyone wishes to input significantly into CML there is no formal exclusion, but there has to be clear value to us. * There must be space for input from the community. It's often difficult to do this at the beginning, but anyone can make assertions, comments, et.c on any BOS. This is not normally possible with manufacturer formats - I cannot influence what Bruker, CambridgeSoft, etc. create. I cannot affect the next distrib of Pipeline Pilot. * The material must be published Openly and must be redistributable and re-usable without explicit permission. It does not have to allow editing and redistribution. (I have serious problems with software companies who take CML, hack it so it is invalid and then redistribute it as if it is CML. It happens, and I have advised them that it does damage to the CML effort but they don't care. CML is actually the most validatable spec in chemistry and this type of action is destructive This is an area where Pistoia might be able to help. Remember also that most of the BO is unfunded and voluntary. It does what it can. Its tools are heavily used by those who have resources and who create commercial products. That's fine - it's part of the ethos. It would be nice to see some support from that sector but we don't demand it. But we do ask that any criticism is generally constructive. P. On Tue, Dec 8, 2009 at 2:17 PM, Waller, Chris <[email protected]>wrote: > Hi Peter, > > > > Good discussion and the primary focus of the Pistoia Alliance. Check out > the activities at http://www.pistoiaalliance.org. > > > > Chris > > > > Chris L. Waller, Ph.D. > > Senior Director, Precompetitive Collaborations > > Research, Development, and Medical Informatics > > Business Technology > > Pfizer, Inc. > > Eastern Point Road, MS 8260-1221 > Groton, CT 06340 > Office: (860) 715-0398 > Mobile: (860) 501-3954 > Fax: (860) 686-5770 > e-mail: [email protected] > > http://www.linkedin.com/in/wallerc > > > > > > > > *From:* Peter Murray-Rust [mailto:[email protected]] > *Sent:* Tuesday, December 08, 2009 6:22 AM > *To:* Noel O'Boyle > *Cc:* Egon Willighagen; BlueObelisk-Discuss > *Subject:* Re: [Blueobelisk-discuss] What is an Open Standard? > > > > If you are using "Standards" in a formal sense then there are very few in > our area. > NO chemistry specifications are standards. > W3C protocols (XML, HTML, CSS) are not standards, they are > "recommendations" > IETF does not produce standards but drafts (e.g. MIME, URIs) > The only standards are those that go through ISO (none in chemistry that > matter) or ECMA. Things like Javascript, MS-OOXML (yes). Not Java. > > So we have to use a looser definition of standard. It's in our mantra. I > think we should define what we regard as useful, not what is formally a > "standard". > > > > > > > -- > Peter Murray-Rust > Reader in Molecular Informatics > Unilever Centre, Dep. Of Chemistry > University of Cambridge > CB2 1EW, UK > +44-1223-763069 > -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069
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