SBOL data model diagram and documentation

Matthew Pocock

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Aug 19, 2011, 12:14:57 PM8/19/11

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Hi,

It was great meeting with some of you at the Newcastle synthetic biology data standards workshop. Since then, we have been beginning to use SBOL in some research applications. I'm working with Neil and Jen's synthetic biology group, with an emphasis on leveraging and contributing to the development of relevant standards.

We were wondering about the core data model diagram displayed in http://www.sbolstandard.org/initiatives/core-data-model. This doesn't match what I remember of the diagram shown at the Newcastle workshop. Is this on-line diagram the current representation of the standard, or is it out of date? There are several diagrams linked at the bottom of that page, and we're unsure how these relate to the one at the top, or which is current or if there is some other diagram that hasn't made it on-line yet.

Is this page the canonical reference for the current SBOL data model, or is there some other on-line source that we should be referring to? Is there any additional documentation describing the entities and properties displayed in this diagram? Also, I have not been able to find any on-line discussions about the development of the SBOL standard - my google-foo may be weak. Is there an open forum in which the development process is conducted? By reading through the archives, I can probably answer many of the questions I have about how to interpret the data model and why things are as they are.

Thanks,

Matthew

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Dr Matthew Pocock

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Herbert Sauro

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Aug 19, 2011, 12:37:23 PM8/19/11

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Matthew, the core model has undergone some changes since I visited
Newcastle. At the moment the group is going round in circles but the
circles are getting smaller ! Mike just released an update to the UML
diagram on sbolstandards.org and I would take that as the current
Gospel. The Java sbol library is also getting a significant
development push with new programmers on board. Eventually we will
also need a more generic C/C++ version but someone needs to take
ownership of that project There is a very active discussion group on
sbol and I would email either Michal Galdzicki, Cesar Rodriquez or
Mandy Wilson (all sbol editors) to get registered with the group. I've
cced this email to all three.

I am hoping that once the core model is ready we can start to decide
on the extensions at which point I am hoping the current community
will delegate the extensions to sub groups so that they can take
ownership. If we don't do this it won't be possible to scale the
development or get comprehensive community buy in across the globe.

sbol...@googlegroups.com

regards
Herbert