BBF RFC 31
Vincent, 16th May 2009
it is a good surprise to read about some new PoBoL development. I fully agree with the authors that the Synthetic Biology community needs an open and standarized data model to represent BioBricks. Please find below some comments about the proposal. I hope they are clear and useful.
> related to [6. Motivation]
What about compatibility with existing DNA sequence standards, and their respective tools ? I understand that SynBio will require some specific features, but is it really required to start from scratch. Defining a standard that would extend on previous standards might help us to avoid reinventing the wheel, as well as reaching out other communities (in terms of people and software solutions / infrastructures). At least, I would be interested to read about the authors' reasons not to consider, at all, any of the existing standards to represent DNA sequences.
I would also find useful if the authors could describe two or three relevant scenarii where such a data format would be required.
> related to [10.1.1 Class BioBrick]
Is there a concept of unicity for a BioBrick ? Or is it accepted for the proposed standard to have duplicates ? For example, two Biobricks with same DNASequences, same Format, but different ShortDescriptions ? Also, if unicity is required, at which level ? in the same lab or in the all world ? Would it be useful to consider unique identifiers ?
"The BioBrick class May be extended at any time". This built-in flexibility might be difficult to deal with when people try to practically implement the scheme.
> related to [10.1.3 BioBrickBasic]
Quick clarification: Let's say that I use direct DNA synthesis to get a 5kb (4 genes) metabolic pathway, with prefix/suffix chosen to satisfy a particular BioBrick standard (+ not incompatible restriction sites in the 5kb). From what I understand, this would constitute a BioBrickBasic instance, no ?
> related to [10.1.5 BioBrickFormat]
Recombinant DNA is a method amongst others to put together 2 pieces of DNA. For example, in vitro recombination could very well become a popular way of physically assembling DNA (no resulting scar). It looks like this proposed scheme only considers Recombinant DNA-type assemblies. Is it a limitation ? Is it ok ? Or are we saying that pieces of DNA using homology recombination for assembly will never be considered as BioBricks ?
At the end, if this proposal is restricted to BioBricks, as opposed to generic "DNA-parts" (or assembled DNA sequences), I would say that it is a limitation of the scope to accomodate future genetic circuit assemblies.
> related to [Class Sample]
What if the sample is a PCR product (linear DNA, no vector) ? How would you distinguish between a mini-prep in buffer, dry DNA, or a stab ?
At the end, I am not sure that this type of information is very useful. I would prefer to see a community agreement on key attributes before getting into those details that are more relevant to a Laboratory Information System.
> General comments
Without denying the descriptive power of RDF, I feel that using a RDF framework, at this stage, might prevent a majority of people within the community to engage with this important process of describing essential features of "DNA-parts". I would prefer to see a "Minimum Information for the description of a DNA-part" discussion before getting into a specific knowledge representation, such as RDF.
Could the authors comment on the impact of such information model on the current MIT registry, and on future registries ?
Characterisation of Biobricks is one of the highest priorities for our community. How the authors suggest to integrate this new type of information in the current scheme ? Will it be part of the standard or will it require a different system ?