I have a collection of biological parts and devices in a particular format that basically stores information of the sequence of the elements. My intention is to move to a more standardized data structure with a particular interest in Synthetic Biology. SBOL 3 looks like a good choice, then the question is if there is a way to kind of "import" data from my sequence-based database into SBOL?
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2 Answers
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For SBOL 2, you can readily import data via the online converter tool at https://converter.sbolstandard.org/ The converter basically just wraps the conversion function found in the SBOL libraries, so if you're coding, you can do the conversion directly from the libraries.
For SBOL 3, there isn't yet an online tool, but James McLaughlin has a converter in his JavaScript library: https://github.com/sboltools/sbolgraph I believe he is working to bring it online shortly, so hopefully this answer will soon need to be updated or replaced by an answer from him.
An anecdote on the difficulty level: I recently started using an SBOL3-->SBOL2-->GenBank conversion using pySBOL3 and pySBOL3. It took a couple of hours to setup the pipeline, and isn't perfect, but it's pretty doable (and ought to be generalized for others to use as well at some point). The other way would be easier, since GenBank contents are pretty simple.
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Further to jakebeal's answer there is also an excel2sbol library (still in alpha) that can take input to a standard template and convert to SBOL2.
For SBOL3 there is also a python library, but using this to create SBOL3 is more involved.
