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SynBioDex / libSBOLj

Java Library for Synthetic Biology Open Language (SBOL)
Apache License 2.0
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GenBank exports lose names #593

Closed jakebeal closed 5 years ago

jakebeal commented 5 years ago

(copy of https://github.com/SynBioHub/synbiohub/issues/944, per evaluation by @cjmyers )

GenBank exports come out with anonymous features. Here is an example: https://synbiohub.org/public/igem/BBa_K808000/1 https://synbiohub.org/public/igem/BBa_K808000/1/BBa_K808000.gb

The SBOL knows the features are AraC, AraO, AraO1, and AraPromoter, but the GenBank loses that information.

I don't know just what the GenBank file should look like (not actually using GenBank much), but it should be able to round-trip from GenBank --> SBOL --> GenBank --> SBOL such that the two SBOL versions are identical.

cjmyers commented 5 years ago

GenBank -> SBOL -> GenBank -> SBOL should work fine.

What you are asking for here is different, you are asking for:

SBOL -> GenBank -> SBOL

This is an inherently lossy translation I’m afraid.

On Jun 4, 2019, at 9:32 AM, Jacob Beal notifications@github.com wrote:

(copy of SynBioHub/synbiohub#944 https://github.com/SynBioHub/synbiohub/issues/944, per evaluation by @cjmyers https://github.com/cjmyers )

GenBank exports come out with anonymous features. Here is an example: https://synbiohub.org/public/igem/BBa_K808000/1 https://synbiohub.org/public/igem/BBa_K808000/1 https://synbiohub.org/public/igem/BBa_K808000/1/BBa_K808000.gb https://synbiohub.org/public/igem/BBa_K808000/1/BBa_K808000.gb The SBOL knows the features are AraC, AraO, AraO1, and AraPromoter, but the GenBank loses that information.

I don't know just what the GenBank file should look like (not actually using GenBank much), but it should be able to round-trip from GenBank --> SBOL --> GenBank --> SBOL such that the two SBOL versions are identical.

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jakebeal commented 5 years ago

I am asking for GenBank -> SBOL -> GenBank -> SBOL (which can be validated by comparing the two SBOLs). Right now, it is not working, per the bug listed.

jakebeal commented 5 years ago

Let's use the '/label' convention

cjmyers commented 5 years ago

Fixed