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SynBioHub / synbiohub

Web application enabling users and software to browse, upload, and share synthetic biology designs
https://wiki.synbiohub.org
BSD 2-Clause "Simplified" License
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Can't download genbank for bacillondex parts #175

Closed jamesamcl closed 7 years ago

jamesamcl commented 7 years ago

Validator says

ComponentDefintion http://synbiohub.org/public/vpr/BO_10000/1 does not have an IUPAC sequence.

jamesamcl commented 7 years ago

Also note there's a typo in "ComponentDefintion" there. not sure whether that should be reported in libSBOLj or the validator.

cjmyers commented 7 years ago

My understanding is GenBank format is not for Protein sequences, see here: https://www.ncbi.nlm.nih.gov/genbank/samplerecord/#MoleculeTypeB and here https://www.ncbi.nlm.nih.gov/Sequin//sequin.hlp.html#SpecifyMolecule If you disagree, can you show me where it says it can be a protein?

Also, where is the typo?

3ach commented 7 years ago

From https://www.ncbi.nlm.nih.gov/books/NBK50679/#RefSeqFAQ.what_is_a_reference_sequence_r,

... Whereas the International Nucleotide Sequence Database Collaboration (INSDC, made up of GenBank, the European Nucleotide Archive, and the DNA Data Bank of Japan) ...

The clear inference is that GenBank represents nucleotide sequences, and nucleotides are not components in proteins -- amino acids are.

Also, there was a slight typo in the error messaging (it was ComponentDefintion, not ComponentDefinition) that I've fixed in libSBOLj.