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In submitting sequences using tbl2asn to NCBI/GenBank, the documentation states that there is a controlled vocabulary for the key "moltype", but no where on the Internet can I find a full list of that vocabulary. "mRNA" and "genomic" are given as examples on several pages, and I can see from Sequin documentation what the GUI descriptors of all the vocabulary terms are (e.g., "genomic DNA"), but I can't find the terms themselves. Any ideas where I can find this list?

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  • $\begingroup$ Kind of a hassle, but could you download Sequin see what it outputs in the fasta for each molecule type? $\endgroup$ – canadianer Mar 28 '18 at 4:57
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    $\begingroup$ I hadn't realized Sequin output fasta files. I just checked, and it doesn't seem to include any of those descriptors in the FASTA file that will be exported when you use the Export command. $\endgroup$ – David Maddison Mar 28 '18 at 20:23
  • $\begingroup$ Sorry, I actually don’t know anything about it. Just a thought I had. $\endgroup$ – canadianer Mar 28 '18 at 20:25
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    $\begingroup$ It was a good thought. As you can see, I (perhaps inappropriately) edited my comment because I tested it out, and it didn't seem to work. $\endgroup$ – David Maddison Mar 28 '18 at 20:28
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There is this "Controlled vocabulary for /mol_type qualifier" page created by the International Nucleotide Sequence Database Collaboration in 2013. It says the allowed values are:

"genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA", "other RNA", "other DNA", "transcribed RNA", "viral cRNA", "unassigned DNA", "unassigned RNA"

I found this as the second result of a Google search on moltype vocabulary.

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    $\begingroup$ I found that too. The issue with this is that in the examples provided by NCBI, "genomic" is one of the valid values "moltype". "genomic" by itself does not appear on that controlled vocabulary list. $\endgroup$ – David Maddison Mar 28 '18 at 20:22
  • $\begingroup$ Of course, another possibility is that the other NCBI documentation if invalid, and that this is the controlled vocabulary they use as well. $\endgroup$ – David Maddison Mar 28 '18 at 23:43
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    $\begingroup$ I just heard back from NCBI. Even though this controlled vocabulary conflicts with their own documentation (which I suspect is out-of-date), it is the vocabulary they now use. $\endgroup$ – David Maddison Mar 29 '18 at 20:05
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I've found an archived version of Sequin for Database Submissions and Updates: A Quick Guide, published by NCBI.

  • moltype should use one of the following values. Example: [moltype=genomic]
    • genomic
    • precursor RNA
    • mRNA
    • rRNA
    • tRNA
    • snRNA
    • scRNA
    • other-genetic
    • cRNA
    • snoRNA
    • transcribed RNA
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  • $\begingroup$ Great job! That looks like it is what I need. Odd that this isn't public. $\endgroup$ – David Maddison Mar 28 '18 at 23:42
  • $\begingroup$ The other possibility is that the OTHER documentation is out of date, and that the controlled vocabulary the mgkrebbs found is the one NCBI also uses. $\endgroup$ – David Maddison Mar 28 '18 at 23:42
  • $\begingroup$ @DavidMaddison Yes, it is odd. It may be worth contacting NCBI about it. $\endgroup$ – canadianer Mar 29 '18 at 0:43
  • $\begingroup$ Yes, I sent NCBI a note asking about this earlier today. I will report back! $\endgroup$ – David Maddison Mar 29 '18 at 4:29
  • $\begingroup$ See my new comment to mgkrebbs answer. $\endgroup$ – David Maddison Mar 29 '18 at 20:05

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