Question: When Is The Best Time To Submit Sequences To Public Databases Like Ncbi?
gravatar for Joseph Hughes
9.1 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

I have always left the submission of sequences to NCBI to the very last minute, i.e. just before submitting a manuscript for review and on occasion, I have left it until I have known that the paper is accepted. In your opinion when is the best time to submit? As soon as you have quality checked the sequences? Once the manuscript is ready for submission? After the manuscript has been accepted?

It would be great to get a general feel of when people tend to submit there sequences.

ncbi database sequence • 3.0k views
ADD COMMENTlink modified 7.7 years ago by Noyk50 • written 9.1 years ago by Joseph Hughes2.7k

This is interesting, I don't (or rather haven't yet) submitted sequence data to NCBI or EBI, but I have submitted to ArrayExpress and GEO. When I do this we just put a release date on the data in the future, generate a private reviewer URL or access for the reviewers and submit the paper. The reviewers can see the data is annotated and deposited, and it's released on publication.

So why isn't this the same for sequence data?

ADD REPLYlink written 9.1 years ago by Daniel Swan13k

But is there any advantage to releasing your data before you have even submitted a manuscript?

ADD REPLYlink written 9.1 years ago by Joseph Hughes2.7k
gravatar for Phis
9.1 years ago by
Phis1.0k wrote:

In the past, I've mostly done it like you, but with the current wealth of sequence data, I guess the relative value of sequences is going down. Therefore, I don't see any reason per se to wait until the paper is submitted/accepted. Unless of course you have something that gives you an advantage over your competition (if applicable) that you don't want them to see before your publication is out.

Note that you can also submit sequences and specify a release date, so it's not necessarily true that sequences become publically available as soon as they're submitted.

In my personal view, the advantage to submitting as early as possible is that you've got it out of the way sooner.

ADD COMMENTlink written 9.1 years ago by Phis1.0k
gravatar for Noyk
9.1 years ago by
Noyk50 wrote:

how about the issue of patenting after submitting the data? will there be any complications since these data are already in public domain

ADD COMMENTlink written 9.1 years ago by Noyk50

if you publish, you need to release the data on a public domain, otherwise your results won't be reproducible (at least for most of the journals). So either publish or patent it, you have to choose.

ADD REPLYlink written 9.1 years ago by Giovanni M Dall'Olio26k

Patenting is a different issue really. I think that a small proportion of sequences are withheld for patenting purposes although there is no way to know what is being stored being the wall of private biotechs. I am interested in knowing what most people do with their sequences: release them a soon as they have been quality checked; wait until they are submitting a manuscript; wait until the manuscript is accepted.

ADD REPLYlink written 9.1 years ago by Joseph Hughes2.7k
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