Can I assemble chloroplast genome of plants using SRA data from NCBI and I can publish it ?
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6 months ago

Hello everyone,I am working on the development of chloroplast genome resources for medicinal plant groups to identify species-specific DNA barcodes for species identification and authentication of herbal products. In this context, I initially checked the availability of chloroplast genomes in NCBI. I noted that SRA data is available in NCBI for 10 plants, submitted by authors for whole genome sequencing purposes.My question is: Can I use the same SRA data for those particular plant species, assemble the chloroplast genomes, and publish the results myself?If it is ethically sound, I would not need to generate the whole genome sequencing data again for the same species.

Chloroplast genome SRA • 723 views
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6 months ago

There is no "ethical" issue here as long as you identify the source of the data.

The bar for publishing may be a bit higher; you have to demonstrate additional value, but that's about it.

One of the main rationales for publishing raw data is to enable others to build upon prior results.

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It would be good practice to let the submitter's know of one's intention to use/publish as a professional courtesy. People release the data to make it immediately available but may retain the first-dibs on publishing.

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I don't think there are any tacit rights, "first dibs," or ethical concerns. In my view there is also absolutely no requirement to let someone know you will use their data or to implicitly or explicitly "ask permission".

In the vast majority of cases, taxpayers supported that effort and the scientists were paid to do the work to benefit everyone else. Publishing is exactly that: putting the data out there for others to use.

The point of publishing the data is not just to verify the results.

While reproducibility may be one reason, it alone would never warrant the massive costs associated with data publishing and storage.

If you manage to publish something using existing data, you are rewarding the original creators of the data with a citation.

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I don't think there are any tacit rights, "first dibs," or ethical concerns.

Legally perhaps not but this has been the accepted principle for a while: https://en.wikipedia.org/wiki/Bermuda_Principles

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requiring that all DNA sequence data be released in publicly accessible databases within twenty-four hours after generation

The above is a different scenario agreed upon during the Human Genome Project where data was released 24h after generation and not as part of a publication

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If you manage to publish something using existing data, you are rewarding the original creators of the data with a citation.

I don't think this is much of an argument, as we reward by citations any quality work by others. That goes whether we used their data in our own research or not. I agree with your argument that publicly funded work should be publicly available, but why not acknowledge those who obtained that funding and performed the work? By this I mean acknowledge them beyond giving them a citation.

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I would definitely let the original authors know once the paper is ready for submission. I would even send them a preprint and ask for comments (but not ask for permission). It is a sign of respect and gratitude for generating the data. Other than that, and assuming their work on nuclear genome was publicly funded and was published, I don't think there are any remaining dibs to be claimed.

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