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Old 02-22-2013, 06:02 AM   #1
fibar
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Default Accession Numbers when publishing

Dear community, is it not obligatory to add an Accession Number whenever publishing results derived from NGS? I think it should be, I have found several articles with no numbers and that has stopped me from doing important comparisons. Thank you for reading and good luck.
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Old 02-22-2013, 06:18 AM   #2
vadim
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I know this may sound weird, but have you considered submitting their data?

Btw, could you share the articles please?
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Old 02-22-2013, 06:43 AM   #3
fibar
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Sorry, but what do you mean by "submitting their data"?
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Old 02-22-2013, 06:46 AM   #4
vadim
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Quote:
Originally Posted by fibar View Post
Sorry, but what do you mean by "submitting their data"?
If the data mentioned in the articles is public but not in the archive. Maybe the authors did not have enough time/resources to submit the data to SRA.
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Old 02-22-2013, 07:21 AM   #5
biznatch
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Journals will have their own requirements, I think usually they do require it, so check what the journal's policy is. If you find an article in a journal that requires the data be made available (on SRA or otherwise) and the data hasn't been made available or an accession isn't given in the paper, contact the journal and ask if they have any information. I did that once and the journal contacted the authors to have them upload their data (most of the data was there they just forgot one of the samples).
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Old 04-30-2015, 07:54 AM   #6
fibar
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Thank you for your replies.
What I meant originally was that NGS raw data should be made public whenever you publish the corresponding paper (which would contain the accession number). In my opinion, it should be the policy of every journal.

Here's a nice additional story: Recently I asked for some raw metagenomic data sets to a research group, and the PhD student said he was very busy and that he was going to be able to upload it in two or three months. Hilarious. I will see if the journal's conditions for submission includes uploading raw data.

And here's a paper for which I couldn't find accession number or uploaded data:
Pyrosequencing Analysis of Bacterial Diversity in 14 Wastewater Treatment Systems in China
Xiaohui Wang, Man Hu, Yu Xia, Xianghua Wen and Kun Ding
Appl. Environ. Microbiol. 2012, 78(19):7042. DOI:
10.1128/AEM.01617-12.
Published Ahead of Print 27 July 2012.

All the best.

Last edited by fibar; 04-30-2015 at 08:02 AM.
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Old 05-04-2015, 05:58 AM   #7
cliffbeall
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If I'm peer reviewing a manuscript I try to make sure that there is an accession number. I would urge everyone else to do the same.

It unfortunately seems to be very common to submit the paper without it and only undertake the hassle of data submission when forced.
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Old 05-15-2015, 12:10 PM   #8
Joann
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Default a point on abstracts and accession numbers

Also when preparing or reviewing an article which should have accession numbers, make sure to see that the accession numbers appear in the article's abstract, which also has been a general requirement of journals for many years. This is important because articles behind paywalls cannot be subjected to open full text mining among other types of machine searching techniques, but the abstracts can.
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