Question: How to create own SRAdb
0
gravatar for Deepak Tanwar
14 months ago by
Deepak Tanwar4.0k
ETH Zürich, Switzerland
Deepak Tanwar4.0k wrote:

Hello,

As SRAdb is outdated, I would like to create my own SRAdb. What is the best way to do that? I am aware of the files I would need to make one: ftp://ftp.ncbi.nlm.nih.gov/sra/reports/

But, I am not an expert in SQL and don't know how to deal with XML files.

sradb sra geo • 513 views
ADD COMMENTlink modified 14 months ago by Sean Davis26k • written 14 months ago by Deepak Tanwar4.0k

Contact Sean Davis and try to work with his team. No point in developing a new one? - waste of time and research funds (?)

ADD REPLYlink written 14 months ago by Kevin Blighe63k

https://github.com/seandavi/SRAdb/issues/24

ADD REPLYlink written 14 months ago by Deepak Tanwar4.0k

ADD REPLYlink modified 14 months ago • written 14 months ago by Kevin Blighe63k

As far as I understood, Sean Davis seems to be working on a replacement of SRAdb. As I have already set up the tool to work with SRAdb, I would like to have an updated one.

ADD REPLYlink written 14 months ago by Deepak Tanwar4.0k

There are functions in R for dealing with both SQL and XML. The ideal situation would be to pull the data in real time from SRA, no? This is how GEOquery (also by Sean Davis) functions.

ADD REPLYlink written 14 months ago by Kevin Blighe63k

The ideal situation would be to pull the data in real time from SRA: Yes!

I was looking for the code which Sean Davis and his team wrote to make this database. But, couldn't find it (that would have been an easy solution)...

ADD REPLYlink modified 14 months ago • written 14 months ago by Deepak Tanwar4.0k
1

They have direct access to SRA, you might just ask them to update the file. I've sent Sean Davis a tweet to ask for his input here.

ADD REPLYlink written 14 months ago by Devon Ryan96k

Unfortunately, I do not have direct access to SRA. I mine the data from multiple publicly available locations at NCBI in what is a non-trivial exercise.

ADD REPLYlink modified 14 months ago • written 14 months ago by Sean Davis26k

If SRAdb is no longer being maintained can a note be added to the GitHub/Bioconductor page that effect? There is currently no indication there.

ADD REPLYlink written 14 months ago by genomax87k

That's incredibly annoying, I had presumed that since you were at NIH you'd have more direct access.

ADD REPLYlink written 14 months ago by Devon Ryan96k

Bold text and ALL CAPS can come across as rude in online communication. For what it's worth, it definitely helps to learn SQL (and even XML). It doesn't take too long and a learning opportunity seems to have presented itself to you!

ADD REPLYlink modified 14 months ago • written 14 months ago by RamRS28k

Sorry, I updated mine comment!

ADD REPLYlink written 14 months ago by Deepak Tanwar4.0k
2
gravatar for Sean Davis
14 months ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Due to growing size of SRA metadata, we have been transitioning to a new approach for building, updating, and distributing the SRA metadata. As a first step, the data are available as public resource on Google BigQuery.

https://seandavi.github.io/2019/06/omicidx-on-bigquery/

Access BigQuery via any language, basically, via the bq command line, or via the cloud console. BigQuery requires a Google Cloud Platform account, but the free credits will cover thousands of queries.

If you are simply interested in searching SRA programmatically, you can try using NCBI Eutils. There is documentation on NCBI.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Sean Davis26k

There are some existing projects that are dependent on SRAdb being the in same format, e.g.:

https://github.com/deweylab/MetaSRA-pipeline

Is there a way to regenerate the SRAdb locally so that the code/data for MetaSRA can be updated, or is the bigquerty the only way forward?

Cheers

ADD REPLYlink written 12 months ago by Dirk80
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