SRA study metadata download

[ersgupta]

Hi Guys,

I am trying to download the metadata of all the studies submitted in SRA but I am not able to find a complete list. Can anybody help me out with this.

I want metadata(mainly abstract and description) (preferably in xml format) of all the studies/samples in SRA till date.

Thnx in advance.

[laura]

You might try

ftp://ftp-trace.ncbi.nlm.nih.gov/sra...Accessions.tab

[ersgupta]

Thanx for the reply.

I have checked it but it doesnt contain the information I want i.e. study abstract and description. It only contains IDs, which I already have.

I am trying few other things lets hope if it works.

[vadim]

Grab the full XML dump and parse it:
ftp://ftp-trace.ncbi.nlm.nih.gov/sra...0111101.tar.gz

[ersgupta]

@vadim... thnx a lot...

This is wht I was looking for. But in this also one issue is that not every SRA id is having study.xml, but its ok. I can live with that.

[vadim]

What do you mean by SRA id? Each SRA run should be associated with a study through SRA experiment. The XML schema might be useful:

http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-3/

or

http://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_3/

Also have a look here for a complete XML dump (including EBI SRA):

http://ftp.sra.ebi.ac.uk/meta/xml/xml.all.tar.gz

[ersgupta]

Both link to same page.

I understand SRA run, they have ID as SRR.

For eg: take this case.

http://www.ncbi.nlm.nih.gov/sra?term=SRA028225

http://www.ncbi.nlm.nih.gov/sra?term=SRA028192

http://www.ncbi.nlm.nih.gov/sra?term=SRA028059

Out of these only SRA028059 folder in the SRA Metadata is having *.study.xml.

SRP = Study
SRX = Experiment
SRS = Sample
SRR = Run

But what basically is SRA for?? I am confused here.

[ersgupta]

This is a reply I got from a person in SRA.

The SRA number acts as a collector for the information. This means that when a center submits metadata or data they create a submission (SRAXXXXXX), but the data or metadata in the submission links to another submission.

This is ok with me, but I don't understand the fact that why have separate SRA ids for same study, even if one has to submit more samples to the same study at a later stage.

[vadim]

SRA* accessions are NCBI submission accessions, similarly ERA* accessions are EBI submission accessions and DRA* are DDBJ submission accessions.
Sometimes study is submitted before the run data, but since metadata dumps are organized by submission accession in such cases run and study metadata end up in separate folders. To get proper association use the livelists:
NCBI: ftp://ftp-trace.ncbi.nlm.nih.gov/sra...Accessions.tab
EBI: ftp://ftp.sra.ebi.ac.uk/meta/list/livelist.gz

As for the submissions you are asking, it appears that the run was submitted in SRA028225, experiment in SRA028192 and the study in SRA028059.

[ersgupta]

yeah... got it... That *.tab file is very useful indeed... thanx...

[ersgupta]

I guess I can conclude this:

"NCBI-SRA doesn't have a single ID using which we can get everything related to it i.e. study, run, experiment, sample", the only way to go about it is use the SRA_Accessions.tab, using study_id *RP* get the *RA*(s) then using *RA*(s) get the *RR*(s)... there is no direct way of getting *RR* from *RP*."

RA = SRA Accessions
RR = Run
RP = Study

[nickloman]

Maybe not relevant for this question but am finding the DNAnexus SRA interface much nicer than the NCBI's: http://sra.dnanexus.com/

[ersgupta]

Maybe not relevant for this question but am finding the DNAnexus SRA interface much nicer than the NCBI's: http://sra.dnanexus.com/

@nickloman...

ok... will have a look at it as well...

[ersgupta]

can anybody explain me dis...

many SRA(accession) ids having same SRP(study) id this is ok... as justified by an answer above...
but many SRP(study) ids having same SRA(accession) id...?

[sdavis]

You might take a look at:

http://www.bioconductor.org/packages/release/bioc/html/SRAdb.html

While this is an R/Bioconductor package, the underlying data are stored in a SQLite database that can be downloaded separately and used directly or from any language with a SQLite driver (most languages). What is done to create the database is to download all the SRA XML files containing metadata, parse those files, and then load them into a relational database. This makes bulk operations on the data easier and more flexible since SQL can be used. Some full-text searching capabilities are also included since SQLite supports that in later versions.