Question: Documenting all available data sets of histone modifications in GEO
gravatar for Saad Khan
5.7 years ago by
Saad Khan400
United States
Saad Khan400 wrote:

Hi All,

I am trying to document the histone modification data sets available in GEO for mammals. Following are the things that I want to retrieve from GEO :-

1.) Species (2). Tissue (3) Disease/normal state (if so which disease). (4.) SRA id (if available) (5) link for analysed data (if available) (6) Cell line/not (7) Type of experiment (ChIP-chip or CHIP-SEQ)

I need to retrieve this information from GEO. I have tried to look at e-utils but it is not well documented or easy to use. I was wondering if there is any other API somebody has written in PERL/Python for achieving the above task or should I instead try to write a web scraping program to achieve the same. I am sure somebody must have already done such a task. I also intend to document DNA methylation (MEDIP-Seq/MIRA-seq) that might be available in mammals and for which tissues in future.


sra geo parser e-utils histones geo • 1.3k views
ADD COMMENTlink modified 5.7 years ago by Sean Davis26k • written 5.7 years ago by Saad Khan400
gravatar for Sean Davis
5.7 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

You may have trouble documenting #3 and #6 for anything except the curated GDS data (which are somewhat older) since GEO does not require that type of information to be present.  That said, you might take a look at the SRAdb and GEOmetadb bioconductor packages, each of which contains a SQL database of metadata from the respective repository meant for doing queries such as the one you are attempting.

ADD COMMENTlink written 5.7 years ago by Sean Davis26k

Yeah SRAdb and GEOmetadb may not be able to satisfy my requirements. But I believe it is something somebody should have already worked on ,at least someone who relies a lot on working with public data. It would be great if someone could share a web crawler he/she has already written to do above or something similar that I can modify rather than manually going through each of the entry.

ADD REPLYlink written 5.7 years ago by Saad Khan400

Is there some information available on a GEO web page that is not in GEOmetadb?  If there is, perhaps we can try to add those details.  Otherwise, I suspect that a web crawler for GEO is not likely to yield more results than GEOmetadb.

ADD REPLYlink written 5.7 years ago by Sean Davis26k
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