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Accessing the information available in the GEO database [Programmatic access for GEO database]

I am trying the access the information available in this GEO link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1289257 through API Entrez - Eutil.

So, I use their pipeline to access the data

Link1 : http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=GSM1289257

Link 2: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=562544

There is some information missing in this particular way of accessing the data.

For example, In the first GEO link, image

But I am seeing the information like Treatment Protocol, Growth Protocol, Data Processing in the eutils result that I got accessing the Link2 above.

Even I tried changing the eutil database as gds

Link1: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gds&term=GSM1289257

Link2: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gds&id=200053268,200053313,100013821,301289257

Not much details in there.

Am I missing something or how should I access these information of interest.

Thanks

rna-seq chip-seq geo entrez
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updated by natasha.sernova natasha.sernova • written by startup_biostar • startup_biostar

1 answer

This post is the answer to your question to some extent:

How to programmatically get GEO accession number ID

Other useful posts describing how to reach some information from GEO, either programmically or not:

How To Compare The Expression Of Two Genes In Large Microarray Dataset Such As Arrayexpress And Geo

RNA-seq:

A: Rna-Seq Data In Public Database

Chip-seqs from Geo:

Documenting all available data sets of histone modifications in GEO

Suggestions For Extracting Data (A Challenge Of Sorts !)

"R and Bioconductor, two great programming tools for doing almost anything you want."

A: Understanding Microarray Datasets

What is the information of your interest,

it's not very easy to understand: yeasts and Rna-seq tools? Is it correct?

And a lot of data are pre-processed and ready to analyse with known tools.

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written by natasha.sernova natasha.sernova

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