Question

Url To Download Sra Experiment_Package Xml File Programmatically

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13.9 years ago

Tim ▴ 350

Given the following Experiment description page from SRA: http://www.ncbi.nlm.nih.gov/sra/SRX001682?report=fullXML

How can I download the visualized XML file as actual XML?

It's driving me crazy that I can only get this weird HTML layout, when what I want is the XML file to parse and transform automatically, without the manual copy&paste step in between.

The page offers a heavily JavaScripted form at the bottom to download as file, but no direct link to that XML file.

xml sra • 5.5k views

ADD COMMENT • link updated 21 months ago by Ram 44k • written 13.9 years ago by Tim ▴ 350

score 3 · Answer 1 · 2011-02-02

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13.9 years ago

Jeremy Leipzig 22k

http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=SRA&term=SRX001682

ADD COMMENT • link 13.9 years ago by Jeremy Leipzig 22k

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Thanks, that works fine! Any notes on where you found the URL and how to find similar URLs for the SRA?

ADD REPLY • link 13.9 years ago by Tim ▴ 350

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i guess http://www.ncbi.nlm.nih.gov/books/NBK25497/ would be a good place to start. hopefully the SRA follows the same syntax standards as the rest of NCBI

ADD REPLY • link 13.9 years ago by Jeremy Leipzig 22k

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This method doesn't seem to work anymore - the link provided only returns WebEnv parameter is required.

ADD REPLY • link 12.6 years ago by Jeff Hussmann ▴ 120

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yes, seems not work anymore. There is a similar post at SO with a solution: http://stackoverflow.com/questions/15855188/extract-xml-from-xml-embebed-in-html

ADD REPLY • link 11.4 years ago by dli ▴ 250

Ram · Answer 2 · 2015-07-21

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=fullxml&term=SRX001682[Experiment]

Sorry this is like 2 years too late but since someone might come across it in a search, here is the new way. I received this in an e-mail from Robert Sanders (NIH/NLM/NCBI) recently when e-mailing the sra-tools help address to get the full XML as actual XML. However the results are what you want, even though they're ugly, you will want to use

xmllint --format DOWNLOADEDFILENAME > srx001682.xml

(however you like) to get readable XML. I myself wanted SRR and it had to be termed SRR1169893[Accession], I'm not sure how important the bit in square brackets is however. It was suggested I try using E-utilities to programmatically retrieve the same information: http://www.ncbi.nlm.nih.gov/books/NBK25500/