[Bioperl-l] From Anand - a question on querying ncbi's genomeprj with Bio::DB::Eutilities

Anand Venkatraman bioperlanand at yahoo.com
Fri Mar 26 21:40:04 EDT 2010


Hi everybody,
 
I have a list of genome project ids & I have a need where I need to gather information from a specific field  & store the output in a file.

As regards what Info I want

For example, for genome project id 30807  http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30807, I need to grab the text information that reads (this is found at the bottom of the page):Anabaena azollae. Anabaena azollae is a cyanobacterial symbiont of the water fern Azolla, commonly known as 'duckweed'. Anabaena azollae is a nitrogen-fixer and provides nitrogen to the host plant.Nostoc azollae 0708. Nostoc azollae 0708, also called Anabaena azollae strain 0708, will be used for comparative analysis.

I need to grab the  same information for a list of genome project ids.

Is this possible using Bio::DB::Eutilities. If yes, what would be the fields/params?

I did try out this: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#What_information_is_available_for_database_.27x.27.3F

to find out what information is available for genomeprj, but I am unable to get the necessary field/param for my need.

Please help.

Alternatively, is there a better way to address my need other than Bio::DB::Eutilities

Thanks in advance,

Anand 


      


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