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Publication Lookup
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Input Format for whatizitlookup
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A simple function for searching Pubmed for articles which mention a particular gene.  This function is a simple wrapper around EBI-web's whatzit function.  Input files should be in the following format:

search query 1	UniProt 1
search query 2	UniProt 2
search query 3	UniProt 3
search query 4	UniProt 4

IDS MUST be UniProt ids.  The whatzit tool will automatically expand these IDS into all of thier common names.  Then on retrieval it will filter the abstracts through a gene-name tagger and ensure tbat the requested gene is actually present.

For example I use this tool to find the number of acticles that mention a gene along with cancer but are not from microarray experiments. Below is an excerpt from one of my lookups.

Cancer NOT microarray	P04217
Cancer NOT microarray	P11245
Cancer NOT microarray	P19022
Cancer NOT microarray	Q9Y243
Cancer NOT microarray	Q9Y3Q0
Cancer NOT microarray	Q9UQQ1
Cancer NOT microarray	O14734
Cancer NOT microarray	Q02094

Example usage:

python whatizitlookup.py -o results.txt inputfile.txt

One quick note, the function allows you to specify the number of parellel workers.  The default is 3, I've noticed this balances the speed or retrieval and the "niceness" on the EBI webserver.  Please don't raise this much over 5 otherwise you'll crash thier server (I know from experience).

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Input format for entrezlookup.py
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Search-Term	List-Name	GeneID
crohn's disease NOT microarray	Common_up	5967
crohn's disease NOT microarray	Common_up	10562
crohn's disease NOT microarray	Common_up	83998
crohn's disease NOT microarray	Common_up	27290
crohn's disease NOT microarray	Common_up	1116
crohn's disease NOT microarray	Common_up	6372
crohn's disease NOT microarray	Common_up	6373
crohn's disease NOT microarray	Common_up	4319
crohn's disease NOT microarray	Common_up	6286

Results are taken from the gene2pubmed lookup table provided by the NCBI.