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================== Publication Lookup ================== =============================== Input Format for whatizitlookup =============================== 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). ================================ Input format for entrezlookup.py ================================ 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.
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A python function for looking up Pubmed articles based on the genes that they mention
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