I would like to search the literature using the Pubmed search engine for a set of genes that are associated with a brain region of interest. Unfortunately, there are a lot of them. It's possible there is no solution if there is a character limit on the query. I think it would be easiest to do this with 'nix tools but I'm open to R libraries or Python implementations too.
The list is 908 genes long. It's from the Gensat annotation search engine, with the filters
Structure IS olfactory bulb &
Expression level IS moderate to strong signal &
Expression pattern IS region-specific.
The list looks like, scraped from the dropdown list in the HTML source with a regular expression:
Aatf Abcb1b Abhd3 Abhd4 Abhd5 ...
The Pubmed query should look like:
(((((((Aatf) OR Abcb1b) OR Abhd3) OR Abhd4) OR Abhd5) OR Abl2) AND olfactory bulb
but with 908 genes separated by OR and parentheses.
Bonus points if you find/write a utility which adds gene synonyms to the query!