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ropensci / rentrez

talk with NCBI entrez using R
https://docs.ropensci.org/rentrez
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new_vignette web history usage example #58

Closed htc502 closed 9 years ago

htc502 commented 9 years ago

Hi @dwinter , happy to pull request again...~_~. I have made some typo checking work and write a paragraph illuminating how to use web history feature of rentrez.. hope it can be helpful..

dwinter commented 9 years ago

Thanks @htc502

Very happy to get the typos and the usage example.

I think I might use the example in the "cookbook" of the wiki (a la this one https://github.com/ropensci/rentrez/wiki/Find-genes-known-to-interact-with-a-given-gene) so that we can keep the vignette as "tight" as possible. But it will definitely be useful.

htc502 commented 9 years ago

lol~. help yourself to it @dwinter . Besides, I have an experience that each time when I want to search something with rentrez, I have to do the following logic: 1) which database is the item i want to search 'belonging to'? 2)is the items the UIDs of that database? if true, use esummary/efetch against that database will do the job; if false, construct a search phrase with 'search builder' provided by NCBI's 'advanced search', do it with esearch. 3)refining the search phrase if necessary, use efetch/esummary with the search result. In the process described above, I have to check this web page(http://www.ncbi.nlm.nih.gov/books/NBK25497/table/chapter2.T._entrez_unique_identifiers_ui/?report=objectonly) to get the uid information and open the corresponding database 'advanced search' web page to do the phrase construction. can we implement a helper function which would help freshman like me to do things above, this will save a lot of time and make rentrez more easy for beginners to use.

dwinter commented 9 years ago

Check out #60 for query building.

What would expect to be the input to a function mimicking this UID table (i.e. would would a user type in)