ncbi.Ncbi

This probabaly is the thinnest wrapper around all the APIs. The main reason for that is that we cover basically the entirety of the NCBI database and you have a lot of options and flexibility for querying. As always with that flexibility comes the burden of verbosity. We will cover some of the endpoints in this tutorial for the rest you can check the E-Utils guide and the NCBI website. One other quirk of this database is, some endpoints return detailed information via the summary endpoint while others return via fetch. You will need to try them out yourself before writing a comprehensive script.

from benchmate.apis.ncbi import Ncbi
ncbi = Ncbi(email=<your email>) # so ncbi can tell you to stop abusing their resources. Also the rate limit increase dramatically when an email or api key is provided, they put you in the nice queue.

# list all the databases:
ncbi.databases

To search a specific database you will need to specifiy it in the search method. This will return their NCBI ids and nothing else.

omim_codes=ncbi.search(db="omim", query="cancer", retmax=1000) # return 1000 items

To get more information about a specific id you can use the summary or fetch method.

mycodes=omim_codes[0:10]
summaries=[ncbi.summary("omim", code)[0] for code in mycodes]

full_record=ncbi.fetch("omim", omim_codes[0])

I’m not going to go into a lot of details partly because there are so many different databases and all of them either have the summary or fetch (or both like genes) method return something and what they return is different in each case. However, the response per call/db is quite consistent and if you know what you are looking for it’s not that difficult to streamline the search and knowledge gathering using these endpoints.