1
$\begingroup$

Is there an up-to-date database of known human proteins that is easily accessible using Python libraries?

$\endgroup$
2
$\begingroup$

GenBank includes human proteins and provides APIs for constructing HTTP requests to make searches. Examples are given in Perl, but if you prefer another programming or scripting language you are expected to write your own:

Equivalent HTTP requests can be constructed in many modern programming languages; all that is required is the ability to create and post an HTTP request.

This approach has always served me well.

Uniprot seems similar in this respect.

SwissProt provides a package for BioPython which may be of interest. I don’t know if this is the library you are referring to — you don’t say, and I don’t use Python.

$\endgroup$
1
$\begingroup$

The human proteome can be retrieved from the UniProt Knowledgebase (http://www.uniprot.org/help/human_proteome).

All data on the UniProt website is accessible programmatically via a REST API. The documentation http://www.uniprot.org/help/programmatic_access also includes a few python code examples (among other programmaing languages).

Please don't hesitate to contact the UniProt helpdesk if you have any additional questions.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.