Biomart Interfaces For Different Languages
Similarly to biomaRt for R I would like to know what other languages have interfaces to BioMart.
The one I'm more interested in is Python, however for completion I would also include:
- Python
- Ruby
- Perl
- Java
- Javascript
- C/C++
- ...
Working examples are welcome.
1 answer
Those that I'm aware of are:
- As you mentioned already, biomaRt for R/Bioconductor
- biomart Ruby library
- biomart-perl (Perl) and martj (Java), both described on this page
There are some third-party interfaces to BioMart, listed at the bottom of the BioMart entry page.
There seem to be less options for other languages. However, the BioMart API can be used to return XML; you may be able to hack your own solution around that. As discussed at this question, Pycogent might be an option for Python.
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Partial duplicate of question Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
There is also a python library.