Question

Biomart Interfaces For Different Languages

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15.0 years ago

Unode ▴ 180

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.

biomart • 5.0k views

ADD COMMENT • link updated 3.1 years ago by Ram 45k • written 15.0 years ago by Unode ▴ 180

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Partial duplicate of question Is There A Non-Perl Alternative To Accessing Ensembl'S Api?

ADD REPLY • link updated 6.2 years ago by Ram 45k • written 15.0 years ago by Neilfws 49k

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There is also a python library.

ADD REPLY • link updated 3.1 years ago by Ram 45k • written 10.2 years ago by Lluís R. ★ 1.2k

Ram · Answer 1 · 2010-11-12

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.