Which other databases should be included in biomartr?

[HajkD]

I would like to trigger a brainstorming around the question which other databases could be useful to be included in biomartr. I would be grateful to receive input from different life science communities working with genomics data.

Many thanks!

[ARamesh123]

Uniprot?

[HajkD]

Hi @ARamesh123

Sounds like a very good idea!

I just checked: http://www.uniprot.org/help/programmatic_access

Should be feasible :) So I will try to get familiar with the API and will implement Uniprot retrieval functions.

I am happy for any further suggestions or for pointing out even more detailed functionality that is needed.

Many thanks!

Hajk

[jvineis]

fungene http://fungene.cme.msu.edu/ Its terribly painful to extract reference genes for functional genes from fungene with appropriate taxonomic strings. It seems as though their data is protected though.

[jvineis]

JGI IMG is critical. Thanks Hajk! https://img.jgi.doe.gov/

[HajkD]

I just finished implementing the proteome retrieval interface to UniProt.

Please see the example here for details.

In short users can now specify:

biomartr::getProteome( db = "uniprot",  organism = "Mus musculus" )

I hope this is useful.

Best, Hajk

[Norbittner]

ensembl plants

[sofsta]

Not sure if this has been covered but:

Homo sapiens (human) genome assembly GRCh38 (hg38)

[HajkD]

This should work with:

biomartr::getGenome(db = "refseq", organism = "GCF_000001405.39")

The refseq id was taken from: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39

Does this solve the human genome issue?