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Which other databases should be included in biomartr? #4

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HajkD opened this issue Jan 19, 2017 · 9 comments
Open

Which other databases should be included in biomartr? #4

HajkD opened this issue Jan 19, 2017 · 9 comments

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@HajkD
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HajkD commented Jan 19, 2017

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
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Uniprot?

@HajkD
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HajkD commented Mar 11, 2017

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
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jvineis commented Nov 3, 2017

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
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jvineis commented Nov 17, 2017

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

@HajkD
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HajkD commented Jan 18, 2018

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
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ensembl plants

@sofsta
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sofsta commented Apr 14, 2020

Not sure if this has been covered but:

Homo sapiens (human) genome assembly GRCh38 (hg38)

@HajkD
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HajkD commented Apr 14, 2020

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?

@WWz33
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WWz33 commented Aug 29, 2024

JGI IMG is critical. Thanks Hajk!JGI IMG 至关重要。谢谢哈吉克! https://img.jgi.doe.gov/

I think so too!

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