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scibiomart

This is just a simple wrapper around the API from BioMart, but I found existing packages were not quite sufficent for what I was wanting to do.

Here you can simply get the list of all genes and perform other biomart functions such as mapping between human and mouse.

Installation

pip install scibiomart

Usage

For the most simple usage, use API which will get the latest mouse and human and map gene IDs to gene names.

Examples

from scibiomart import SciBiomartApi

sb = SciBiomartApi()

# Get only the default for those genes
results_df = sb.get_mouse_default({'ensembl_gene_id': 'ENSMUSG00000029844,ENSMUSG00000032446'})

# Select attributes
results_df = sb.get_mouse_default({'ensembl_gene_id': 'ENSMUSG00000020875,ENSMUSG00000038210'},
                                     attr_list=['entrezgene_id'])
# Get all genes
results_df = sb.get_mouse_default()

# Sort the results based on TSS (takes direction into account)
results_df = sb.sort_df_on_starts(results_df)

# Get human
results_df = sb.get_human_default()

Examples extended

If you are interested in more than the simple API, see the tests for all examples, however, you can list the datasets etc, and query other attributes.

Print marts

sb = SciBiomart()
marts = sb.list_marts()
print('\n'.join(marts))

Print datasets

sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
err = sb.list_datasets()

List attributes

sb = SciBiomart()  
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('fcatus_gene_ensembl')
err = sb.list_attributes()

List configs

sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('fcatus_gene_ensembl')
err = sb.list_configs()

List filters

sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('fcatus_gene_ensembl')
err = sb.list_filters()

Run generic query

Here we show a generic query for two genes (as a comma separated list) and the attributes we're interested in are 'ensembl_gene_id', 'hgnc_symbol', 'uniprotswissprot'.

Run query: def run_query(self, filter_dict: dict, attr_list: list): i.e. you can pass it a filter dictionary and a list of attributes. This will make it quicker, you can also run it and it will get all genes (i.e. if filter_dict is empty).

sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('hsapiens_gene_ensembl')
results = sb.run_query({'ensembl_gene_id': 'ENSG00000139618,ENSG00000091483'},
                       ['ensembl_gene_id', 'hgnc_symbol', 'uniprotswissprot'])
print(results)

Match mouse to human

Get mouse orthologs for human genes

sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('hsapiens_gene_ensembl')
attributes = ['ensembl_gene_id', 'mmusculus_homolog_ensembl_gene', 'mmusculus_homolog_perc_id_r1']
results = sb.run_query({'ensembl_gene_id': 'ENSG00000139618,ENSG00000091483'},  attributes)
print(results)

See tests for more examples.

Biomart information below

[[https://m.ensembl.org/biomart/martservice]]

Martservices usage:

(a) Querying BioMart

To submit a query using our webservices generate an XML document conforming to our Query XML syntax. This can be achieved simply by building up your query using MartView and hitting the XML button. This XML should be posted to http://www.ensembl.org/martservice attached to a single parameter of query. For example you could either:

  • submit using wget replacing MY_XML with the XML obtained above, first removing any new lines.
wget -O results.txt 'http://www.ensembl.org/biomart/martservice?query=MY_XML' 

(b) Retrieving Meta Data:

  • to retrieve registry information:
http://www.ensembl.org/biomart/martservice?type=registry
  • to retrieve datasets available for a mart:
http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL
  • to retrieve attributes available for a dataset:
http://www.ensembl.org/biomart/martservice?type=attributes&dataset=mpahari_gene_ensembl
  • to retrieve filters available for a dataset:
http://www.ensembl.org/biomart/martservice?type=filters&dataset=mpahari_gene_ensembl
  • to retrieve configuration for a dataset:
http://www.ensembl.org/biomart/martservice?type=configuration&dataset=mpahari_gene_ensembl

More documentation at: [[http://www.biomart.org/other/user-docs.pdf]]

At the time of writing this the version of biomart was 0.7.

http://www.ensembl.org/biomart/martservice?query=type=registry</Query>

http://www.ensembl.org/biomart/martservice?query=<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" ><Dataset name = "hsapiens_gene_ensembl" interface = "default" ><Filter name = "ensembl_gene_id" value = "ENSG00000139618,ENSG00000091483"/><Attribute name = "ensembl_gene_id" /></Dataset></Query>

http://www.ensembl.org/biomart/martservice?query=<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" ><Dataset name = "hsapiens_gene_ensembl" interface = "default" >< Filter name = "ensembl_gene_id" value = "ENSG00000139618,ENSG00000091483" /><Attribute name = "ensembl_gene_id" /><Attribute name = "hgnc_symbol" /><Attribute name = "uniprotswissprot" /></Dataset></Query>

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